diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/Duplications_per_Orthogroup.tsv b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/Duplications_per_Orthogroup.tsv new file mode 100644 index 0000000000000000000000000000000000000000..1f3722fb729ef5525c6b4d503de0636de8017fcb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/Duplications_per_Orthogroup.tsv @@ -0,0 +1,1987 @@ +Orthogroup Duplications (all) Duplications (50% support) +OG0000000 33 31 +OG0000001 19 18 +OG0000002 13 9 +OG0000003 12 8 +OG0000004 10 6 +OG0000005 19 15 +OG0000006 7 3 +OG0000007 1 1 +OG0000008 5 5 +OG0000009 2 1 +OG0000010 7 7 +OG0000011 4 4 +OG0000012 4 3 +OG0000013 6 6 +OG0000014 4 2 +OG0000015 1 1 +OG0000016 1 1 +OG0000017 1 1 +OG0000018 2 1 +OG0000019 4 4 +OG0000020 1 1 +OG0000021 2 2 +OG0000022 1 1 +OG0000023 3 3 +OG0000024 1 1 +OG0000025 1 0 +OG0000026 2 2 +OG0000027 0 0 +OG0000028 1 1 +OG0000029 3 3 +OG0000030 3 3 +OG0000031 1 0 +OG0000032 2 2 +OG0000033 1 0 +OG0000034 2 1 +OG0000035 2 2 +OG0000036 2 1 +OG0000037 2 2 +OG0000038 2 2 +OG0000039 1 1 +OG0000040 2 2 +OG0000041 2 2 +OG0000042 1 1 +OG0000043 2 2 +OG0000044 2 2 +OG0000045 3 3 +OG0000046 1 0 +OG0000047 2 2 +OG0000048 2 2 +OG0000049 2 2 +OG0000050 1 0 +OG0000051 2 2 +OG0000052 2 2 +OG0000053 1 1 +OG0000054 1 1 +OG0000055 2 1 +OG0000056 1 1 +OG0000057 2 2 +OG0000058 1 1 +OG0000059 1 1 +OG0000060 1 1 +OG0000061 1 1 +OG0000062 1 1 +OG0000063 1 1 +OG0000064 1 1 +OG0000065 1 1 +OG0000066 1 1 +OG0000067 1 1 +OG0000068 1 1 +OG0000069 1 1 +OG0000070 1 1 +OG0000071 1 1 +OG0000072 1 1 +OG0000073 1 1 +OG0000074 1 1 +OG0000075 1 1 +OG0000076 1 1 +OG0000077 1 1 +OG0000078 1 1 +OG0000079 1 1 +OG0000080 1 1 +OG0000081 1 1 +OG0000082 1 1 +OG0000083 1 1 +OG0000084 1 1 +OG0000085 1 1 +OG0000086 1 1 +OG0000087 1 1 +OG0000088 1 0 +OG0000089 1 1 +OG0000090 1 1 +OG0000091 1 1 +OG0000092 1 1 +OG0000093 1 1 +OG0000094 1 1 +OG0000095 1 1 +OG0000096 2 2 +OG0000097 2 2 +OG0000098 1 1 +OG0000099 2 1 +OG0000100 1 0 +OG0000101 1 1 +OG0000102 1 1 +OG0000103 1 1 +OG0000104 1 1 +OG0000105 1 1 +OG0000106 1 1 +OG0000107 1 1 +OG0000108 1 1 +OG0000109 1 1 +OG0000110 1 1 +OG0000111 1 0 +OG0000112 1 1 +OG0000113 1 1 +OG0000114 1 1 +OG0000115 1 1 +OG0000116 1 1 +OG0000117 1 1 +OG0000118 1 1 +OG0000119 1 1 +OG0000120 1 1 +OG0000121 1 1 +OG0000122 1 1 +OG0000123 1 1 +OG0000124 1 1 +OG0000125 1 1 +OG0000126 1 1 +OG0000127 1 1 +OG0000128 1 1 +OG0000129 1 1 +OG0000130 1 1 +OG0000131 1 1 +OG0000132 1 1 +OG0000133 1 1 +OG0000134 1 0 +OG0000135 1 1 +OG0000136 1 1 +OG0000137 1 1 +OG0000138 2 2 +OG0000139 1 1 +OG0000140 1 1 +OG0000141 1 0 +OG0000142 1 1 +OG0000143 1 1 +OG0000144 1 1 +OG0000145 1 0 +OG0000146 1 1 +OG0000147 1 1 +OG0000148 2 2 +OG0000149 1 1 +OG0000150 1 1 +OG0000151 1 0 +OG0000152 1 1 +OG0000153 1 0 +OG0000154 1 1 +OG0000155 1 0 +OG0000156 1 1 +OG0000157 1 0 +OG0000158 1 1 +OG0000159 1 1 +OG0000160 2 2 +OG0000161 1 0 +OG0000162 1 0 +OG0000163 1 1 +OG0000164 1 1 +OG0000165 1 1 +OG0000166 1 1 +OG0000167 1 0 +OG0000168 1 1 +OG0000169 1 1 +OG0000170 1 1 +OG0000171 1 1 +OG0000172 2 1 +OG0000173 2 1 +OG0000174 0 0 +OG0000175 0 0 +OG0000176 0 0 +OG0000177 0 0 +OG0000178 0 0 +OG0000179 0 0 +OG0000180 0 0 +OG0000181 0 0 +OG0000182 0 0 +OG0000183 0 0 +OG0000184 0 0 +OG0000185 0 0 +OG0000186 0 0 +OG0000187 0 0 +OG0000188 0 0 +OG0000189 0 0 +OG0000190 0 0 +OG0000191 0 0 +OG0000192 0 0 +OG0000193 0 0 +OG0000194 0 0 +OG0000195 0 0 +OG0000196 0 0 +OG0000197 1 1 +OG0000198 0 0 +OG0000199 0 0 +OG0000200 0 0 +OG0000201 0 0 +OG0000202 0 0 +OG0000203 0 0 +OG0000204 0 0 +OG0000205 0 0 +OG0000206 0 0 +OG0000207 0 0 +OG0000208 0 0 +OG0000209 0 0 +OG0000210 0 0 +OG0000211 0 0 +OG0000212 0 0 +OG0000213 0 0 +OG0000214 0 0 +OG0000215 0 0 +OG0000216 0 0 +OG0000217 0 0 +OG0000218 0 0 +OG0000219 0 0 +OG0000220 0 0 +OG0000221 0 0 +OG0000222 0 0 +OG0000223 0 0 +OG0000224 0 0 +OG0000225 0 0 +OG0000226 0 0 +OG0000227 0 0 +OG0000228 0 0 +OG0000229 0 0 +OG0000230 0 0 +OG0000231 0 0 +OG0000232 0 0 +OG0000233 0 0 +OG0000234 0 0 +OG0000235 0 0 +OG0000236 0 0 +OG0000237 0 0 +OG0000238 0 0 +OG0000239 0 0 +OG0000240 0 0 +OG0000241 0 0 +OG0000242 0 0 +OG0000243 0 0 +OG0000244 0 0 +OG0000245 0 0 +OG0000246 0 0 +OG0000247 0 0 +OG0000248 0 0 +OG0000249 0 0 +OG0000250 0 0 +OG0000251 0 0 +OG0000252 0 0 +OG0000253 0 0 +OG0000254 0 0 +OG0000255 0 0 +OG0000256 0 0 +OG0000257 0 0 +OG0000258 0 0 +OG0000259 0 0 +OG0000260 0 0 +OG0000261 0 0 +OG0000262 0 0 +OG0000263 0 0 +OG0000264 0 0 +OG0000265 0 0 +OG0000266 0 0 +OG0000267 0 0 +OG0000268 0 0 +OG0000269 0 0 +OG0000270 0 0 +OG0000271 0 0 +OG0000272 0 0 +OG0000273 0 0 +OG0000274 0 0 +OG0000275 0 0 +OG0000276 0 0 +OG0000277 0 0 +OG0000278 0 0 +OG0000279 0 0 +OG0000280 0 0 +OG0000281 0 0 +OG0000282 0 0 +OG0000283 0 0 +OG0000284 0 0 +OG0000285 0 0 +OG0000286 0 0 +OG0000287 0 0 +OG0000288 0 0 +OG0000289 0 0 +OG0000290 0 0 +OG0000291 0 0 +OG0000292 0 0 +OG0000293 0 0 +OG0000294 0 0 +OG0000295 0 0 +OG0000296 0 0 +OG0000297 0 0 +OG0000298 0 0 +OG0000299 0 0 +OG0000300 0 0 +OG0000301 0 0 +OG0000302 0 0 +OG0000303 0 0 +OG0000304 0 0 +OG0000305 0 0 +OG0000306 0 0 +OG0000307 0 0 +OG0000308 0 0 +OG0000309 0 0 +OG0000310 0 0 +OG0000311 0 0 +OG0000312 0 0 +OG0000313 0 0 +OG0000314 0 0 +OG0000315 0 0 +OG0000316 0 0 +OG0000317 0 0 +OG0000318 0 0 +OG0000319 0 0 +OG0000320 0 0 +OG0000321 0 0 +OG0000322 0 0 +OG0000323 0 0 +OG0000324 0 0 +OG0000325 0 0 +OG0000326 0 0 +OG0000327 0 0 +OG0000328 0 0 +OG0000329 0 0 +OG0000330 0 0 +OG0000331 0 0 +OG0000332 0 0 +OG0000333 0 0 +OG0000334 0 0 +OG0000335 0 0 +OG0000336 0 0 +OG0000337 0 0 +OG0000338 0 0 +OG0000339 0 0 +OG0000340 0 0 +OG0000341 0 0 +OG0000342 0 0 +OG0000343 0 0 +OG0000344 0 0 +OG0000345 0 0 +OG0000346 0 0 +OG0000347 0 0 +OG0000348 0 0 +OG0000349 0 0 +OG0000350 0 0 +OG0000351 0 0 +OG0000352 0 0 +OG0000353 0 0 +OG0000354 0 0 +OG0000355 0 0 +OG0000356 0 0 +OG0000357 0 0 +OG0000358 0 0 +OG0000359 0 0 +OG0000360 0 0 +OG0000361 0 0 +OG0000362 0 0 +OG0000363 0 0 +OG0000364 0 0 +OG0000365 0 0 +OG0000366 0 0 +OG0000367 0 0 +OG0000368 0 0 +OG0000369 0 0 +OG0000370 0 0 +OG0000371 0 0 +OG0000372 0 0 +OG0000373 0 0 +OG0000374 0 0 +OG0000375 0 0 +OG0000376 0 0 +OG0000377 0 0 +OG0000378 0 0 +OG0000379 0 0 +OG0000380 0 0 +OG0000381 0 0 +OG0000382 0 0 +OG0000383 0 0 +OG0000384 0 0 +OG0000385 0 0 +OG0000386 0 0 +OG0000387 0 0 +OG0000388 0 0 +OG0000389 0 0 +OG0000390 0 0 +OG0000391 0 0 +OG0000392 0 0 +OG0000393 0 0 +OG0000394 0 0 +OG0000395 0 0 +OG0000396 0 0 +OG0000397 0 0 +OG0000398 0 0 +OG0000399 0 0 +OG0000400 0 0 +OG0000401 0 0 +OG0000402 0 0 +OG0000403 0 0 +OG0000404 0 0 +OG0000405 0 0 +OG0000406 0 0 +OG0000407 0 0 +OG0000408 0 0 +OG0000409 0 0 +OG0000410 0 0 +OG0000411 0 0 +OG0000412 0 0 +OG0000413 0 0 +OG0000414 0 0 +OG0000415 0 0 +OG0000416 0 0 +OG0000417 0 0 +OG0000418 1 1 +OG0000419 1 1 +OG0000420 1 1 +OG0000421 0 0 +OG0000422 0 0 +OG0000423 0 0 +OG0000424 0 0 +OG0000425 1 1 +OG0000426 0 0 +OG0000427 0 0 +OG0000428 0 0 +OG0000429 0 0 +OG0000430 0 0 +OG0000431 0 0 +OG0000432 1 1 +OG0000433 0 0 +OG0000434 0 0 +OG0000435 0 0 +OG0000436 0 0 +OG0000437 0 0 +OG0000438 0 0 +OG0000439 0 0 +OG0000440 0 0 +OG0000441 0 0 +OG0000442 0 0 +OG0000443 0 0 +OG0000444 0 0 +OG0000445 0 0 +OG0000446 0 0 +OG0000447 0 0 +OG0000448 0 0 +OG0000449 0 0 +OG0000450 0 0 +OG0000451 0 0 +OG0000452 0 0 +OG0000453 0 0 +OG0000454 0 0 +OG0000455 0 0 +OG0000456 0 0 +OG0000457 0 0 +OG0000458 0 0 +OG0000459 0 0 +OG0000460 0 0 +OG0000461 0 0 +OG0000462 0 0 +OG0000463 0 0 +OG0000464 0 0 +OG0000465 0 0 +OG0000466 0 0 +OG0000467 0 0 +OG0000468 0 0 +OG0000469 0 0 +OG0000470 0 0 +OG0000471 0 0 +OG0000472 0 0 +OG0000473 0 0 +OG0000474 0 0 +OG0000475 0 0 +OG0000476 0 0 +OG0000477 0 0 +OG0000478 0 0 +OG0000479 0 0 +OG0000480 0 0 +OG0000481 0 0 +OG0000482 0 0 +OG0000483 0 0 +OG0000484 0 0 +OG0000485 0 0 +OG0000486 0 0 +OG0000487 0 0 +OG0000488 0 0 +OG0000489 0 0 +OG0000490 0 0 +OG0000491 0 0 +OG0000492 0 0 +OG0000493 0 0 +OG0000494 0 0 +OG0000495 0 0 +OG0000496 0 0 +OG0000497 0 0 +OG0000498 0 0 +OG0000499 0 0 +OG0000500 0 0 +OG0000501 0 0 +OG0000502 0 0 +OG0000503 0 0 +OG0000504 0 0 +OG0000505 0 0 +OG0000506 0 0 +OG0000507 0 0 +OG0000508 0 0 +OG0000509 0 0 +OG0000510 0 0 +OG0000511 0 0 +OG0000512 0 0 +OG0000513 0 0 +OG0000514 0 0 +OG0000515 0 0 +OG0000516 0 0 +OG0000517 0 0 +OG0000518 0 0 +OG0000519 0 0 +OG0000520 0 0 +OG0000521 0 0 +OG0000522 0 0 +OG0000523 0 0 +OG0000524 0 0 +OG0000525 0 0 +OG0000526 0 0 +OG0000527 0 0 +OG0000528 0 0 +OG0000529 0 0 +OG0000530 0 0 +OG0000531 0 0 +OG0000532 0 0 +OG0000533 0 0 +OG0000534 0 0 +OG0000535 0 0 +OG0000536 0 0 +OG0000537 0 0 +OG0000538 0 0 +OG0000539 0 0 +OG0000540 0 0 +OG0000541 0 0 +OG0000542 0 0 +OG0000543 0 0 +OG0000544 0 0 +OG0000545 0 0 +OG0000546 0 0 +OG0000547 0 0 +OG0000548 0 0 +OG0000549 0 0 +OG0000550 0 0 +OG0000551 0 0 +OG0000552 0 0 +OG0000553 0 0 +OG0000554 0 0 +OG0000555 0 0 +OG0000556 0 0 +OG0000557 0 0 +OG0000558 0 0 +OG0000559 0 0 +OG0000560 0 0 +OG0000561 0 0 +OG0000562 0 0 +OG0000563 0 0 +OG0000564 0 0 +OG0000565 0 0 +OG0000566 0 0 +OG0000567 0 0 +OG0000568 0 0 +OG0000569 0 0 +OG0000570 0 0 +OG0000571 0 0 +OG0000572 0 0 +OG0000573 2 2 +OG0000574 1 1 +OG0000575 1 1 +OG0000576 1 1 +OG0000577 1 1 +OG0000578 0 0 +OG0000579 0 0 +OG0000580 0 0 +OG0000581 0 0 +OG0000582 0 0 +OG0000583 0 0 +OG0000584 0 0 +OG0000585 0 0 +OG0000586 0 0 +OG0000587 0 0 +OG0000588 0 0 +OG0000589 0 0 +OG0000590 0 0 +OG0000591 0 0 +OG0000592 0 0 +OG0000593 0 0 +OG0000594 0 0 +OG0000595 1 1 +OG0000596 0 0 +OG0000597 0 0 +OG0000598 0 0 +OG0000599 0 0 +OG0000600 0 0 +OG0000601 0 0 +OG0000602 0 0 +OG0000603 0 0 +OG0000604 0 0 +OG0000605 0 0 +OG0000606 0 0 +OG0000607 0 0 +OG0000608 0 0 +OG0000609 0 0 +OG0000610 0 0 +OG0000611 0 0 +OG0000612 0 0 +OG0000613 0 0 +OG0000614 0 0 +OG0000615 0 0 +OG0000616 0 0 +OG0000617 0 0 +OG0000618 0 0 +OG0000619 0 0 +OG0000620 0 0 +OG0000621 0 0 +OG0000622 0 0 +OG0000623 0 0 +OG0000624 0 0 +OG0000625 0 0 +OG0000626 0 0 +OG0000627 0 0 +OG0000628 0 0 +OG0000629 0 0 +OG0000630 0 0 +OG0000631 0 0 +OG0000632 0 0 +OG0000633 0 0 +OG0000634 0 0 +OG0000635 0 0 +OG0000636 0 0 +OG0000637 0 0 +OG0000638 0 0 +OG0000639 0 0 +OG0000640 0 0 +OG0000641 0 0 +OG0000642 0 0 +OG0000643 0 0 +OG0000644 0 0 +OG0000645 0 0 +OG0000646 0 0 +OG0000647 0 0 +OG0000648 0 0 +OG0000649 0 0 +OG0000650 0 0 +OG0000651 0 0 +OG0000652 0 0 +OG0000653 0 0 +OG0000654 0 0 +OG0000655 0 0 +OG0000656 0 0 +OG0000657 0 0 +OG0000658 0 0 +OG0000659 0 0 +OG0000660 0 0 +OG0000661 0 0 +OG0000662 0 0 +OG0000663 0 0 +OG0000664 0 0 +OG0000665 0 0 +OG0000666 0 0 +OG0000667 0 0 +OG0000668 0 0 +OG0000669 0 0 +OG0000670 0 0 +OG0000671 0 0 +OG0000672 0 0 +OG0000673 0 0 +OG0000674 0 0 +OG0000675 0 0 +OG0000676 0 0 +OG0000677 0 0 +OG0000678 0 0 +OG0000679 0 0 +OG0000680 0 0 +OG0000681 0 0 +OG0000682 0 0 +OG0000683 0 0 +OG0000684 0 0 +OG0000685 0 0 +OG0000686 0 0 +OG0000687 0 0 +OG0000688 0 0 +OG0000689 0 0 +OG0000690 0 0 +OG0000691 0 0 +OG0000692 0 0 +OG0000693 0 0 +OG0000694 0 0 +OG0000695 0 0 +OG0000696 0 0 +OG0000697 0 0 +OG0000698 0 0 +OG0000699 0 0 +OG0000700 0 0 +OG0000701 0 0 +OG0000702 0 0 +OG0000703 0 0 +OG0000704 0 0 +OG0000705 0 0 +OG0000706 0 0 +OG0000707 0 0 +OG0000708 0 0 +OG0000709 0 0 +OG0000710 0 0 +OG0000711 0 0 +OG0000712 0 0 +OG0000713 0 0 +OG0000714 0 0 +OG0000715 0 0 +OG0000716 0 0 +OG0000717 0 0 +OG0000718 0 0 +OG0000719 0 0 +OG0000720 0 0 +OG0000721 0 0 +OG0000722 0 0 +OG0000723 0 0 +OG0000724 0 0 +OG0000725 0 0 +OG0000726 0 0 +OG0000727 0 0 +OG0000728 0 0 +OG0000729 0 0 +OG0000730 0 0 +OG0000731 0 0 +OG0000732 0 0 +OG0000733 0 0 +OG0000734 0 0 +OG0000735 0 0 +OG0000736 0 0 +OG0000737 0 0 +OG0000738 0 0 +OG0000739 0 0 +OG0000740 0 0 +OG0000741 0 0 +OG0000742 0 0 +OG0000743 0 0 +OG0000744 0 0 +OG0000745 0 0 +OG0000746 0 0 +OG0000747 0 0 +OG0000748 0 0 +OG0000749 0 0 +OG0000750 0 0 +OG0000751 0 0 +OG0000752 0 0 +OG0000753 0 0 +OG0000754 0 0 +OG0000755 0 0 +OG0000756 0 0 +OG0000757 0 0 +OG0000758 0 0 +OG0000759 0 0 +OG0000760 0 0 +OG0000761 0 0 +OG0000762 0 0 +OG0000763 0 0 +OG0000764 0 0 +OG0000765 0 0 +OG0000766 0 0 +OG0000767 0 0 +OG0000768 0 0 +OG0000769 0 0 +OG0000770 0 0 +OG0000771 0 0 +OG0000772 0 0 +OG0000773 0 0 +OG0000774 0 0 +OG0000775 0 0 +OG0000776 0 0 +OG0000777 0 0 +OG0000778 0 0 +OG0000779 0 0 +OG0000780 0 0 +OG0000781 0 0 +OG0000782 0 0 +OG0000783 0 0 +OG0000784 0 0 +OG0000785 0 0 +OG0000786 0 0 +OG0000787 0 0 +OG0000788 0 0 +OG0000789 0 0 +OG0000790 0 0 +OG0000791 0 0 +OG0000792 0 0 +OG0000793 0 0 +OG0000794 0 0 +OG0000795 0 0 +OG0000796 0 0 +OG0000797 0 0 +OG0000798 0 0 +OG0000799 0 0 +OG0000800 0 0 +OG0000801 0 0 +OG0000802 0 0 +OG0000803 0 0 +OG0000804 0 0 +OG0000805 0 0 +OG0000806 0 0 +OG0000807 0 0 +OG0000808 0 0 +OG0000809 0 0 +OG0000810 0 0 +OG0000811 0 0 +OG0000812 0 0 +OG0000813 0 0 +OG0000814 0 0 +OG0000815 0 0 +OG0000816 0 0 +OG0000817 0 0 +OG0000818 0 0 +OG0000819 0 0 +OG0000820 0 0 +OG0000821 0 0 +OG0000822 0 0 +OG0000823 0 0 +OG0000824 0 0 +OG0000825 0 0 +OG0000826 0 0 +OG0000827 0 0 +OG0000828 0 0 +OG0000829 0 0 +OG0000830 0 0 +OG0000831 0 0 +OG0000832 0 0 +OG0000833 0 0 +OG0000834 0 0 +OG0000835 0 0 +OG0000836 0 0 +OG0000837 0 0 +OG0000838 0 0 +OG0000839 0 0 +OG0000840 0 0 +OG0000841 0 0 +OG0000842 0 0 +OG0000843 0 0 +OG0000844 0 0 +OG0000845 0 0 +OG0000846 0 0 +OG0000847 0 0 +OG0000848 0 0 +OG0000849 0 0 +OG0000850 0 0 +OG0000851 0 0 +OG0000852 0 0 +OG0000853 0 0 +OG0000854 0 0 +OG0000855 0 0 +OG0000856 0 0 +OG0000857 0 0 +OG0000858 0 0 +OG0000859 0 0 +OG0000860 0 0 +OG0000861 0 0 +OG0000862 0 0 +OG0000863 0 0 +OG0000864 1 1 +OG0000865 0 0 +OG0000866 0 0 +OG0000867 0 0 +OG0000868 0 0 +OG0000869 0 0 +OG0000870 0 0 +OG0000871 0 0 +OG0000872 0 0 +OG0000873 0 0 +OG0000874 0 0 +OG0000875 0 0 +OG0000876 0 0 +OG0000877 0 0 +OG0000878 0 0 +OG0000879 0 0 +OG0000880 0 0 +OG0000881 0 0 +OG0000882 0 0 +OG0000883 0 0 +OG0000884 0 0 +OG0000885 0 0 +OG0000886 0 0 +OG0000887 0 0 +OG0000888 0 0 +OG0000889 0 0 +OG0000890 0 0 +OG0000891 0 0 +OG0000892 0 0 +OG0000893 0 0 +OG0000894 0 0 +OG0000895 0 0 +OG0000896 0 0 +OG0000897 0 0 +OG0000898 0 0 +OG0000899 0 0 +OG0000900 0 0 +OG0000901 0 0 +OG0000902 0 0 +OG0000903 0 0 +OG0000904 0 0 +OG0000905 0 0 +OG0000906 0 0 +OG0000907 0 0 +OG0000908 0 0 +OG0000909 0 0 +OG0000910 0 0 +OG0000911 0 0 +OG0000912 0 0 +OG0000913 0 0 +OG0000914 0 0 +OG0000915 0 0 +OG0000916 0 0 +OG0000917 0 0 +OG0000918 0 0 +OG0000919 0 0 +OG0000920 0 0 +OG0000921 0 0 +OG0000922 0 0 +OG0000923 0 0 +OG0000924 0 0 +OG0000925 0 0 +OG0000926 0 0 +OG0000927 0 0 +OG0000928 0 0 +OG0000929 0 0 +OG0000930 0 0 +OG0000931 0 0 +OG0000932 0 0 +OG0000933 0 0 +OG0000934 0 0 +OG0000935 0 0 +OG0000936 0 0 +OG0000937 0 0 +OG0000938 0 0 +OG0000939 0 0 +OG0000940 0 0 +OG0000941 0 0 +OG0000942 0 0 +OG0000943 0 0 +OG0000944 0 0 +OG0000945 0 0 +OG0000946 0 0 +OG0000947 0 0 +OG0000948 0 0 +OG0000949 0 0 +OG0000950 0 0 +OG0000951 0 0 +OG0000952 0 0 +OG0000953 0 0 +OG0000954 0 0 +OG0000955 0 0 +OG0000956 0 0 +OG0000957 0 0 +OG0000958 0 0 +OG0000959 0 0 +OG0000960 0 0 +OG0000961 0 0 +OG0000962 0 0 +OG0000963 0 0 +OG0000964 0 0 +OG0000965 0 0 +OG0000966 0 0 +OG0000967 0 0 +OG0000968 0 0 +OG0000969 0 0 +OG0000970 0 0 +OG0000971 0 0 +OG0000972 0 0 +OG0000973 0 0 +OG0000974 0 0 +OG0000975 0 0 +OG0000976 0 0 +OG0000977 0 0 +OG0000978 0 0 +OG0000979 0 0 +OG0000980 0 0 +OG0000981 0 0 +OG0000982 0 0 +OG0000983 0 0 +OG0000984 0 0 +OG0000985 0 0 +OG0000986 0 0 +OG0000987 0 0 +OG0000988 0 0 +OG0000989 0 0 +OG0000990 0 0 +OG0000991 0 0 +OG0000992 0 0 +OG0000993 0 0 +OG0000994 0 0 +OG0000995 0 0 +OG0000996 0 0 +OG0000997 0 0 +OG0000998 0 0 +OG0000999 0 0 +OG0001000 0 0 +OG0001001 0 0 +OG0001002 0 0 +OG0001003 0 0 +OG0001004 0 0 +OG0001005 0 0 +OG0001006 0 0 +OG0001007 0 0 +OG0001008 0 0 +OG0001009 0 0 +OG0001010 0 0 +OG0001011 0 0 +OG0001012 0 0 +OG0001013 0 0 +OG0001014 0 0 +OG0001015 0 0 +OG0001016 0 0 +OG0001017 0 0 +OG0001018 0 0 +OG0001019 0 0 +OG0001020 0 0 +OG0001021 0 0 +OG0001022 0 0 +OG0001023 0 0 +OG0001024 0 0 +OG0001025 0 0 +OG0001026 0 0 +OG0001027 0 0 +OG0001028 0 0 +OG0001029 0 0 +OG0001030 0 0 +OG0001031 0 0 +OG0001032 0 0 +OG0001033 0 0 +OG0001034 0 0 +OG0001035 0 0 +OG0001036 0 0 +OG0001037 0 0 +OG0001038 0 0 +OG0001039 0 0 +OG0001040 0 0 +OG0001041 0 0 +OG0001042 0 0 +OG0001043 0 0 +OG0001044 0 0 +OG0001045 0 0 +OG0001046 0 0 +OG0001047 0 0 +OG0001048 0 0 +OG0001049 0 0 +OG0001050 0 0 +OG0001051 0 0 +OG0001052 0 0 +OG0001053 0 0 +OG0001054 0 0 +OG0001055 0 0 +OG0001056 0 0 +OG0001057 0 0 +OG0001058 0 0 +OG0001059 0 0 +OG0001060 0 0 +OG0001061 0 0 +OG0001062 0 0 +OG0001063 0 0 +OG0001064 0 0 +OG0001065 0 0 +OG0001066 0 0 +OG0001067 0 0 +OG0001068 0 0 +OG0001069 0 0 +OG0001070 0 0 +OG0001071 0 0 +OG0001072 0 0 +OG0001073 0 0 +OG0001074 0 0 +OG0001075 0 0 +OG0001076 0 0 +OG0001077 0 0 +OG0001078 0 0 +OG0001079 0 0 +OG0001080 0 0 +OG0001081 0 0 +OG0001082 0 0 +OG0001083 0 0 +OG0001084 0 0 +OG0001085 0 0 +OG0001086 0 0 +OG0001087 0 0 +OG0001088 0 0 +OG0001089 0 0 +OG0001090 0 0 +OG0001091 0 0 +OG0001092 0 0 +OG0001093 0 0 +OG0001094 0 0 +OG0001095 0 0 +OG0001096 0 0 +OG0001097 0 0 +OG0001098 0 0 +OG0001099 0 0 +OG0001100 0 0 +OG0001101 0 0 +OG0001102 0 0 +OG0001103 0 0 +OG0001104 0 0 +OG0001105 0 0 +OG0001106 0 0 +OG0001107 0 0 +OG0001108 0 0 +OG0001109 0 0 +OG0001110 0 0 +OG0001111 0 0 +OG0001112 0 0 +OG0001113 0 0 +OG0001114 0 0 +OG0001115 0 0 +OG0001116 0 0 +OG0001117 0 0 +OG0001118 0 0 +OG0001119 0 0 +OG0001120 0 0 +OG0001121 0 0 +OG0001122 0 0 +OG0001123 0 0 +OG0001124 0 0 +OG0001125 0 0 +OG0001126 0 0 +OG0001127 0 0 +OG0001128 0 0 +OG0001129 0 0 +OG0001130 0 0 +OG0001131 0 0 +OG0001132 0 0 +OG0001133 0 0 +OG0001134 0 0 +OG0001135 0 0 +OG0001136 0 0 +OG0001137 0 0 +OG0001138 0 0 +OG0001139 0 0 +OG0001140 0 0 +OG0001141 0 0 +OG0001142 0 0 +OG0001143 0 0 +OG0001144 0 0 +OG0001145 0 0 +OG0001146 0 0 +OG0001147 0 0 +OG0001148 0 0 +OG0001149 0 0 +OG0001150 0 0 +OG0001151 0 0 +OG0001152 0 0 +OG0001153 0 0 +OG0001154 0 0 +OG0001155 0 0 +OG0001156 0 0 +OG0001157 0 0 +OG0001158 0 0 +OG0001159 0 0 +OG0001160 0 0 +OG0001161 0 0 +OG0001162 0 0 +OG0001163 0 0 +OG0001164 0 0 +OG0001165 0 0 +OG0001166 0 0 +OG0001167 0 0 +OG0001168 0 0 +OG0001169 0 0 +OG0001170 0 0 +OG0001171 0 0 +OG0001172 0 0 +OG0001173 0 0 +OG0001174 0 0 +OG0001175 0 0 +OG0001176 0 0 +OG0001177 0 0 +OG0001178 0 0 +OG0001179 0 0 +OG0001180 0 0 +OG0001181 0 0 +OG0001182 0 0 +OG0001183 0 0 +OG0001184 0 0 +OG0001185 0 0 +OG0001186 0 0 +OG0001187 0 0 +OG0001188 0 0 +OG0001189 0 0 +OG0001190 0 0 +OG0001191 0 0 +OG0001192 0 0 +OG0001193 0 0 +OG0001194 0 0 +OG0001195 0 0 +OG0001196 0 0 +OG0001197 0 0 +OG0001198 0 0 +OG0001199 0 0 +OG0001200 0 0 +OG0001201 0 0 +OG0001202 0 0 +OG0001203 0 0 +OG0001204 0 0 +OG0001205 0 0 +OG0001206 0 0 +OG0001207 0 0 +OG0001208 0 0 +OG0001209 0 0 +OG0001210 0 0 +OG0001211 0 0 +OG0001212 0 0 +OG0001213 0 0 +OG0001214 0 0 +OG0001215 0 0 +OG0001216 0 0 +OG0001217 0 0 +OG0001218 0 0 +OG0001219 0 0 +OG0001220 0 0 +OG0001221 0 0 +OG0001222 0 0 +OG0001223 0 0 +OG0001224 0 0 +OG0001225 0 0 +OG0001226 0 0 +OG0001227 0 0 +OG0001228 0 0 +OG0001229 0 0 +OG0001230 0 0 +OG0001231 0 0 +OG0001232 0 0 +OG0001233 0 0 +OG0001234 0 0 +OG0001235 0 0 +OG0001236 0 0 +OG0001237 0 0 +OG0001238 0 0 +OG0001239 0 0 +OG0001240 0 0 +OG0001241 0 0 +OG0001242 0 0 +OG0001243 0 0 +OG0001244 0 0 +OG0001245 0 0 +OG0001246 0 0 +OG0001247 0 0 +OG0001248 0 0 +OG0001249 0 0 +OG0001250 0 0 +OG0001251 0 0 +OG0001252 0 0 +OG0001253 0 0 +OG0001254 0 0 +OG0001255 0 0 +OG0001256 0 0 +OG0001257 0 0 +OG0001258 0 0 +OG0001259 0 0 +OG0001260 0 0 +OG0001261 0 0 +OG0001262 0 0 +OG0001263 0 0 +OG0001264 0 0 +OG0001265 0 0 +OG0001266 0 0 +OG0001267 0 0 +OG0001268 0 0 +OG0001269 0 0 +OG0001270 0 0 +OG0001271 0 0 +OG0001272 0 0 +OG0001273 0 0 +OG0001274 0 0 +OG0001275 0 0 +OG0001276 0 0 +OG0001277 0 0 +OG0001278 0 0 +OG0001279 0 0 +OG0001280 0 0 +OG0001281 0 0 +OG0001282 0 0 +OG0001283 0 0 +OG0001284 0 0 +OG0001285 0 0 +OG0001286 0 0 +OG0001287 0 0 +OG0001288 0 0 +OG0001289 0 0 +OG0001290 0 0 +OG0001291 0 0 +OG0001292 0 0 +OG0001293 0 0 +OG0001294 0 0 +OG0001295 0 0 +OG0001296 0 0 +OG0001297 0 0 +OG0001298 0 0 +OG0001299 0 0 +OG0001300 0 0 +OG0001301 0 0 +OG0001302 0 0 +OG0001303 0 0 +OG0001304 0 0 +OG0001305 0 0 +OG0001306 0 0 +OG0001307 0 0 +OG0001308 0 0 +OG0001309 0 0 +OG0001310 0 0 +OG0001311 0 0 +OG0001312 0 0 +OG0001313 1 1 +OG0001314 0 0 +OG0001315 0 0 +OG0001316 0 0 +OG0001317 0 0 +OG0001318 0 0 +OG0001319 0 0 +OG0001320 0 0 +OG0001321 0 0 +OG0001322 0 0 +OG0001323 0 0 +OG0001324 0 0 +OG0001325 0 0 +OG0001326 0 0 +OG0001327 0 0 +OG0001328 0 0 +OG0001329 0 0 +OG0001330 0 0 +OG0001331 0 0 +OG0001332 0 0 +OG0001333 0 0 +OG0001334 0 0 +OG0001335 0 0 +OG0001336 0 0 +OG0001337 0 0 +OG0001338 0 0 +OG0001339 0 0 +OG0001340 0 0 +OG0001341 0 0 +OG0001342 0 0 +OG0001343 0 0 +OG0001344 0 0 +OG0001345 0 0 +OG0001346 0 0 +OG0001347 0 0 +OG0001348 0 0 +OG0001349 0 0 +OG0001350 0 0 +OG0001351 0 0 +OG0001352 0 0 +OG0001353 0 0 +OG0001354 0 0 +OG0001355 0 0 +OG0001356 0 0 +OG0001357 0 0 +OG0001358 0 0 +OG0001359 0 0 +OG0001360 0 0 +OG0001361 0 0 +OG0001362 0 0 +OG0001363 0 0 +OG0001364 0 0 +OG0001365 0 0 +OG0001366 0 0 +OG0001367 0 0 +OG0001368 0 0 +OG0001369 0 0 +OG0001370 0 0 +OG0001371 0 0 +OG0001372 0 0 +OG0001373 0 0 +OG0001374 0 0 +OG0001375 0 0 +OG0001376 0 0 +OG0001377 0 0 +OG0001378 0 0 +OG0001379 0 0 +OG0001380 0 0 +OG0001381 0 0 +OG0001382 0 0 +OG0001383 0 0 +OG0001384 0 0 +OG0001385 0 0 +OG0001386 0 0 +OG0001387 0 0 +OG0001388 0 0 +OG0001389 0 0 +OG0001390 0 0 +OG0001391 0 0 +OG0001392 0 0 +OG0001393 0 0 +OG0001394 0 0 +OG0001395 0 0 +OG0001396 0 0 +OG0001397 0 0 +OG0001398 0 0 +OG0001399 0 0 +OG0001400 0 0 +OG0001401 0 0 +OG0001402 0 0 +OG0001403 0 0 +OG0001404 0 0 +OG0001405 0 0 +OG0001406 0 0 +OG0001407 0 0 +OG0001408 0 0 +OG0001409 0 0 +OG0001410 0 0 +OG0001411 0 0 +OG0001412 0 0 +OG0001413 0 0 +OG0001414 0 0 +OG0001415 0 0 +OG0001416 0 0 +OG0001417 0 0 +OG0001418 0 0 +OG0001419 0 0 +OG0001420 0 0 +OG0001421 0 0 +OG0001422 0 0 +OG0001423 0 0 +OG0001424 0 0 +OG0001425 0 0 +OG0001426 0 0 +OG0001427 0 0 +OG0001428 0 0 +OG0001429 0 0 +OG0001430 0 0 +OG0001431 0 0 +OG0001432 0 0 +OG0001433 0 0 +OG0001434 0 0 +OG0001435 0 0 +OG0001436 0 0 +OG0001437 0 0 +OG0001438 0 0 +OG0001439 0 0 +OG0001440 0 0 +OG0001441 0 0 +OG0001442 0 0 +OG0001443 0 0 +OG0001444 0 0 +OG0001445 0 0 +OG0001446 0 0 +OG0001447 0 0 +OG0001448 0 0 +OG0001449 0 0 +OG0001450 0 0 +OG0001451 0 0 +OG0001452 0 0 +OG0001453 0 0 +OG0001454 0 0 +OG0001455 0 0 +OG0001456 0 0 +OG0001457 0 0 +OG0001458 0 0 +OG0001459 0 0 +OG0001460 0 0 +OG0001461 0 0 +OG0001462 0 0 +OG0001463 0 0 +OG0001464 0 0 +OG0001465 0 0 +OG0001466 0 0 +OG0001467 0 0 +OG0001468 0 0 +OG0001469 0 0 +OG0001470 0 0 +OG0001471 0 0 +OG0001472 0 0 +OG0001473 0 0 +OG0001474 0 0 +OG0001475 0 0 +OG0001476 0 0 +OG0001477 0 0 +OG0001478 0 0 +OG0001479 0 0 +OG0001480 0 0 +OG0001481 0 0 +OG0001482 0 0 +OG0001483 0 0 +OG0001484 0 0 +OG0001485 0 0 +OG0001486 0 0 +OG0001487 0 0 +OG0001488 0 0 +OG0001489 0 0 +OG0001490 0 0 +OG0001491 0 0 +OG0001492 0 0 +OG0001493 0 0 +OG0001494 0 0 +OG0001495 0 0 +OG0001496 0 0 +OG0001497 0 0 +OG0001498 0 0 +OG0001499 0 0 +OG0001500 0 0 +OG0001501 0 0 +OG0001502 0 0 +OG0001503 0 0 +OG0001504 1 1 +OG0001505 0 0 +OG0001506 0 0 +OG0001507 0 0 +OG0001508 0 0 +OG0001509 0 0 +OG0001510 0 0 +OG0001511 0 0 +OG0001512 0 0 +OG0001513 0 0 +OG0001514 0 0 +OG0001515 0 0 +OG0001516 0 0 +OG0001517 0 0 +OG0001518 0 0 +OG0001519 0 0 +OG0001520 0 0 +OG0001521 0 0 +OG0001522 0 0 +OG0001523 0 0 +OG0001524 0 0 +OG0001525 0 0 +OG0001526 0 0 +OG0001527 0 0 +OG0001528 0 0 +OG0001529 0 0 +OG0001530 0 0 +OG0001531 0 0 +OG0001532 0 0 +OG0001533 0 0 +OG0001534 0 0 +OG0001535 0 0 +OG0001536 0 0 +OG0001537 0 0 +OG0001538 0 0 +OG0001539 0 0 +OG0001540 0 0 +OG0001541 0 0 +OG0001542 0 0 +OG0001543 0 0 +OG0001544 0 0 +OG0001545 0 0 +OG0001546 0 0 +OG0001547 0 0 +OG0001548 0 0 +OG0001549 0 0 +OG0001550 0 0 +OG0001551 0 0 +OG0001552 0 0 +OG0001553 0 0 +OG0001554 0 0 +OG0001555 0 0 +OG0001556 0 0 +OG0001557 0 0 +OG0001558 0 0 +OG0001559 0 0 +OG0001560 0 0 +OG0001561 0 0 +OG0001562 0 0 +OG0001563 0 0 +OG0001564 0 0 +OG0001565 0 0 +OG0001566 0 0 +OG0001567 0 0 +OG0001568 0 0 +OG0001569 0 0 +OG0001570 1 1 +OG0001571 1 1 +OG0001572 0 0 +OG0001573 0 0 +OG0001574 0 0 +OG0001575 0 0 +OG0001576 0 0 +OG0001577 0 0 +OG0001578 0 0 +OG0001579 0 0 +OG0001580 0 0 +OG0001581 0 0 +OG0001582 0 0 +OG0001583 0 0 +OG0001584 0 0 +OG0001585 0 0 +OG0001586 0 0 +OG0001587 0 0 +OG0001588 0 0 +OG0001589 0 0 +OG0001590 0 0 +OG0001591 0 0 +OG0001592 0 0 +OG0001593 0 0 +OG0001594 0 0 +OG0001595 0 0 +OG0001596 0 0 +OG0001597 0 0 +OG0001598 0 0 +OG0001599 0 0 +OG0001600 0 0 +OG0001601 0 0 +OG0001602 0 0 +OG0001603 0 0 +OG0001604 0 0 +OG0001605 0 0 +OG0001606 0 0 +OG0001607 0 0 +OG0001608 0 0 +OG0001609 0 0 +OG0001610 0 0 +OG0001611 0 0 +OG0001612 0 0 +OG0001613 0 0 +OG0001614 0 0 +OG0001615 0 0 +OG0001616 0 0 +OG0001617 0 0 +OG0001618 0 0 +OG0001619 0 0 +OG0001620 0 0 +OG0001621 0 0 +OG0001622 0 0 +OG0001623 0 0 +OG0001624 1 1 +OG0001625 0 0 +OG0001626 0 0 +OG0001627 0 0 +OG0001628 0 0 +OG0001629 0 0 +OG0001630 0 0 +OG0001631 1 1 +OG0001632 0 0 +OG0001633 0 0 +OG0001634 0 0 +OG0001635 0 0 +OG0001636 0 0 +OG0001637 0 0 +OG0001638 0 0 +OG0001639 0 0 +OG0001640 1 1 +OG0001641 2 2 +OG0001642 0 0 +OG0001643 0 0 +OG0001644 0 0 +OG0001645 0 0 +OG0001646 0 0 +OG0001647 0 0 +OG0001648 0 0 +OG0001649 0 0 +OG0001650 0 0 +OG0001651 0 0 +OG0001652 0 0 +OG0001653 0 0 +OG0001654 0 0 +OG0001655 0 0 +OG0001656 0 0 +OG0001657 0 0 +OG0001658 0 0 +OG0001659 0 0 +OG0001660 0 0 +OG0001661 0 0 +OG0001662 0 0 +OG0001663 0 0 +OG0001664 0 0 +OG0001665 0 0 +OG0001666 0 0 +OG0001667 0 0 +OG0001668 0 0 +OG0001669 0 0 +OG0001670 0 0 +OG0001671 0 0 +OG0001672 0 0 +OG0001673 0 0 +OG0001674 0 0 +OG0001675 0 0 +OG0001676 0 0 +OG0001677 0 0 +OG0001678 0 0 +OG0001679 0 0 +OG0001680 0 0 +OG0001681 0 0 +OG0001682 0 0 +OG0001683 0 0 +OG0001684 0 0 +OG0001685 0 0 +OG0001686 0 0 +OG0001687 0 0 +OG0001688 0 0 +OG0001689 0 0 +OG0001690 0 0 +OG0001691 0 0 +OG0001692 0 0 +OG0001693 0 0 +OG0001694 0 0 +OG0001695 0 0 +OG0001696 0 0 +OG0001697 0 0 +OG0001698 0 0 +OG0001699 0 0 +OG0001700 0 0 +OG0001701 0 0 +OG0001702 0 0 +OG0001703 0 0 +OG0001704 0 0 +OG0001705 0 0 +OG0001706 0 0 +OG0001707 0 0 +OG0001708 0 0 +OG0001709 0 0 +OG0001710 0 0 +OG0001711 0 0 +OG0001712 0 0 +OG0001713 0 0 +OG0001714 0 0 +OG0001715 0 0 +OG0001716 0 0 +OG0001717 0 0 +OG0001718 0 0 +OG0001719 0 0 +OG0001720 0 0 +OG0001721 0 0 +OG0001722 0 0 +OG0001723 0 0 +OG0001724 0 0 +OG0001725 0 0 +OG0001726 1 1 +OG0001727 0 0 +OG0001728 0 0 +OG0001729 0 0 +OG0001730 0 0 +OG0001731 0 0 +OG0001732 0 0 +OG0001733 0 0 +OG0001734 0 0 +OG0001735 0 0 +OG0001736 0 0 +OG0001737 0 0 +OG0001738 0 0 +OG0001739 0 0 +OG0001740 0 0 +OG0001741 0 0 +OG0001742 0 0 +OG0001743 0 0 +OG0001744 0 0 +OG0001745 0 0 +OG0001746 0 0 +OG0001747 0 0 +OG0001748 0 0 +OG0001749 0 0 +OG0001750 0 0 +OG0001751 0 0 +OG0001752 0 0 +OG0001753 0 0 +OG0001754 0 0 +OG0001755 0 0 +OG0001756 0 0 +OG0001757 0 0 +OG0001758 0 0 +OG0001759 1 1 +OG0001760 2 2 +OG0001761 2 2 +OG0001762 1 1 +OG0001763 1 1 +OG0001764 1 1 +OG0001765 1 1 +OG0001766 1 1 +OG0001767 2 1 +OG0001768 3 3 +OG0001769 3 3 +OG0001770 0 0 +OG0001771 1 1 +OG0001772 0 0 +OG0001773 0 0 +OG0001774 0 0 +OG0001775 0 0 +OG0001776 0 0 +OG0001777 0 0 +OG0001778 0 0 +OG0001779 0 0 +OG0001780 0 0 +OG0001781 0 0 +OG0001782 0 0 +OG0001783 0 0 +OG0001784 0 0 +OG0001785 0 0 +OG0001786 0 0 +OG0001787 1 1 +OG0001788 0 0 +OG0001789 0 0 +OG0001790 0 0 +OG0001791 0 0 +OG0001792 0 0 +OG0001793 0 0 +OG0001794 0 0 +OG0001795 0 0 +OG0001796 0 0 +OG0001797 0 0 +OG0001798 0 0 +OG0001799 0 0 +OG0001800 0 0 +OG0001801 0 0 +OG0001802 0 0 +OG0001803 0 0 +OG0001804 0 0 +OG0001805 0 0 +OG0001806 0 0 +OG0001807 0 0 +OG0001808 0 0 +OG0001809 0 0 +OG0001810 0 0 +OG0001811 0 0 +OG0001812 0 0 +OG0001813 0 0 +OG0001814 0 0 +OG0001815 0 0 +OG0001816 0 0 +OG0001817 0 0 +OG0001818 0 0 +OG0001819 0 0 +OG0001820 0 0 +OG0001821 1 1 +OG0001822 2 2 +OG0001823 0 0 +OG0001824 0 0 +OG0001825 0 0 +OG0001826 0 0 +OG0001827 0 0 +OG0001828 0 0 +OG0001829 0 0 +OG0001830 0 0 +OG0001831 0 0 +OG0001832 0 0 +OG0001833 0 0 +OG0001834 0 0 +OG0001835 0 0 +OG0001836 0 0 +OG0001837 0 0 +OG0001838 0 0 +OG0001839 0 0 +OG0001840 1 1 +OG0001841 0 0 +OG0001842 0 0 +OG0001843 0 0 +OG0001844 0 0 +OG0001845 0 0 +OG0001846 0 0 +OG0001847 0 0 +OG0001848 0 0 +OG0001849 0 0 +OG0001850 0 0 +OG0001851 0 0 +OG0001852 0 0 +OG0001853 0 0 +OG0001854 0 0 +OG0001855 0 0 +OG0001856 0 0 +OG0001857 0 0 +OG0001858 0 0 +OG0001859 0 0 +OG0001860 1 1 +OG0001861 0 0 +OG0001862 0 0 +OG0001863 0 0 +OG0001864 0 0 +OG0001865 0 0 +OG0001866 0 0 +OG0001867 0 0 +OG0001868 0 0 +OG0001869 0 0 +OG0001870 0 0 +OG0001871 0 0 +OG0001872 0 0 +OG0001873 2 2 +OG0001874 0 0 +OG0001875 0 0 +OG0001876 0 0 +OG0001877 0 0 +OG0001878 0 0 +OG0001879 0 0 +OG0001880 0 0 +OG0001881 1 1 +OG0001882 0 0 +OG0001883 1 1 +OG0001884 0 0 +OG0001885 0 0 +OG0001886 0 0 +OG0001887 0 0 +OG0001888 0 0 +OG0001889 0 0 +OG0001890 0 0 +OG0001891 0 0 +OG0001892 0 0 +OG0001893 0 0 +OG0001894 0 0 +OG0001895 0 0 +OG0001896 0 0 +OG0001897 0 0 +OG0001898 0 0 +OG0001899 0 0 +OG0001900 0 0 +OG0001901 0 0 +OG0001902 0 0 +OG0001903 0 0 +OG0001904 0 0 +OG0001905 0 0 +OG0001906 0 0 +OG0001907 0 0 +OG0001908 0 0 +OG0001909 0 0 +OG0001910 0 0 +OG0001911 0 0 +OG0001912 1 1 +OG0001913 0 0 +OG0001914 0 0 +OG0001915 0 0 +OG0001916 0 0 +OG0001917 0 0 +OG0001918 2 2 +OG0001919 0 0 +OG0001920 0 0 +OG0001921 0 0 +OG0001922 0 0 +OG0001923 0 0 +OG0001924 0 0 +OG0001925 0 0 +OG0001926 0 0 +OG0001927 0 0 +OG0001928 0 0 +OG0001929 0 0 +OG0001930 0 0 +OG0001931 0 0 +OG0001932 0 0 +OG0001933 0 0 +OG0001934 0 0 +OG0001935 0 0 +OG0001936 0 0 +OG0001937 0 0 +OG0001938 1 1 +OG0001939 1 1 +OG0001940 0 0 +OG0001941 0 0 +OG0001942 0 0 +OG0001943 0 0 +OG0001944 0 0 +OG0001945 0 0 +OG0001946 0 0 +OG0001947 0 0 +OG0001948 0 0 +OG0001949 0 0 +OG0001950 0 0 +OG0001951 0 0 +OG0001952 0 0 +OG0001953 1 1 +OG0001954 1 1 +OG0001955 0 0 +OG0001956 0 0 +OG0001957 0 0 +OG0001958 0 0 +OG0001959 0 0 +OG0001960 0 0 +OG0001961 0 0 +OG0001962 0 0 +OG0001963 0 0 +OG0001964 0 0 +OG0001965 0 0 +OG0001966 0 0 +OG0001967 0 0 +OG0001968 0 0 +OG0001969 0 0 +OG0001970 0 0 +OG0001971 0 0 +OG0001972 0 0 +OG0001973 0 0 +OG0001974 0 0 +OG0001975 0 0 +OG0001976 1 1 +OG0001977 2 2 +OG0001978 2 2 +OG0001979 2 2 +OG0001980 2 2 +OG0001981 2 2 +OG0001982 3 3 +OG0001983 3 3 +OG0001984 3 3 +OG0001985 3 3 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/Duplications_per_Species_Tree_Node.tsv b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/Duplications_per_Species_Tree_Node.tsv new file mode 100644 index 0000000000000000000000000000000000000000..27c4afeb14eecdf33285cba573064750aa6b09de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/Duplications_per_Species_Tree_Node.tsv @@ -0,0 +1,10 @@ +Species Tree Node Duplications (all) Duplications (50% support) +N1 22 15 +GCF_023573625 18 18 +GCF_005280335 137 137 +N2 30 13 +GCF_002008305 43 43 +N3 7 7 +GCF_003691675 26 26 +N0 37 8 +GCF_020097155 106 106 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv new file mode 100644 index 0000000000000000000000000000000000000000..a671181846569a4cc7a8398fa02989f49c27c51a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/Orthogroups_SpeciesOverlaps.tsv @@ -0,0 +1,6 @@ + GCF_002008305 GCF_003691675 GCF_005280335 GCF_020097155 GCF_023573625 +GCF_002008305 2095 1989 1922 1841 1983 +GCF_003691675 1989 2104 1919 1843 2013 +GCF_005280335 1922 1919 2108 1884 1914 +GCF_020097155 1841 1843 1884 2035 1867 +GCF_023573625 1983 2013 1914 1867 2096 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/OrthologuesStats_Totals.tsv b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/OrthologuesStats_Totals.tsv new file mode 100644 index 0000000000000000000000000000000000000000..4845a7e5c26ccddcdc29e77c1f66cff8478bd3d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/OrthologuesStats_Totals.tsv @@ -0,0 +1,6 @@ + GCF_002008305 GCF_003691675 GCF_005280335 GCF_020097155 GCF_023573625 +GCF_002008305 0.0 2117.0 1982.0 1885.0 2103.0 +GCF_003691675 2089.0 0.0 1986.0 1881.0 2139.0 +GCF_005280335 2028.0 2045.0 0.0 2012.0 2029.0 +GCF_020097155 1926.0 1914.0 1986.0 0.0 1947.0 +GCF_023573625 2053.0 2119.0 1949.0 1893.0 0.0 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/OrthologuesStats_many-to-many.tsv b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/OrthologuesStats_many-to-many.tsv new file mode 100644 index 0000000000000000000000000000000000000000..d21cb111666da03e7145c1a2605a839bdfec504b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/OrthologuesStats_many-to-many.tsv @@ -0,0 +1,6 @@ + GCF_002008305 GCF_003691675 GCF_005280335 GCF_020097155 GCF_023573625 +GCF_002008305 0.0 2.0 12.0 3.0 8.0 +GCF_003691675 3.0 0.0 18.0 2.0 4.0 +GCF_005280335 12.0 14.0 0.0 17.0 16.0 +GCF_020097155 3.0 2.0 15.0 0.0 2.0 +GCF_023573625 4.0 2.0 16.0 2.0 0.0 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/OrthologuesStats_many-to-one.tsv b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/OrthologuesStats_many-to-one.tsv new file mode 100644 index 0000000000000000000000000000000000000000..87188fb64d5c6a5f4ac5f6cfb017efe7d0caf405 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/OrthologuesStats_many-to-one.tsv @@ -0,0 +1,6 @@ + GCF_002008305 GCF_003691675 GCF_005280335 GCF_020097155 GCF_023573625 +GCF_002008305 0.0 86.0 76.0 59.0 92.0 +GCF_003691675 44.0 0.0 71.0 52.0 50.0 +GCF_005280335 168.0 187.0 0.0 185.0 179.0 +GCF_020097155 133.0 113.0 134.0 0.0 125.0 +GCF_023573625 19.0 22.0 29.0 28.0 0.0 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/OrthologuesStats_one-to-many.tsv b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/OrthologuesStats_one-to-many.tsv new file mode 100644 index 0000000000000000000000000000000000000000..5135c9d0f4e8e6659348426d0cc5abf43824a999 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/OrthologuesStats_one-to-many.tsv @@ -0,0 +1,6 @@ + GCF_002008305 GCF_003691675 GCF_005280335 GCF_020097155 GCF_023573625 +GCF_002008305 0.0 19.0 78.0 58.0 9.0 +GCF_003691675 32.0 0.0 81.0 49.0 10.0 +GCF_005280335 32.0 28.0 0.0 55.0 10.0 +GCF_020097155 25.0 21.0 82.0 0.0 12.0 +GCF_023573625 36.0 20.0 80.0 55.0 0.0 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/OrthologuesStats_one-to-one.tsv b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/OrthologuesStats_one-to-one.tsv new file mode 100644 index 0000000000000000000000000000000000000000..81db82eeb3e82724a9e9b0e15d2d513c979e0cfa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/OrthologuesStats_one-to-one.tsv @@ -0,0 +1,6 @@ + GCF_002008305 GCF_003691675 GCF_005280335 GCF_020097155 GCF_023573625 +GCF_002008305 0.0 2010.0 1816.0 1765.0 1994.0 +GCF_003691675 2010.0 0.0 1816.0 1778.0 2075.0 +GCF_005280335 1816.0 1816.0 0.0 1755.0 1824.0 +GCF_020097155 1765.0 1778.0 1755.0 0.0 1808.0 +GCF_023573625 1994.0 2075.0 1824.0 1808.0 0.0 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/Statistics_Overall.tsv b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/Statistics_Overall.tsv new file mode 100644 index 0000000000000000000000000000000000000000..c8acb9f15b1bc4f5e0c2f0730bd8fbef89ea1e9d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/Statistics_Overall.tsv @@ -0,0 +1,53 @@ +Number of species 5 +Number of genes 11758 +Number of genes in orthogroups 11058 +Number of unassigned genes 700 +Percentage of genes in orthogroups 94.0 +Percentage of unassigned genes 6.0 +Number of orthogroups 2370 +Number of species-specific orthogroups 41 +Number of genes in species-specific orthogroups 98 +Percentage of genes in species-specific orthogroups 0.8 +Mean orthogroup size 4.7 +Median orthogroup size 5.0 +G50 (assigned genes) 5 +G50 (all genes) 5 +O50 (assigned genes) 1017 +O50 (all genes) 1087 +Number of orthogroups with all species present 1709 +Number of single-copy orthogroups 1563 +Date 2026-05-20 +Orthogroups file Orthogroups.tsv +Unassigned genes file Orthogroups_UnassignedGenes.tsv +Per-species statistics Statistics_PerSpecies.tsv +Overall statistics Statistics_Overall.tsv +Orthogroups shared between species Orthogroups_SpeciesOverlaps.tsv + +Average number of genes per-species in orthogroup Number of orthogroups Percentage of orthogroups Number of genes Percentage of genes +<1 600 25.3 1764 16.0 +'1 1753 74.0 8972 81.1 +'2 8 0.3 93 0.8 +'3 3 0.1 49 0.4 +'4 1 0.0 23 0.2 +'5 3 0.1 79 0.7 +'6 1 0.0 32 0.3 +'7 0 0.0 0 0.0 +'8 0 0.0 0 0.0 +'9 1 0.0 46 0.4 +'10 0 0.0 0 0.0 +11-15 0 0.0 0 0.0 +16-20 0 0.0 0 0.0 +21-50 0 0.0 0 0.0 +51-100 0 0.0 0 0.0 +101-150 0 0.0 0 0.0 +151-200 0 0.0 0 0.0 +201-500 0 0.0 0 0.0 +501-1000 0 0.0 0 0.0 +'1001+ 0 0.0 0 0.0 + +Number of species in orthogroup Number of orthogroups +1 41 +2 249 +3 130 +4 241 +5 1709 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv new file mode 100644 index 0000000000000000000000000000000000000000..a4d2a11263893b98817acbb40e6b9646ff0c487d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv @@ -0,0 +1,100 @@ + GCF_002008305 GCF_003691675 GCF_005280335 GCF_020097155 GCF_023573625 +Number of genes 2252 2257 2623 2432 2194 +Number of genes in orthogroups 2192 2203 2300 2205 2158 +Number of unassigned genes 60 54 323 227 36 +Percentage of genes in orthogroups 97.3 97.6 87.7 90.7 98.4 +Percentage of unassigned genes 2.7 2.4 12.3 9.3 1.6 +Number of orthogroups containing species 2095 2104 2108 2035 2096 +Percentage of orthogroups containing species 88.4 88.8 88.9 85.9 88.4 +Number of species-specific orthogroups 1 1 13 26 0 +Number of genes in species-specific orthogroups 2 5 30 61 0 +Percentage of genes in species-specific orthogroups 0.1 0.2 1.1 2.5 0.0 + + +Number of genes per-species in orthogroup Number of orthogroups Number of orthogroups Number of orthogroups Number of orthogroups Number of orthogroups +'0 275 266 262 335 274 +'1 2044 2056 1983 1923 2065 +'2 36 32 98 84 21 +'3 7 4 16 18 2 +'4 2 2 4 7 2 +'5 4 6 2 1 3 +'6 1 1 1 0 2 +'7 0 2 1 1 0 +'8 0 0 1 0 0 +'9 0 0 1 0 0 +'10 0 0 0 0 1 +11-15 0 1 0 0 0 +16-20 0 0 1 1 0 +21-50 1 0 0 0 0 +51-100 0 0 0 0 0 +101-150 0 0 0 0 0 +151-200 0 0 0 0 0 +201-500 0 0 0 0 0 +501-1000 0 0 0 0 0 +'1001+ 0 0 0 0 0 + +Number of genes per-species in orthogroup Percentage of orthogroups Percentage of orthogroups Percentage of orthogroups Percentage of orthogroups Percentage of orthogroups +'0 11.6 11.2 11.1 14.1 11.6 +'1 86.2 86.8 83.7 81.1 87.1 +'2 1.5 1.4 4.1 3.5 0.9 +'3 0.3 0.2 0.7 0.8 0.1 +'4 0.1 0.1 0.2 0.3 0.1 +'5 0.2 0.3 0.1 0.0 0.1 +'6 0.0 0.0 0.0 0.0 0.1 +'7 0.0 0.1 0.0 0.0 0.0 +'8 0.0 0.0 0.0 0.0 0.0 +'9 0.0 0.0 0.0 0.0 0.0 +'10 0.0 0.0 0.0 0.0 0.0 +11-15 0.0 0.0 0.0 0.0 0.0 +16-20 0.0 0.0 0.0 0.0 0.0 +21-50 0.0 0.0 0.0 0.0 0.0 +51-100 0.0 0.0 0.0 0.0 0.0 +101-150 0.0 0.0 0.0 0.0 0.0 +151-200 0.0 0.0 0.0 0.0 0.0 +201-500 0.0 0.0 0.0 0.0 0.0 +501-1000 0.0 0.0 0.0 0.0 0.0 +'1001+ 0.0 0.0 0.0 0.0 0.0 + +Number of genes per-species in orthogroup Number of genes Number of genes Number of genes Number of genes Number of genes +'0 0 0 0 0 0 +'1 2044 2056 1983 1923 2065 +'2 72 64 196 168 42 +'3 21 12 48 54 6 +'4 8 8 16 28 8 +'5 20 30 10 5 15 +'6 6 6 6 0 12 +'7 0 14 7 7 0 +'8 0 0 8 0 0 +'9 0 0 9 0 0 +'10 0 0 0 0 10 +11-15 0 13 0 0 0 +16-20 0 0 17 20 0 +21-50 21 0 0 0 0 +51-100 0 0 0 0 0 +101-150 0 0 0 0 0 +151-200 0 0 0 0 0 +201-500 0 0 0 0 0 +501-1000 0 0 0 0 0 +'1001+ 0 0 0 0 0 + +Number of genes per-species in orthogroup Percentage of genes Percentage of genes Percentage of genes Percentage of genes Percentage of genes +'0 0.0 0.0 0.0 0.0 0.0 +'1 90.8 91.1 75.6 79.1 94.1 +'2 3.2 2.8 7.5 6.9 1.9 +'3 0.9 0.5 1.8 2.2 0.3 +'4 0.4 0.4 0.6 1.2 0.4 +'5 0.9 1.3 0.4 0.2 0.7 +'6 0.3 0.3 0.2 0.0 0.5 +'7 0.0 0.6 0.3 0.3 0.0 +'8 0.0 0.0 0.3 0.0 0.0 +'9 0.0 0.0 0.3 0.0 0.0 +'10 0.0 0.0 0.0 0.0 0.5 +11-15 0.0 0.6 0.0 0.0 0.0 +16-20 0.0 0.0 0.6 0.8 0.0 +21-50 0.9 0.0 0.0 0.0 0.0 +51-100 0.0 0.0 0.0 0.0 0.0 +101-150 0.0 0.0 0.0 0.0 0.0 +151-200 0.0 0.0 0.0 0.0 0.0 +201-500 0.0 0.0 0.0 0.0 0.0 +501-1000 0.0 0.0 0.0 0.0 0.0 +'1001+ 0.0 0.0 0.0 0.0 0.0 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000007.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000007.fa new file mode 100644 index 0000000000000000000000000000000000000000..f50d76316a276d57d49bd9a55d2be421f2add433 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000007.fa @@ -0,0 +1,51 @@ +>PROKKA_00158 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_01033 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKAEDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_01293 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_01383 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_02076 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_01016 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_01103 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_01111 +MRVVLLPAVADRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_01115 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_02022 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_01213 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_00589 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_00591 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_01251 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_01338 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_01886 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>PROKKA_02204 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000066.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000066.fa new file mode 100644 index 0000000000000000000000000000000000000000..e88790c4344cbe4902257b82111d128575e42705 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000066.fa @@ -0,0 +1,37 @@ +>PROKKA_00198 +MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG +PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL +ALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAGYILLSRRAGTHLPGVQGLA +LATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQVLRRMPTALFSL +LTCLSPIAAALTAWAVRGQELTPLDLAGMLLVIAACAAAVWTSRSPGVAGGGRG +>PROKKA_02026 +MAVAVYPLAFYTSIHWAGVAIGSVVSLASAPLASGLLERIVEYRRLSRWWMLAAALGGTG +AALLCLSQLDQEAASSTATLAGVLLGLVAGATYATYSWAAHRLIHDGISRAASMGAVFGA +GGALLLPVLVLTGAPLIATPQAFAVAAYMALVPMFLGYVLFGYGLTRVPASTATTITLTE +PAIAAILAVAVVGERLTPVGWTGLGIIAAVLFILALTPTNTTADRHGRTPTSEAIQPALA +PSPRRHNERTSPRDDAGRGSDVMWVSQTMRCQGATRPSRWEGVRGRFRKPYRLRPVSPDH +GRATCGERTEIMRPARGLDARSVLAATMET +>PROKKA_02194 +MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG +PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL +ALAGIGVLGREGFSADGRIGGAGLDPVGVALALAAAACWAAYILLSQRAGTHLPGVQGLA +LATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQVLRRMPTALFSL +LTCLSPIAAALTAWAVRGQQLTPLDLAGMLLVIAACAAAVWTSRSPGVSGGARG +>PROKKA_00197 +MRLIPLVLLSLLCQQLGASVAGLMFGTTGPAGMVALRLAFSALVLLVLTRPRMRTLAGLS +RRGWVAVVMLGVTMAGMNLLIYAAFDRIPQGVAVTFEVLGPLALSVLANRRWLSVVWAAL +AFAGIALLGRDGFSAGMDGAGLDPLGVAFALAAAACWAGFILANRHAGTHLPGVQGLALA +MVVGSAVAVPVGAADAGPVLLEPWVLAVGLGVALLSSSIPYGIEMQVLRTMPTGLFSLIT +CLSPVVAALTAWAVRGQRLAVLDLGGMGLVVLACGAAVWAAERAARPSRRAPRTS +>PROKKA_00149 +MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG +PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL +ALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSRRAGTHLPGVQGLA +LATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQVLRRMPTALFSL +LTCLSPIAAALTAWAVRGQELTPLDLAGMLLVIAACAAAVWTSRSPGVAGGGRG +>PROKKA_00198 +MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG +PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL +ALVGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSRRAGTHLPGVQGLA +LATAAGSLVALPVGVATAGTALLSPVVLGVGLAVALLSTAVPYGIDLQVLRHMPTALFSL +LTCLSPIAAALTAWAVRGQELTPLDLAGMLLVIAACAAAVWTGRSPGVAGGGRS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000092.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000092.fa new file mode 100644 index 0000000000000000000000000000000000000000..a220b3717450984d166f38d4f70a73081eb3e923 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000092.fa @@ -0,0 +1,25 @@ +>PROKKA_00554 +MSALVRPLRPEDHEAVAELTLASYVDGGHIAPDDAYVKTLMDVADRAGRAEVLVAEVDGE +VAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLAEIVARARAEEGVDAV +VLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGPFLVYRLALD +>PROKKA_00279 +MSALVRPLRPEDHEAVAELTLASYVDGGHIAPDDAYVKTLMDVADRAGRAEVLVAEVDGE +VAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLAEIVARARAEEGVDAV +VLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGPFLVYRLALD +>PROKKA_00640 +MERPAPTAEICPVRPEDTDAVVALWERTLPEYGDPTRPQRAPRPSIRRKLDWGDGLFWLA +VSDEEVVGTVMAGYDGHRGWIYSLAVHPDHRRGGLGTALVAHAEQELARLGCPKVNLQVL +ATNADGAEFWAATGYQPDPVLGLGKRLGG +>PROKKA_02391 +MTETAPTVPTPPARPQVRPLRPEDHEAVAALTVASYVDGGHIAPGSRYVKTLRDVAGRAA +RAEVLVAEVDGQVAGSVVLTPLGSPMAETAAPGEYEFRMLAVHPDHHRRGVARTLMAVIE +ERARALPGIEAIALTTMPTMTDAHRLYEALGYVRVPERDWYLRDVIPDLDPADETGPFLV +YRLPLA +>PROKKA_02275 +MSDVTVRALRPEDHEAVAALTLASYTTGGHFEAESDYLETLADVAGRAAVAEVLVAELDG +QVAGSLVLTPHGSPMAETSVPGEYEFRMLAVDPAVHRRGVATALLAEVVRRARATPGVEA +IALSTMTSMTDAHRMYERLGFVRVPDRDWRLSDLEPGLDPAEDAGPFLVYRLPLT +>PROKKA_00557 +MSALVRPLRPEDHEAVAELTLASYVDGGHIAPDDAYVKTLMDVADRAGRAEVLVAEVDGE +VAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLAEIVARARAEEGVDAV +VLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGPFLVYRLALD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000098.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000098.fa new file mode 100644 index 0000000000000000000000000000000000000000..1da7895ed55ae1687819fe9b9dc6d33dc61b02f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000098.fa @@ -0,0 +1,33 @@ +>PROKKA_00626 +MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSAREWSDAHAANAVLDAHAGDP +EFGYRFLADELRGRGLAVSDHQVLKACRLVRVRCCHWFRRGSGKRPGPAVHDDLVRREFR +AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLALDALQMALARR +GGKAEVQGCRVHSDRGSQGGFNRSSQHPLGITGGMGDGKQGLGEEDQ +>PROKKA_00371 +MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP +EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR +AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALARR +GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV +LNRRRWQSFDQLRLAIVSWIERTYHRRRRQARLRKLTPVEFEMVQSVQAAAAA +>PROKKA_00392 +MTYPVVKDLARDGIPVRLCCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP +EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR +AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALARR +GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV +LNRRRWQSFDQLRLAIVSWIERTYHRRRRQAPLGRLTPVEFEMVQSVQAAAAA +>PROKKA_00411 +MTYPVVKDLARDGIPVRLCCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP +EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR +AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFLKRPGSDEDS +>PROKKA_02188 +MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYPWLAEPVSAREWSDAHAANAVFDAHADDP +EFGYRFLADELRGRGLDVSDHQVLKACRLVRVRCCHSIRRGSGKRPGPAVHDDLVRRQFR +ADKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSIDRRMSSQLAVDALQMALARR +GGKAGVQGCRVHSDRGSQFRARRFVETLRVNSLIGSMGRVGAAGDNAAMESFFALLQKNV +LNRRRWDSFAQLRLAIVSWIERTYHRRRRQARLGKLTPVEFEMVQSVQAAAAA +>PROKKA_00605 +MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP +EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFA +AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALGRR +GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV +LNRRRWQSFDQLRLAIVSWIERTYHRRRRQARLGKLTPVEFEMVQSVQAAAAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000100.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000100.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a7e9fe8d8165361e849a98c567be9ab8e2e4d5b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000100.fa @@ -0,0 +1,36 @@ +>PROKKA_00644 +MTSVPTVPFHDGQQIPQLGFGVWKVEDDVAADVVEQAIRAGYRHIDTAAIYGNEEGVGRG +IAASGVAREELFLTTKVWNSDQGYEEALAALDVSLDKLGTDYVDLYLIHWAKPAQGKYLE +TWKALIEAQKQGKVRSIGVSNFPAAQLEEIIEATGVVPVIHQVETHPYWQQRELREVEGR +HGIVHESWSPLGQGGDLLADPVVTEIAEARGATPAQVVIAWHLAHGFVVIPKSVTPERIV +SNLEAAGVELTDDDVARIDALDREDGRLGPDPAVIDF +>PROKKA_00381 +MTDVPTVPFHDGQQIPQLGLGVWQVEDDVAADVVEQAIRAGYRHIDTAAIYGNEEGVGRG +IAASGVAREELFLTTKVWNSDQGYEEALAALDVSLDKLGTDYVDLYLIHWAKPAQGKYLD +TWKALIEAQKRGKVRSIGVSNFPAAQLEEIIEATGVVPVIHQVETHPYWQQRELREVEGR +HGIVHESWSPLGQGGDLLADPVVTEIAEVRGATPAQVVIAWHLAQGFVVIPKSVTPERIV +SNLEAAGVELTDDDVARIDALDREDGRLGPDPAVIDF +>PROKKA_02319 +MTSVPTVPFHDGQSIPQLGYGVWRVEDEVAADVVAQAIRAGYRHIDTAAIYGNEEGVGRA +VAASGVPREELFITTKVWNSAHGYDEALAALEESLGKLGTDYVDLWLIHWAKPTQGRYVD +TWKALIEAQRQGKVRSIGVSNFPAEQLEEIIEATGVVPVIHQVETHPYWQQRELRELEER +HGILHESWSPLGQGGELLEDPEITAIAEAHGATPAQVVIAWHLAKGFVVIPKSVTSERIV +SNLAAADVELTEDEVARIDALDREDGRIGPDPATIEF +>PROKKA_00584 +MSTDSRHTAIPVDETPVPETLTLTGTGVDGVEMPRIGLGTWPLRGAEARDAVEQALRIGY +RHVDTAQNYGNEDAVGEGIAAAIHAGVLDRDQLFVTTKVNREHHGDARTVRAAVECRLRV +LGLEHVDLVLVHWPNPDQDRYLETAWSLSELAEDGRIRAWGVSNFTPAHLDRLAGAGLRA +PVDQIEVGPLRQSPAWQEGVRAHGAAITAYSPLGRADQDLGALEPVAAAAARTGRTPAQV +VLRWHLQSGRAAVPKSVDPARQAQNLDVFSFALTAEEMAAIDALDTGEGPRRHPDEFGH +>PROKKA_02178 +MTTVPQTPFRDGQSIPQLGYGVWQVEDAVAADVVEQAVRAGYRHIDTAAVYGNEEGVGRA +VAAAGVPREELFITTKVWNSDQGYDEALAALEASLAKLGTDYVDLWLIHWAKPAQGKYVD +TWKALIEAQRQGRARSIGVSNFPAEQLEEIISATGVVPVIHQVETHPYWQQRELREVESR +HGIVHESWSPLGQGGELLSDPVITAIAEAHGATPAQVVIAWHLAEGFVVIPKSVTPERIV +SNLTAAELELTAEEVDQIRGLDRADGRIGPDPASITF +>PROKKA_00614 +MTDVPTVPFHDGQQIPQLGLGVWQVEDDVAADVVEQAIRAGYRHIDTAAIYGNEEGVGRG +IAASGVAREELFLTTKVWNSDQGYEEALAALDASLDKLGTDYVDLYLIHWAKPAQGKYLD +TWKALIEAQKQGKVRSIGVSNFPAAQLEKIIEATGVVPAIHQVETHPYWQQRELREVEGR +HGIVHESWSPLGQGGDLLADPVVTEIAEARGATPAQVVIAWHLAQGFVVIPKSVTPERIV +SNLEAAGVELTADDVARIDALDREDGRLGPDPAVIDF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000127.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000127.fa new file mode 100644 index 0000000000000000000000000000000000000000..d86c8e0921bb65a3f52988a8b59a10c1c42ccea9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000127.fa @@ -0,0 +1,81 @@ +>PROKKA_01369 +MSSARRDPLVGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHPHLAEDPVLV +GRFEQEAKTTARLSHPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSP +REALRFLRPLVDGLAAAHGAGLVHRDVKPENVLVRDDGRVTVADFGLSRAATAHTMAGQA +VVGTPAYLAPEHIAGAPADARSDVYAVGIILFELLTGRQPYTAATALQVAYRHVHERVPV +PSTLHPGLPEDLDDLVLWCTEPDPADRPAGAGELLHRIEAVAAGLDPDAPDRRPAAQPAE +GPGADPAPAGPAADGLEDAAPDGNLETRALDAGDHHATRVLPALAESDLDEDMTDVIDTR +VATHGGDPRPAARPAEPIGPLGLDPAPADRHPGRGSRRRLRRAARRPALDLGQGTGRAAA +IGAAVTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREAAEERLTAAGFTAAVTAR +HDELRTEGTVVASSPAAGEPAGRGAPVELTVSAGPAPVPVPDLTGVVIRQAHGVARDARF +TVEVAERRTDPAVPAGAVIEQHPAPGEQATPGTAVRVVLSEGRAVRPVPDMTGQDPETAH +TTLADEGWDARVHRLPLPLSARGESRVLHQSPAAGTALPEGTAVHVWVG +>PROKKA_01953 +MSLPDARWHVVSPSPFEHEQQGLDILREVLPDESPFQVWTNFEFPDEDGQWHEVDALVLA +RTKFILVELKYYSGVLRGTGLRWERPGHSPQRSPLALAKKKAERFRSLLERTIESKMPGA +GRQRIVPYVDYAVFLHHDRFRNEMAPQDSGRLFGLPHNETASNLPSIEHLVLAPATDRFP +LIGEPREQVLVALMEHLNLADARQPEVGSWLLEERLGEPTPDGQDWLASHRFQERHFARI +RFQQPREGAPSSDLARVREAARREFDLTRALHHEGLLTASDRVDNELGVGLVFPYDESLA +PLPLWLESRAATLSQQNRLDLLRQLAETLEYVHSNGIVHRALSPEALWVKTPKQGEPRIL +VADWQLAGVADRDKVDHAASLTQLSTQFGTTVRSTEELAPTSGALFRAPEDARRVSSLGR +YKLDVFSVGALAAYLLTGAPAANTVAELHEHLATHQGLDVSVALPSVPEPVRQAILHATD +PRPTARTATLNDFLAGLTEAQATAPQPASPALDPLEAAPGQALDSRFTLVRRLGKGSTAV +GLLVDDAQTGSRQVLKVALDDEAATRLDDEAQVLRLLPLHKRLVRLLDGPFDVGGRRALL +LTSAGTRTLSEVLRERQRLSLDHLERFGSELLEAAQALDAAGLRHRDVKPANIGVVRTPK +HGEHLVLFDFSLARARSTDVRAGTPPYLDPFLEQGGRTGYDSAAELYAVAVVLYEMASGQ +KPFYGDPEANPAAVRDDLTVPDGIFDPSLQAPLSALFERALARDAQARFHTVAELAAAWE +ALFRNDADPVTAQDAETLAARATLETPLSEAGLSARGLSALEAIKVTAGPGGVAVEPHDV +RTVRDLVLVDPIKLNSLAGSTTETRAEVRARAKQWRAAFKKELMRQATQVPQGTLPTPLD +AAELLLRHAGAAHAEGVRAQLRLVLGLDGEVPALSTHAVLADARGVTPGLVPQLFGRAQQ +AWTDVAETRSLLDSLDGALRAAVAERGGVSTPDELTSALEQTLSPATPAEVRDAEPRRIV +QGLLWLLLDRERAAARGEADVPALVQRRREGRVVAVAEMPVLLDVAETLGAAAEAAVDGA +GDPESALVPADLVQTRVAAVLDAVDGLPEALRSWRRAAALAAHVSATTCLSAAGEWHHRL +LAPATAAHHALQGASGTVQLSRERAAERVGARFPALSPLPRDAALDRVLAEAELGLVFDE +DLGPQGAYRSRQTLAPTTGFATRAETRLVEHQRPLSELGVEGQRLLDSQRNRSYLALGVP +AQRLARLESALVRRFHAEPLDLTDLFIRLLKDQAAAHPKMTWDHVTAADAEPDGSRPAQG +LNVLVRNLLPELEQHLSRTIGDPGRAASPVLLTGAAVLARYGHLGVLARWADLAEYRARP +VWLVVPQVAGNVGPRLDGVSVPKNTPGQYVPLTPEWIDGLAALMAAQPLTEESRT +>PROKKA_01089 +MSSARRDPLVGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHPHLAEDPVLV +GRFEQEAKTTARLSHPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSP +REALRFLRPLVDGLAAAHRAGLVHRDVKPENVLVRDDGRVTVADFGLSRAATAHTMAGQA +VVGTPAYLAPEHIAGAPADARSDVYAVGIILFELLTGRQPYTAATALQVAYRHVHERVPV +PSTLHPGLPEDLDDLVLWCTEPDPADRPAGAGELLHRIDAVAAGLDPDEPDRHPAEGPGA +EPAVAAPAADGPEDAAPDGNLQTRALDAGDHHATRVLPALAESDLDADMTDVIDTRAATR +GADRRPAAHPAEPIGPLGLDPAPADRHPGRESPRRLRRAARRPALDLGQGTGRAAAIGAA +VTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREAAEERLTAAGFTAAVTARHNEL +RTEGTVVASSPAAGEPAGRGTPVELTVSAGPAPVPVPDLTGVVIRRAHGVARDARFTVEV +AERRTDPAVPAGAVIEQHPAPGEQATPGTAVRVVLSEGRAVRPVPDVTGQDPETARTTLA +DDGWDARVHRLPLPLAGRGESRVLHQSPAAGTALPEGTAVHVWVG +>PROKKA_01524 +MSSTRRDPLVGGIVDGRYEVLARLARGGMSTVYLALDTRLDREVALKVMHPHLAEDPVLV +GRFEQEAKTAARLSHPHVVAVLDQGHTEDASGEVLAYLVMEHVPGHTLRTVIREQAPLTP +REALRHLRPLVDGLAAAHRAGLVHRDAKPENVLVRTDGRITVADFGLSRAATAHTSAGQA +VVGTPAYLAPEHIAGAPADARSDVYAAGIILFELLTGRQPFTAGTALQVAYRHVHERVPV +PSSLQPGLPEALDDLVLWCTEPDPADRPADAGEVLDRLDAVAAELGPAELDRPPVLVPDA +VEGRPGPEHDETTTLDALDRLDPKDPLDDADGDETTSLDAGDHHATRVLPSLPADALPTE +ALAADDVVRRSPARRRRRP +>PROKKA_01419 +MSSTRRDPLIGDLVDGRYEVLDRVARGGMSTVYRALDHRLDREVALKVMHPHLAEDPALV +GRFEREAKTAARISHPHVVAVLDQGHTADEAGDVLAYLVMEHVPGRTLRAVIREEAPVAP +RRAVALLEPVVEGLAAAHRAGLVHRDVKPENVLVRTDGRITVADFGLSRAATGHTSAGQT +VFGTPAYLAPELISGTGGDARADVYGVGIMLFELLTGTQPFTAATPLQVAYRHVHERVPV +PSSVRPGLPEALDDIVLWCTEPRPADRPEDAAALLPELRRVAALLPQTAPADEAPAADDA +PTVALAVSPTVPTVPVPDAADATARLEPRRPDPRRAEPVPTPATATAASPSSDLSSAVPE +APRPAPVAPRPASARQRRRTARTPEVVLGAGMGRTVAVGAAVTLLLAGMALLLGWILGSG +GISGPAGVVVPPLWGLEQQEAAARLAEAGLTSAVVSRHDERFSDGVVLDVSPAAGSTVDA +GGPVRLTVSDGPAPVPAPDLAGLTVTDAHAVAEDGRVGVVVADRVADRAVPAGAVVSQSP +EAGAEMTPGDEVAVVLSTGPATHPLPDLGGLTVGEARTRLADLGFVPDVRTLPLPGPSGD +AARVLRQGTPAGTVLPEGASVQLWTL +>PROKKA_01324 +MSSARRDPLVGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHPHLAEDPVLV +GRFEQEAKTTARLSHPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSP +REALRFLRPLVDGLAAAHRAGLVHRDVKPENVLVRDDGRVTVADFGLSRAATAHTMAGQA +VVGTPAYLAPEHIAGAPADARSDVYAVGIILFELLTGRQPYTAATALQVAYRHVHERVPV +PSTLHPGLPEDLDDLVLWCTEPDPADRPAGAGELLHRIDAVAAGLDPDEPDRRPAEGPGT +DPAAAAPAADGLEGAAPDGDLPTRALDAGDHHATRVLPALAESALDDDVTDVIDTRAATH +GGDPRPAARPAEPVGPLAVDPAPADRHPGRGSRRRLRRAARRPALDLGQGTGRAAAIGAA +VTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREAAEERLTAAGFTAAVTARHDEL +RTEGTVVDSSPAAGEPAGRGAPVELTVSAGPAPVPVPDLTGVVIRQAHGVARDARFTVEV +AERRTDPAVPAGAVIEQHPAPGEQATPGTAVRVVLSEGRAVRPVPDMTGQDPETAHTTLA +DEGWDARVHRLPLPLSARGESRVLHQSPAAGTALPEGTAVHVWVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000143.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000143.fa new file mode 100644 index 0000000000000000000000000000000000000000..7b1188f6be2be9c0ebd3054b7958df25fdb42c7a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000143.fa @@ -0,0 +1,37 @@ +>PROKKA_01687 +MPDVTPPPPSRSWTRRSVLGGTGLAIAAGVAGCGRDEQAEQSSEGDEQATRLPAPDIITT +AQWGAMQPNYYLQTLNERPSYLVIHHTTTPNVTDGSREAAESIAQVVQNAHMGSANDWGD +TGQHFTVSRGGFAMEGRHGSRHALEGGQTFMLGVHALGFNAYALGIECEGLYMLNPPPQS +LYAGLVPLVAYICQQYELPPSRIIGHRDVTATSCCGDAFYAKLPILREDVRLSLASGEYH +VSEGFGADNLFDDAHVTPEYVEEERG +>PROKKA_01391 +MPDVTPPPLPHSWTRRSVLGGTGLAIAAGVAGCGRDEQAEQSSEGDEQATRLPAPDIITT +AQWGAMQPNYYLQTLNERPSYLVIHHTTTPNVTDGSREAAESIAQVVQNAHMSPANDWGD +TGQHFTVSRGGFAMEGRHGSRHALEGGQTFMLGVHALGFNAYALGIECEGLYMLNPPPQS +LYAGLVPLVAYICQQYELPPSRIIGHRDVTATSCCGDAFYAKLPILREDVRLSLASGEYH +VSEGFGADNLFDDAHVTPEYVEEERG +>PROKKA_01191 +MPEQSPTPSSRPWARRTVLGGTGLAIAAGVAGCSRPEAGEEAEETEAAPKRLPAPDILTT +AQWGALQPNYHLQTLDERPSYLVIHHTTTPNVTDGSREAAESIAKSIQNAHMSTLNDWGD +TGQHFTVSRGGFALEGRHGSRYTLEQGQTFMLGVHALGFNAYALGIECEGLYTLNPPPQS +LYAGLVPLAAYICQQYELPPSRIIGHRDVTATSCCGDAFYGKLPVLREDVRLSLATGEYH +VSEGFGADNLFDDAHVTPDYLQEQGY +>PROKKA_00038 +MKHALPRHVQHAPVPPAAASPGRRAVLVGGLAAAGAAGAAAAGAVPAAAFAGPVVHSTAQ +WGARSPRSAAEVVRARPTRLVIHHMASPNTAETSLAHAYGLARACQQDHMGRGFDDSGQH +FTVSRGGHCLEGRAGSLAALRAGDRHVKGAHVSGQNTGKIGIECEGSYVTGLPTPAQYRA +LVQLAAHICRQYGIRPADIVGHGDLMATQCPGGAFHARLGVLRADVARTLATGRLSVSDP +SGRAASIPADPRRAATTTPSAAAPASRRVLGPGSRGADVKRVQALLTTAGHRVPRTGLYA +ARTTAAVRAFQRRSGLAQDGFTGPLTWAALEAAGRR +>PROKKA_01121 +MPDHQILSSSWPRRAVLGGAGLAIAGTVAGCGTGGDAAQSTSADGSAASTGPRLPEPEIL +STIDWGARIPENWQQTLYEKPSYLVIHHTTTPNVTDGSRDAAIALAQRVQNQHINQQWGD +SGQQFTMSRGGFAMEGRHGSLYALQGGETFILGVHALGFNAYAVGIECEGFYMVSPPPQS +LYAGLVKLSAFICQQYELPPSRIIGHRDVVKTSCCGDAFYAKLPILREDVKRSLETGEYQ +ITEGFGADNLLDDAKINVENYEDFQKRS +>PROKKA_01616 +MPDVTPPPLPHSWTRRSVLGGTGLAIAAGVAGCGRDEQAEQSSEGDEQATRLPAPDIITT +AQWGAMQPNYYLQTLNERPSYLVIHHTTTPNVTDGSREAAESIAQVVQNAHMSPANDWGD +TGQHFTVSRGGFAMEGRHGSRHALEGGQTFMLGVHALGFNAYALGIECEGLYMLNPPPQS +LYAGLVPLVAYICQQYELPPSRIIGHRDVTATSCCGDAFYAKLPILREDVRLSLASGEYH +VSEGFGADNLFDDAHVTPEYVEEERG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000144.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000144.fa new file mode 100644 index 0000000000000000000000000000000000000000..a97eed27dfce789d91c48f861dc9f65fa4eb4b31 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000144.fa @@ -0,0 +1,44 @@ +>PROKKA_01779 +MSTAPALPPLPGAPGGPALPSVEELLADAVAVAVPMRVRFRGTDLRHALLLRGPAGWGEF +SPFPEYGPHESAAWLAAAIEAGWQGWPAPVRETIPVNATVPAVDADDVEAVLARYGDGIT +AVKVKVAEHGPEGGLVPGGREADLARVRRVRALLPHAQVRVDANAGWTPAEAVDVLTELA +DVGLEYAEQPVPGITDLAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAADLIVVK +VQPLGGVRRAAAIVAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACGLGTAALFEH +DVVAPAWRPRAGALPAPGERAPAPDPELLDRIRADGTRQAWWADRVRAAHAVLAAQG +>PROKKA_01486 +MSTAPALPPLPGAPGGPALPSVEELLADAVAVALPMRVRFRGTDLRHALLLRGPAGWAEF +SPFPEYGPHECAAWLAAAIEAGWQGWPGPVRQTVPVNATVPAVAADDVEAVLARYGDGIT +AVKVKVAEHGPEGGLVPGGREADLARVRRVRALLPHAQVRVDANAGWTPAEAVDVLTALA +DVGLEYAEQPVPGITALAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAADLIVVK +VQPLGGVRRAAAIVAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACGLGTAALFEH +DVVAPAWRPRAGALPAPGERAPAPDPELLDRIRADGTRQAWWADRLRAAHAVLAAQG +>PROKKA_01098 +MRVRFRGTDARQALLLRGPAGWAEFSPFPEYGPAESSAWLAAAIEAGWQGWPAPVRDVVP +VNATVPAVEAEAVESVLARYGEGITAVKVKVAEHRPGGGLVPGSHSADLARVRRVRELLP +DAHVRIDANAGWTPAEAIAMLTDLADVGLEYAEQPVPGIKKLARVRRELRARGVSTPIAA +DEAVRKAEDPLAVAAAGAADLIVVKVQPLGGVRRAAAVVAAAGLPAVVSSALDTSVGIAG +GAALATHLPALPHACGLGTAALFDDDVVTPAWTPRQGVLEAPGERAPEPDPALLARVRAD +ERTHAWWRDRVAAAHAVLAAGGR +>PROKKA_01022 +MTVPAAHDDADPRPGSALPPLPGAPGGPALPDVDELLEHAVAVTLPMTVRFRGTTERRAL +LLRGPAGWAEFSPFPEYGPAEASRWLAAAVEAGWQGWPAPVRSEVPVNATVPAVDAADVE +SVLARYGDGITAVKVKVAEHRPGGGLVDPTHAADVARVRRVRELLPEAAVRIDANAGWDE +DRAFAVLGALQDVGLEYAEQPVPGIAGLAALRSRLRAAGIATPIAADEAVRKETDPLAVA +QAGAADLIVVKVQPLGGVRRAAAIVAAAGLDAVVSSALDTSVGIAGGAALAAHLPSLPFA +CGLGTASLFAHDVVSPAWRPADGSLPAPGERAPEPDPALLAAARADAAEHAWWAERLRAA +HAVLAARGR +>PROKKA_01806 +MSPAPGQAPVSVAAVRRHRHRAPLLHPFVTAARRTEAVEYVVVEVELSDGTVGQGSAAET +VAVTGEDAASIETAVDGVFGPALTGATGGLDGLLARLPAPARGATSARSAVDVAVHDAVA +RAAGVPLTALLAPAGTAVKQTLENDMTVSLEDPATMAARAAEAVAAGTRILKIKLGRDVA +EDRRRLHAVLEAAPQARLRLDANQGWSVEDAIAIISGMEDEGLPVDLVEQPVAAADVAGL +ARVRAAVTTPIMADEALWSSEDARRLIEAGAADLFNVKLAKTGGLADAVAIADLAAEHGI +GCMVGSMMEPRISIAAAVQLSLAHPAVTMVDLDAPLWFASDAPAGGYTQEGADLRLLPGE +GLALERLDPGTDPV +>PROKKA_01708 +MSTAPALPPLPGAPGGPALPSIEELLADAVAVALPMRVRFRGTDLRHALLLRGPAGWAEF +SPFPEYGPHESAAWLAAAIEAGWQGWPAPVRQAVPVNATVPAVDAADVEAVLARYGDGIT +AVKVKVAEHGPEGELVPGSREADLARVRRVRALLPHAQVRVDANAGWTPTEAVDVLTALA +DVGLEYAEQPVPGITDLAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAADLIVVK +VQPLGGVRRAAAIVAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACGLGTAALFEH +DVVAPAWRPRAGALPAPGERASAPDPELLDRVRADGARQAWWADRVRAAHAVLAAQG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000159.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000159.fa new file mode 100644 index 0000000000000000000000000000000000000000..052d7b9bda91759533578e83c913caa7b6876c49 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000159.fa @@ -0,0 +1,22 @@ +>PROKKA_02070 +MSTTTSITAAGLETMNGPEGCCTLSAGPVDSVEAERIASLLKALSDPTRLRLLSHVAAQG +CNSVCACDLTEPLGISQPTVSHHMKKLVDAGLLTREQKGRWAHYSVVPSAFAELRSFLDI +A +>PROKKA_01107 +MDVKVYVPEFAVEFDTCQYVPMSMSGLSARDAALGYCTPLAREPITPAQAEGVSRMLKAL +ADPVRLRLMSMILSHEGAEACAMCDLTEGFDLSQSTLSHHLKVLHDAGLVDRDKRGVWVY +YKARTEAMDALRTLFSGDLAAPQLA +>PROKKA_00560 +MTACSVPVSTAAAPVLADDCCSLADGPLGAEDAAELAVLLKALADPMRLRLLSHVAARGC +ADVCACDLTEELGIAQPTVSHHMKRLVDAGLLTREQRGRWAHYTVVPEAFARLRRVLVLG +>PROKKA_00743 +MVATTTIPAPEDTDRPEGDDALGSVACCSLSAGPIDAAQAQRAAGMFKALADPMRLRLLS +HVAAQGCAAVCSCDLTEELGISQPTVSHHMKKLVEAGLLTREQRGRWAHYTVVPAAFAEL +GRMLELG +>PROKKA_00486 +MTTTAPSPSDTCCAPAGPALLPAEHAARLAAVFKALADPTRVRVLAHVAASPEGTVCACH +LPEPLGISQPTLSHHLKTLTAAGLVTREQRGRWAHYTAVPAALDAARAFLADPAGA +>PROKKA_01998 +MSTTTAITAAGLETMNGPEECCTLSAGPVDSVEAERIASLLKALSDPTRLRLLSHVAAQG +CNSVCACDLTEPLGISQPTVSHHMKKLVDAGLLTREQKGRWAHYSVVPSAFAELRSFLDI +A diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000199.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000199.fa new file mode 100644 index 0000000000000000000000000000000000000000..2c12f084d083d33776957275c826f2d7a86d5d7f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000199.fa @@ -0,0 +1,33 @@ +>PROKKA_00040 +MAKGVKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQL +VNHDDAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDVDPRHVHLVGVYSE +LPVVCVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSPEPMDAAELPGAGERM +ALEIAASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQ +ARAEAEAGAAVVDGADPAGHGDDDARHPVWDVALAWLKAADSELVQAFVGVARGRRGASS +R +>PROKKA_02053 +MAKGVKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQL +VNHDDAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGGVDPRHVHLVGVYSE +LPVVCVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSAEPMDAAELPGAGERM +ALEIAASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQ +ARAQAEAGAAVVDGADPAGQGDDDARHPGWDVALAWLKAADSELVQAFVGVARGRRGASS +R +>PROKKA_00360 +MGPRRGLPEGEGPLSGARGGRGAGRQRASRGGPARSTRTGGRAGAKGGGPQRAGSGSRAG +GEGRRRAPSAPADLAAPPETLFLATIPGATPSTWVDRFTTRQRVVQLVNHDEASQLAHLA +HDDAGMPRHPLPQLGYVRRRRDVEAEEMLRAAGVDPRRVHLVGVYAELPVVCVGRDHLLA +AWDAEADGPVPLAELDSHEELDPARFAAAPVEDPLDSAELPGAGERMALEIAASGAGHVV +LPMSVARMFGRKDVVVLPLASALDDTVGMSRADREAAATRAEVEADAGDAGTAAAGPGEA +DDDAARHPGWDVALAWLKEADSELVQSFVGVARGRRGNSSR +>PROKKA_00301 +MPAAPADLPTPPETLFLATIPGATPSTWVQRFSSRARTVQLVNHEEAQQAAHLAHDAAGA +PLHPLPQLGYVRWLRDAGVESVLRESGVDPRFVHVVGVYSELPVVCVGKEHLLAAWDLEA +DGPVPLAELDPAEHMDPARFAPEPGAASNPLDSAELPGAGERMALEIVASGVGHVVLPQS +VARVFGRKDVVVLPVACELDDVVGLSRADREAAATRAEVAEEGDGVVPDGADAPATTAPR +HPGWDVGLAWLKEQDSELVQSFVGVARGRRGGTSR +>PROKKA_00035 +MKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQLVNHD +DAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDIDPRHVHLVGVYSELPVV +CVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSPEPMDAAELPGAGERMALEI +AASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQARAE +AEAGAAVVDGADPAGQGDDEARHPGWDVALAWLKAADSELVQAFVGVARGRRGASSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000276.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000276.fa new file mode 100644 index 0000000000000000000000000000000000000000..abeedb8767d45f27be39ef436f1bed1b85d1a66e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000276.fa @@ -0,0 +1,23 @@ +>PROKKA_00143 +MAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAMVTDRYLHVRHHETVAAFTE +WAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGLSAEVRAASSAVLSIAQYGS +TRSINAGVAAGIAMHAWIRQHAAVP +>PROKKA_02157 +MLDHYRYWSLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRW +NRRGAMVTDRYLHVRHHETVAAFTEWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFG +QEGPGLSAEVRAASSAVLSIAQYGSTRSINAGVAAGIAMHAWIRQHAAVP +>PROKKA_00241 +MGPGTSENSPETREKREEREGREEREVGVGPWEGPWPEDPRYDPELLRDGDRRNVVDGYR +YWTLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHVIGRRRWNRRGAM +VTDRYLHVRHHATVEEFTAWAAAEGLPVLGVDLFPESVPLESFELPRECVLVFGQEGPGL +SEEVRAASAAVLSIAQYGSTRSINAGVAAGIAMHAWVRQHGGVPTSSS +>PROKKA_00175 +MGSGEGVDAREVGREVGAPPWEGPWPEDPRYDPALLRDGDRRNVADRYRYWTVEAIVADL +DRTRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAMVTDRYLHVHHH +ETVEAFTAWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGLSEEVRAASEAV +LSIAQYGSTRSINAGVAAGIAMHAWIRQHGGPAPV +>PROKKA_00151 +MPREVGVGPWLGPWPEDPRYDPELLAHGDRRNVLDRYRYWRLEAIVADLDARRHPFHVAI +ENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAMVTDRYLHVRHHETVAAFTEWAA +GEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGLSAEVRAASSAVLSIAQYGSTRS +INAGVAAGIAMHAWIRQHAAVP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000311.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000311.fa new file mode 100644 index 0000000000000000000000000000000000000000..5d5247259631484636a65ae98e97162e2451458e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000311.fa @@ -0,0 +1,15 @@ +>PROKKA_00213 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDEILAQAR +TAAEEMLSNPVIEDVVNVAVLDEAEGAR +>PROKKA_02206 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGKVTDEILAQAR +TAAEEMLSNPVIEDVVNVAVLDEAEGAR +>PROKKA_00173 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDAVLDQAR +RAAEELLSNPVIEDVVNVAVLDEAEGAR +>PROKKA_00122 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTEEVLAAAR +TAAEEMLSNPVIEDVVNVAVLDEDAA +>PROKKA_00213 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDEILAQAR +TAAEEMLSNPVIEDVVNVAVLDEAEGAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000340.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000340.fa new file mode 100644 index 0000000000000000000000000000000000000000..fdf639b57d6403f9938e4cbc7c2da5a26eb95e6e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000340.fa @@ -0,0 +1,20 @@ +>PROKKA_00261 +MTTPAPVASAARARRRAARSGPRPQLRMGLNGFLVAWLLPNLVMAAVVAVLAVVPGLQAF +GSLTPLLTVVGVAGLVVGLPLCLLVNWAFRHVLNQWVHVLAYALIGMLYGLVVLTQGAAG +ILPMLIPVIGFPAAVLMALGRTAARPLVRTVTPEPSPAEPA +>PROKKA_02274 +MTTPAPVASAARARRRAARSGPRPQLRMGLNGFLVAWLLPNLVMAAVVAILAVVPGLQAF +GSLTPLLTVVGVAGLVVGLPLCLLVNWAFRHVLNQWVHVLAYALIGMLYGLVVLTQGAAG +ILPMLIPVIGFPAAVLMALGRTAARPLVRTVTPEPSPAEPA +>PROKKA_00106 +MGLNGFLVAWLLPNLVMAALVAVLAVLPGLQAFGSLTPLLTVVGIAGLVVGLPLCLLVNF +AFRHVLNQWVHVLAYALIGMLYGLVVLTQGAAGILPMLIPVIGFPAAVLMALGRMAARPL +VQVVTPGQEAEARSAAQTASPADPEPSERAARGA +>PROKKA_00076 +MTTPAPVKSTARARRKAARAVSGPRPRLRMGLNGFLVAWLLPNLLMAAVVLALTLIPSLQ +RFGTLTPLLTVVGIAGLVIGLPLCLLVNRAFRHVLNQWVHVLAYALVGMLYGLVVLAQGV +GGVLPMLIPVIGFPAAVLMGLGRLAARPLVDVVPGAEPRS +>PROKKA_00259 +MTTPAPVASAARARRRAARSGPRPQLRMGLNGFLVAWLLPNLVMAAVVAVLAVVPGLQAF +GSLTPLLTVVGVAGLVVGLPLCLLVNWAFRHVLNQWVHVLAYALIGMLYGLVVLTQGAAG +ILPMLIPVIGFPAAVLMALGRTAARPLVRTVTPEPSPAEPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000341.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000341.fa new file mode 100644 index 0000000000000000000000000000000000000000..0992987b83c892843b2f201f24362f8861311d03 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000341.fa @@ -0,0 +1,35 @@ +>PROKKA_00262 +MKLPSPAPSAPGEVHHSASSVPVDGVEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD +PHARRGRERRALAELEAAVSGTVLAAETANALHTAAIADGEVAPSPAARALRGLGGLAVG +GAVAAVALRTAGLNDRIDGAVVRGLQRVGVPAPRVALAAAASLAMLLANEDARRTRRDAV +ELAVTGPAGLDEDPVDEVEPEATAELPVEVRVLLETLLDPALAEGRDLPGAEALRSQLPH +ARTVASVAEAIREAGEVPDWVPLVVQTDDDVRRAVPNDCVWPVRGRFASGSAGGHELELR +LQVIDGEIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLAFHVDGDRRA +>PROKKA_02275 +MKLPSPAPSAPGEVHHSASSVPVDGVEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD +PHARRGRERRALAELEAAVSGTVLAAETANALHTAAIADGEVAPSPAARALRGLGGLAVG +GAVAAVTLRATGLNDRIDGALVRGLQRVGVPAPRVALAAAASLAMLLANEDARRTRRDAV +ELAVTGPAGLDEDPVDEVEPEATAELPVEVRVLLETLLDPALAEGRDLPGAEALRSQLPH +ARTVASVAEAIREAGEVPDWVPLVVQTDDDVRRAVPNDCVWPVRGRFASGSAGGHELELR +LQVIDGEIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLAFHVDGDRRA +>PROKKA_00105 +MRQNSPVPGSLPARYVDDPAAAFPALRQRALAPGGRPYGLLAAAVVGALTLVDPHRMGAA +ERRGLARTEAAASGAFVAAEAASSLRLAGLPGRVGPAAGGLAAGAATAALALSTVPLNDR +IDGALVRFLERAGASAPRAVLAGTAALSVLAGNESVRRERRNALEEAAWPAWDDLSEEEQ +SEPTAPLPVEVRVLLETLLDPALAEGRELPGAAALRAQLPHVRTVASMAEAIRDEDEVPD +WTPLVVETDGPVDRAVPHDHVWPVRGRFAVGEDGHEVELRLQVIDGELGALVITLPADED +ADPDAWDAFQELEAFPGVEDLTFQVDGERRD +>PROKKA_00075 +METPRTPETRTDPPADRLAEPQHPAHADAPVVHDTAVPESERIERTVSTRTGETRPPVVR +TVVTESERIERPVVEVRDARVPGRLLWWIGGGTLAAGSLAALVRVLRERLATPEPTPLER +LADAGRGAGLPLALSLAGTAAGVGVSLRARRRRRTEEVLAAPAVPFLLGEAVSAEAGEDD +VDGLPPVNEASDAYPAGALETEALPLEVVVLLDTLLDPSLDEGRELPGAAALRAQLPHVR +TAASVAEEIREDGKVPDWTPLVVEEETGVARAIPNDMVWPVRGRFTTEDGHELELRLQVI +DGELGALVITLPEDVEDGVAAWDAFQELEAFPGVEELTFTVDGDRRP +>PROKKA_00260 +MKLPSPAPSVPGEVHHSASSVPVDDAEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD +PHARRGRERRALAELEAAVSGTFLAAETAGALHTAAIAEGEVAPSPAARALRGLGGLAVG +GAVAAVALRATGLNDRIDGAVVRGLQRVGVPAPRVALAAAASLAMLLANEDARRTRRDAV +ELAVTGPAGLDEDAVDEVEPEATAELPVEVCVLLETLLDPALAEGRDLPGAEALRSQLPH +ARTVTSVAEAIREAGEVPDWVPLVVETDDDIRRAVPNDCVWPVRGRFASGSAGGHELELR +LQVIDGEIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLTFHVDGDRRV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000353.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000353.fa new file mode 100644 index 0000000000000000000000000000000000000000..dfecc11dc4c38e0cc66b3fcf76d27d8d4354401a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000353.fa @@ -0,0 +1,15 @@ +>PROKKA_00280 +MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH +RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR +>PROKKA_02295 +MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH +RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR +>PROKKA_00073 +MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH +RAGEDAEAAEVARRMAEAVSGVAATGRLDVLRRDGGRWVPVPAGPGR +>PROKKA_00059 +MPSYRARLQIGDVLPGHRPEEVLDTAEAAIGATHEVAAKDVEVVARVPRIVLRFTVPAAH +RAAEDAEAAAVAGRMAEAVADVATVGRLDVLRREGGRWLPVSAR +>PROKKA_00279 +MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQASHVLAAKDIEVVARVPRIVLRFTVHGSH +RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGPGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000357.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000357.fa new file mode 100644 index 0000000000000000000000000000000000000000..7bc431403f00d3366d8b8e629a81413bb743d205 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000357.fa @@ -0,0 +1,20 @@ +>PROKKA_00288 +MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV +GADEHLILLDERGTAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRVWSLS +PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA +>PROKKA_02310 +MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV +GADEHLILLDERGAAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRVWSLS +PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA +>PROKKA_00066 +MSVRVLAIGKKHEAWVSEGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV +GADEHLILLDERGTAFDSPGLARHLQSRFDVGAPVTVVIGGAYGVDARVHARADRVWSLS +PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA +>PROKKA_00045 +MMVLMAVRVVAIGKRHESWVSEGITRYEKRLKKPWDLTWQLLPHSSRQEDAARAEESERI +LAKVGPDEQLILLDERGRGFDSPGLSAHLQGQFDLGRTVTLVIGGAYGVDASVHARADRV +WSLSGLVFPHQLVRLILAEQVYRAQEIAGGRPYHHA +>PROKKA_00294 +MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV +GADEHLILLDERGAAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRVWSLS +PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000375.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000375.fa new file mode 100644 index 0000000000000000000000000000000000000000..b8803b22a4120d609ff039c1473ee30cd2d2ad7d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000375.fa @@ -0,0 +1,40 @@ +>PROKKA_00314 +MTASAPVPPVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQC +EVADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWRI +FLMEDADRMTERATNVLLKAIEEPPARTIWMLCTPSPADVLPTVRSRCRLITLSIPAVEQ +VAELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDAM +ALAATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRRR +RRAVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGTAGDSAEVLARI +DAVTTTRERIAANVPEQLALEAMMLALLPRRVRTPRRR +>PROKKA_00029 +MTAPAPAVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQCEV +ADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWRIFL +MEDADRMTERATNVLLKAIEEPPARTIWMLCAPSPADVLPTVRSRCRLITLSIPAVEQVA +ELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDAMAL +AATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRRRRR +AVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGAAGDSAEVLARIDA +VTTARERIAANVPEQLALEAMMLALLPRRVRTPRRR +>PROKKA_00023 +MTALPDAVPAVFADLAGQGSAVEQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQ +CEAPDPAARGCGRCHACRTVLAGTHPDVTVLATEAVTYRIEDVRSLVEAAQSTPATGRWR +IFLMEDADRMTERATNVLLKAVEEPPARTVWMLCTPSPADVLPTVRSRCRLVTLSIPAVE +DVADLLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLEATSVSDA +MALAATLADVSKAEAESSAEARDAEELETLRRSLGLEPGEPVPPKLRQHVKRLEEDQTRR +RRRSVRDSLDRAMIDVMGLFRDVLRVQLGAEGELINEHRRAEVEAYARGAAGDSAEVLAR +IDAVATARERIAANVPEQLALEAMMLALLPRRVRTPRRR +>PROKKA_00019 +MTGAPDVYSDLAGQDAAVAQLRRAATEDRPTHAWLFTGPPGSGRSTAARAFAAALQCEQP +DPANRGCGACHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAAQSTPATGRWRIFLM +EDADRMTERATNVLLKAIEEPPPRTIWMLCSPSPADVLPTIRSRCRLVTLRIPAPEDVAA +LLHRRDGLDEATALMTARISQSHVGMARRLARDPEALARREDVLSLPLQATAVSDAMAMA +ARLAEVSHAEAESSAAARDAEELAALRRQLGVAEGEAVPPKLRQQVKRLEEDQSRRRTRV +TRDALDRAMIDVIGLFRDVLRVQLGAGGDLVNEHRRAEIERYAAGAAGSSAEVVARIDAV +HLARERLGQNVPEQLALEAMMLALLPARVRTPRGRR +>PROKKA_00321 +MTAPAPAVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQCEV +ADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWRIFL +MEDADRMTERATNVLLKAIEEPPARTIWMLCAPSPADVLPTVRSRCRLITLSIPAVEQVA +ELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDAMAL +AATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRRRRR +AVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGAAGDSAEVLARIDA +VTTARERIAANVPEQLALEAMMLALLPRRVRTPRRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000384.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000384.fa new file mode 100644 index 0000000000000000000000000000000000000000..3b0bf80842a11c3fe0a7c6b2ba5c5513791421a3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000384.fa @@ -0,0 +1,45 @@ +>PROKKA_00324 +MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLRHCLESVAAARAAGLDLDAVVVLTPP +AGADAGRVAAEVDAGPRLDVPVHCVPGGAERADSVRAGLAAASHALADLAPAGAPRRVLV +HDAARALTPPSVFGAVTAALETGAVAAIPGLPLTDTVKQVTPGRGGVDVVAATPARAGLR +AIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFKVTAP +ADLDLARLELARRAPQEEAPMDQPARPAAAPAPLPRVGIGTDVHAWAPEDAPRPLWLGGI +HWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRPEMADASGADMLREVLRL +LTEAGLAVGNVAVQVVAPRPKVGARRAEMEAALSAALGGAPVSVSAATTDRLGFIGRKEG +LVGIATALVIPAA +>PROKKA_00039 +MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLRHCLESVAAARAAGLGLDAVVVLTPP +AEADAGRVAAEVDAGPRLDVPVHCVPGGAERADSVRAGLAAASGALADLAPAGAPRCVLV +HDAARALTPPSVFGAVTAALGTGAVAAVPGLPLTDTVKQVTPGRGGVDVVAATPARAGLR +AIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFKVTAP +ADLDLARLELARRAPQEEAPMDQPARPAAAPAPLPRVGIGTDVHAWAPEDAPRPLWLGGI +HWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRPEMADASGADMLREVLRL +LTEAGLAVGNVAVQVVAPRPKVGARRAEMEAALSAALGGAPVSVSAATTDRLGFIGRKEG +LVGIATALVIPAA +>PROKKA_00013 +MPTALVIAAAGAGTRLGAGMPKALVPLADGRTLLRHCLDSVAAARAAGAAVDAVVVLAPP +AEEDAARVAAEVDAGPGLGAPVACVPGGAERADSVRAGLAAAADALNALGPAAGPRRVLV +HDAARALTPPAVFAAVEAALDAGAVAVVPGIAVTDTVKQVAPGPGGAEVVTTTPPRAALR +AVQTPQGFDLDALLAAHEAVRADPALDAAALTDDAMVMEAAGHPVAVVAGDAAAFKVTAP +ADLELARLELARRADAPTPEEDPAMDQYGTAPGTGPEADAATDPAGPRPGAALPRVGVGT +DVHRWAPEDAPRPLWLGGVHWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVD +RPEMADASGTAMLAEVLRLLTEAGLAVGNVAVQVVAPRPKVGTRRAEMEAALSAALGGAP +VSVSAATTDRLGFIGRGEGLVGIATALVAPTA +>PROKKA_00009 +MPTALVIAAAGSGTRLGAGVPKALAPLTDGRPLLDHCLESVAAARATGLGLDALVVLVPP +AADHARAVADVVARHETAVGAPVTCVPGGVERADSVRAGLAAADAALADRGHPAGQGVRH +VLVHDAARAFTPPAVFEAVAGALVSGEVAAVPGLPLTDTVKEVTGADGREVVVATPARSA +LRAVQTPQGFDLDVLLAAHAAAQADPAADAAALTDDAMAMEAAGHAVVVVPGDERAFKVT +SPADLEAAARILAVRDAQSGPGTPSPAAVPAAPPLPRTGIGTDVHRWAPDDAPRPLWLGC +VEWPGQNGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRWEMRGASGAAMLAEVLR +LVTEAGCRIGSVAVQVVAPRPKVGTRRAEMEAAMSAALGGAPVAVSAATTDGLGFIGAGE +GLVGLATALVVPAA +>PROKKA_00331 +MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLHHCLASVATARAAGLALDAVVVLTPP +AEADAGRVAAEVDAGPRLDVPVHCVSGGAERADSVRAGLAAASYALADLAPAGAPRRVLV +HDAARALTPPSVFGAVTAALETGVVAAVPGLPLTDTVKQVTPGRGGVDVVAATPARAGLR +AIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFKVTAP +ADLDLARLELARRAPREEAPMDQPARPAAAPAPLPRVGIGTDVHAWAPEDAPRPLWLGGI +HWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRPEMADASGADMLREVLRL +LTEAGVAVGNVAVQVVAPRPKVGTRRAEMEAALSAALGGAPVSVSAATTDRLGFIGRREG +LVGIATALVVPAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000419.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000419.fa new file mode 100644 index 0000000000000000000000000000000000000000..c2497e01bc2558a9281d9713f8f106fbcaca5d07 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000419.fa @@ -0,0 +1,41 @@ +>PROKKA_00374 +MTSEHTSETRRLRSRTSFVLLAVFGVAAIVALLTSAVEPWPPLVLAPGLIAGLWLLSQWH +REVAAPTRWAVLALGTLTWALSALWDLTPLGALAFALAGALEVMWSRHARAVVTLLVLTV +GSAAGALVFVTDPQALWVYVGMGALLTGVACVTIPVSRISFDLMRLQDQRAEQERAASLD +AERLRFSQDLHDIQGHALHVVKLKIAVAQRMLSTDTDAAQRELDEAQQTLRQTMAETKAL +AQDGHTLTLRGELANSVALLEATGITVTTDDDGGPRGEEFEHVAGVVIREGTTNILRHSD +ARRVEISLAPGHVVISNDGAAGVSAEDHTGGLDNLRSRLAGVGGRLDVSCVDGRFTLGAR +WEADEEESV +>PROKKA_01001 +MTPPSPLAPEPVPDRAPAQDPGSGHAPSPASAALPPGHRPTGALPVAPGFDRDLHRLWWY +TAAGLLSAVVVVAGFLVFVMARRLAVAEGPDASPLAVTVLVAGIAAAVAAAVGQTLATLR +LRRAWEEEREPLRRTAVAALLPALLVALTPLAVPSLSAWPVLSLWLSVCLIAPQAAAHVR +TAVLTSGAAATLGLTALALVRTPAGPADSAVGVLLWWAMVLLVVLPTVWVWRVAVRLEEA +RAQAGELAVARERLRFAADLHDVQGHHLQVIALQAELAGRLLEKGRTDQAGAALRDVREQ +AAEALGETRALVRGLRQVSVASEIENAREVLAATGAVVEVDVDPAAARLAREAARLVGLA +VREATTNALRHAEPRRVRLALGPADGAAGGVRLTVTNDGARPPAAPPGTGLAGLAARAAE +VSGRLSAGPDDDGGFRLELTVPSSSGATTRTDPTTTTGEDA +>PROKKA_02588 +MTSEPTSETRRLRSRTSFVLLAVFGVAAIVALLTSAVEPWPPLVLAPGLIAGLWLLSQWH +REVAAPTRWAVLALGTLTWALSALWELTPLGALAFALAGALEVMWSRHARAVVTLLVLTV +GAAAGALVFVTDPPALWVYVGMGALLTGVACVTIPVSRTSFDLMRLQDQRAEQERAASLD +AERLRFSQDLHDIQGHALHVVKLKIAVAQRMLSTDTDAARRELDEAQQTLRQTMAETKAL +AQDGHTLTLRGELANSVALLEAAGITVTTDDDGDPRREEFEHVAGVVIREGTTNILRHSD +ARRVEISLAPGHVVISNDGVAGAPAEDHTGGLDNLRSRLAGVGGRLDVSCGDGRFTLEAR +WEADEEETV +>PROKKA_01178 +MSPAGGPPAPARPTVGTAEHDPAVLPLHLWPSTMGFAGVWLISFGFVLVELLRRAFTPGD +GRGEAILGVAAIAVFILVYLAAFVVPRPVRAWPAWANTVLTWFVLAGCVAVLTRILGVHA +LLYSPFLVATWIFPHRLRVGLTGAGATMAAALATGLLFFPGDPALPVVLGNLAVLLVVLV +GMRLAIARDDRVVEMTHELDLAGQRERLGRDLHDILGHSLTTINVKTQLVHRLIDTDPAR +AKEEAAEVIALSRTALAEARAAVAELAAPELGGQLSLSVGALRDAGMAVEAPPPGAVTEV +PQRRRALAAWIVREAVTNVLRHAGARRVRISLDAHHVAVLDDGAGLPAAVVAGVGPRTLA +ERAAAEGARLEVGPGLGGAGTGVAVHWGGTTPEAARGVLPATEGRMDA +>PROKKA_00381 +MTSEHTSETRRLRSRTSFVLLAVFGVAAIVALLTSAVEPWPPLVLAPGLIAGLWLLSQWH +REVAAPTRWAVLALGTLTWALSALWDLTPLGALAFALAGALEVMWSRHARAVVTLLVLTV +GSAAGALVFVTDPQALWVYVGMGALLTGVACVTIPVSRISFDLMRLQDQRAEQERAASLD +AERLRFSQDLHDIQGHALHVVKLKIAVAQRMLSTDTDAAQRELDEAQQTLRQTMAETKAL +AQDGHTLTLRGELANSVALLEATGITVTTDDDGGPRGEEFEHVAGVVIREGTTNILRHSD +ARRVEISLAPGHVVISNDGAAGVSAEDHTGGLDNLRSRLAGVGGRLDVSCVDGRFTLGAR +WEADEEESV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000421.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000421.fa new file mode 100644 index 0000000000000000000000000000000000000000..159ee35fad0d20b80f9218dcf1d8ec881d8427f5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000421.fa @@ -0,0 +1,40 @@ +>PROKKA_00379 +MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE +GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA +AAVTYVLGLLFGANVG +>PROKKA_00103 +MSAAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRILLGEHAENPPRPSFRRVLLRWLARIFGSVFVLALAQRAESDTPYEKDQDAPE +GMAADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGAALLFTGGVVGLLSGSSPLARGLRQLAIGYGA +AAVTYVLGLLFGANVG +>PROKKA_02576 +MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRALLGEHAENPPRPSVHRILLRWLARIFGSVFVLALAQRAESDTPYAKDQDAPE +GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELTLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGYGA +AAVTYVLGLLFGANVG +>PROKKA_02448 +MSPAHAATPAALPEPTREQVRRWRRYLADEIAEGQIYRDIAASKDGVERDILIGLAEAEK +RHEEHWRALLGEHAAHPPRPSVHRILLRALARVFGSVFVLALAQRAESDTPYAKDQDATE +HMAADEQIHEEVVRGLASRGREQLAGSFRAAVFGMNDGLVSNLALVMGIGATGVASSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAEHLDLDRNELELVYLARG +MTPEDAKHRALERLGYLSCDCNPQFSARPDGSKGPVDHSESFAEIGSAWGASLSSFCFFA +SGALIPILPYLFGMTGLGALVVAAVLVGIALLFTGGVVGLLSGSSPLWRGLRQLMIGYGA +AAVTYLLGLLVGGSIG +>PROKKA_00385 +MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE +GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA +AAVTYVLGLLFGANVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000430.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000430.fa new file mode 100644 index 0000000000000000000000000000000000000000..5a53e2b73ada0d9ebfd736efb63c1041488f560c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000430.fa @@ -0,0 +1,41 @@ +>PROKKA_00391 +MPAASDAPTPAPRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMAFTGY +GSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGDLRTT +VRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDDTVVV +TSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQTLTRF +LGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQHDPEI +YAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRRSTPGIPWCYGPDGATLSNQLEDL +GILPVEFVDVQPEAWREDILGDDEAPATLDAAAQRDDRSTDEEAAR +>PROKKA_00115 +MPAASDAPTPAPRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMAFTGY +GSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGDLRTT +VRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDDTVVV +TSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQTLTRF +LGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQHDPEI +YAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRHSTPGIPWCYGPDGATLSNQLEDL +GILPVEFVDVQPEAWREDILGDDEAPATLDAPGQRDGRPADEEAAR +>PROKKA_02565 +MSAVSDAAPVSPRRTRLAALGDPTPVENVATHLQEGWNRWHRSRALRAGHVPTIMAFTGY +GSTSWVRILSRVVIAPDEEFLNGRRISKVVADGVRGWRNFVAPPMAYAEVEVEVGGTRTT +VRTDRMGVVDAVLDVEMEPGWRTATLHVGDDEHVTMDLYICHPDARIGLVSDIDDTVVVT +SLPRPLLAAWNSFVIDEHARTPTPGMAVLLRRVAELEPKAPVLYLSTGAWNVAQTLTRFL +GRNLYPLGALLLTSWGPTKDRWFRSGQEHKKTQLERLAEQFPDIKWILVGDDGQHDPEIY +ADFAQRHPDRVAAIVIRQLTPSEALLAGGRAEDTRRSTPGIPWCYGPDGASLSNQLEDLG +ILPVGFVDVQPEGWKEDILGDDEVLSAAEHGAAALGDEADAPDTAAEPRVPAGEAAVGDG +AADEAEAAEAGGSR +>PROKKA_02436 +MPASESASIAAQNDPARRQRLAAAGGPTPAENVATHLQEQWNRWHRSRALRRGFVPTVMA +FTGYGTTSWVRVLSRVVLAKDEDFLNGRRLSKVVADGVHGWRNFVAPPMAYAEVEVEVGD +LVTTVRADRMGVVDVVLDVELEPGWRTAVLRVGDEEEVTTDLYIASPDAKVGLVSDIDDT +VVVTSLPRPLLAAWNSFVIDEHARTPTPGMAVLLRRIAAAEPMAPVLYLSTGAWNVAQTL +TRFLGRNLYPLGALLLTSWGPTKDRWFRSGQEHKVTQLERLAQQFPDLQWILVGDDGQHD +PEIYADFATKHPDKVKAIVIRQLTPSEALLAGGRAEATRHSTPGIPWCYGPDGAALSNQL +EDLGILPVDFVDVHPEGWLEDILGEDEASAAGRDGDEHGVHGGRADQDEARDVDVSAQD +>PROKKA_00397 +MPAASDAPTPAPRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMAFTGY +GSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGDLRTT +VRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDDTVVV +TSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQTLTRF +LGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQHDPEI +YAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRHSTPGIPWCYGPDGATLSNQLEDL +GILPVEFVDVQPEAWREDILGDDEAPATLDAAAQRDGRSADEEAAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000435.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000435.fa new file mode 100644 index 0000000000000000000000000000000000000000..b2c03f4ef8ce07a843005d9fab94a6cc695f0437 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000435.fa @@ -0,0 +1,46 @@ +>PROKKA_00397 +MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQ +VGGVLWLALHAVPVTVTTAMPTAPDHLITGTAWLVPWGLTLLPLALSWRAGRRLARASYR +DQAWQAFVGAVGAYALVGLAVAFLPGTDELTAHPAPAALLPALLFGVAALAGARREAGTW +AHLIGLDLTERISRRSQYERWAGSYAWSVVRAAAVAVLALTGLNALLVAGRLAVEWTAVV +TVAEAIGGGPLGGLLLALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPA +LPALGALPGTWSPWQLLLLAVPIGAGAVAGVWLLREGENHLDDWLHTRHGSRAVSLTLST +LALAVLTGLLTGLLLLVPLALTSGTLGLGALTDLGSHVWAVSAAVAGWVALGCAAGYLTA +LAVAGHRDGTTTVPRSGDRASGLRDRPSPRRARD +>PROKKA_00121 +MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQ +VGGVLWLALHAVPVTVATAMPTAPDHLITGTAWLVPWGLTLVPLALSWRAGRRLARASYR +DQAWQAFVGAVGAYALVGLAVAFLPGTDELTAHPAPAALLPALLFGVAALAGARREAGTW +AHLIGLDLTERISRRSQYERWAGSYAWSVVRAAAVAVLALTGLNALLVAGRLAVEWTAVV +TVAQAIGGGPLGGLLVALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPA +LPALGALPGTWSPWQLLLLAVPISAGVVAGVWLLREGENHLDDWLHTRHGSRAVSLTLST +LALAVLTGLLAGLLLLVPLALTSGTLGLGTLTDIGPHVWAVCAAVAGWVALGCAAGYLTA +LAVAGHRDGTTTVPRSGDRASGLRDRPSPRRARD +>PROKKA_02560 +MTALLSLLAVMIPTLVVWATGGFQRPTIEGALQVGGTLWLALHAVPVTVATVLPTAEGHV +LSGTAWLVPWGLTLIPLLLSWRAGRRLARASYRDQAWQAFAGAVVGYALAGLTVAFLPGT +PELRVSPWAAALLPALLFGIAALAGARREAGTWAHLIGLDLTERIARRSQYERWAGSYAW +SVVRAAVVALLVLAALSALLVAVRLAVEWPAVVTLAQAIDAGPFGGLLLAVLQIGWLPTL +TGWAIAWTAGPGFSVGSDSLYSVFGATPAAAPALPALGALPAAWAPWHPLFLAVPIAAGV +AAGVWLLREGENHLDDWLDARTGHRAVSLALSTLALAVLTGLLAGLLLLVPLALTSGTLG +VGTLTDIGANVWAVCAAVAGWVALGCAAGYLVALALAGRRFIPPAEAAVAAERPRPRRSR +D +>PROKKA_02431 +MSPRVPSLLRPVPLPLWLQGVVEALVTALTSLALVLVPTLAVWITGGFSSTRIEDVLQTG +GALWLGLHAVPLAVTTVVAQADTPTVTGTVWLVPWALTALPVWLSWRAGRRLARASYREQ +AWQALAGAVAAYAVVALACALLPGEGRITVHPLPSVLLPCLLFTTSAVAGARREAGTWAH +LIGLDLTERIARRSQYERWAGTYAWSVLRGAGVGLAALAGLHALLVTVAVLVRWPRIIEV +QQMVGAGPVGGLMLALLEIGWLPTFTAWAVAWTAGPGFAVGADGHYSVFGTTPAPVPALP +LLEALPAPWAPWHPAFLLVPVLAGAVAGWWLLREGENHLDDWIDSRITARWASLTLSTLA +LALLLGLVSGVAVLVPLALTNGTLGVGSMREIGSNAPLVALAVAGWMALGCALGYLVALA +VVDRPVRGRRRISLPLPGSAPRAVTGRARRLPPRRLPRGVADAEADEPEVAAPAAAREEI +PGRETPAQETPSEEPPAAARPAPRRAGAPRVPRVPRPAPRRARD +>PROKKA_00403 +MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQ +VGGVLWLALHAVPVTVATAMPTAPDHLITGTAWLVPWGLTLVPLALSWRAGRRLARASYR +DQAWQAFVGAVGAYALVGLAVAFLPGTDELTVHPAPAALLPALLFGVAALAGARREAGTW +AHLIGLDLTERISRRSQYERWAGSYAWSVVRAAVLAVLALTGLNALLVAGRLAVEWTAVV +TVAEAIGAGPLGGLLLALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPA +LPALGALPGTWSPWQLLLLAVPIGAGAVAGVWLLREGENHLDDWLHTRHGSRAVSLTLST +LALAVLTGLLTGLLLLVPLALTSGTLGLGTLTDIGSHVWAVCAAVAGWVALGCAAGYLTA +LAVAGHRDGTTTVPRSGDRASGPRDRPSPRRARD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000501.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000501.fa new file mode 100644 index 0000000000000000000000000000000000000000..37bfcea5322bf0578c39e14f2a6566594e94d479 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000501.fa @@ -0,0 +1,25 @@ +>PROKKA_00479 +MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDEPGAVDQRIELSGRVTVNWAAKFAGLL +GAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEGDSPAAVLTDRPEAWPDPSVAV +FAVALPRGLEPEFDGPAVDPAVVDVAAEIRAQPDALPGPVDHVRPASIPAGADVAPDDDG +PRPRLTWAGVRAALEAWDAGRAVTVRP +>PROKKA_00197 +MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDEPGAVDQRIELSGRVTVNWAAKFTGLL +GAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEGDSPAAVLTDRPEAWPDPSVAV +FAVALPRGLEPEFDGPATDPAVVDVAAEIRAQPDALPGPVDHVRPASIPAGTDVAPDDDG +PRPRLTWAGVRAALEAWDAGRAVTVRP +>PROKKA_02468 +MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPGEHGAVDQRIELSGRVTVNWAAKTAGLL +ADEGLGPGDPVALDLPAHWLSHALALGVLCAGAEPADDGAAPAAVLTDRPERWTDPATAV +FAVALPRGLELPTGGAVADPSVVDVAAEILGQPDALPGPVDHVRPEALPAADVAAADGDA +RTDEDQDDDGPRPRLTWAGMRAVLQAWDAGRAVQVRP +>PROKKA_02352 +MVSLSAPRPDGPLVTRLASSPRPALVQEPAPAGEAAGAAHGAVDQRIELSGSVTVNWAAK +AAGLLLDEGVAPGDAVLLDLPDHWLSRALALGVLCAGARPAFVAGPADRAQEAPDDAAAV +LTDRPEHWDDPVLTVVAVRLPRGIEPDFGDDDAGDPSVVDLAAEIRAQPDALPGRVDHVT +VDAVPADPADAAGPLTEGGVGVGRARLDAPALRASLEAWDAGRAAHVPA +>PROKKA_00479 +MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDEPGAVDQRIELSGRVTVNWAAKFAGLL +GAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEGDSPAAVLTDRPEAWPDPSVAV +FAVALPRGLEPEFDGPAVDPAVVDVAAEIRAQPDALPGPVDHVRPASIPAGADVAPDDDG +PRPRLTWAGVRAALEAWDAGRAVTVRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000517.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000517.fa new file mode 100644 index 0000000000000000000000000000000000000000..f053fea6835f142a98a3677ed63ba461572ca86d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000517.fa @@ -0,0 +1,30 @@ +>PROKKA_00501 +MAERVEPAHGEDGGAVAAPQPHRPRLPFWASLLLNVVVALAVVAVVQALWVKVYSVPSGS +MENTLEVGDRMLVNRTAYPDGAADAQDVVVFTANEDWAHPMPPEGAVENAVRTFGDLTGI +GRSHEQALVKRVIGTAGQTVECCTAEGAVTVDGEPLDEPYIHNDLPFIRDELDCESEVMS +ARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQAGDCARFVTREDIVGEVFVTVW +PPTHWGGH +>PROKKA_00222 +MAERVEPAHGEDGGAVAAPQPHRPRLPFWASLLLNVVVALAVVAVVQALWVKVYSVPSGS +MENTLEVGDRMLVNRTAYPDGMADAQDVVVFTANEDWAHPMPPEGAVENAVRTFGDLTGI +GRSHEQALVKRVVGTAGQTVECCTAEGAVTVDGEPVDEPYIHNDLPFIRDELDCESEVMS +ARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQAGDCARFVTREDIVGEVFVTVW +PPTHWGGH +>PROKKA_02448 +MAERVEPVRGEDGDDGSVAAPERRRSRLPGWASVLLNVVVAIAVVAVVQALWVKVYSVPS +GSMEQTLEVGDRMLVNRTAYPDGMAASQDVVVFNANEDWAQPLPPEGPVENAVRTFGDIT +GIGRSHDQALVKRVVGTEGQTVECCTSEGRVTVDGQPLDEPYLHNDLPFAPGRLDCESDV +MSARCFGPITVPEDSMLVLGDHRSNSADSVIGCRGLPAEQAEGCARFVTREDVVGEVFVT +IWPPSNWGGH +>PROKKA_02332 +MAHTPDAVPARDEAACDEAVRDDAAPAPASSAAAPGRRRRVQLPFWASVLLNVAVALLVV +SVVQALWVKVYSVPSGSMEQTLQVGDRMLVNRTAYPDGVAERQDIVVFDANETWGVDTVG +EEGPVEGAVRTFGDLTGIGRSHENALVKRVIGLPGETVECCTSQGAVTVGGTPLEEDYLY +EDLPFVPGTLDCTTTPRSSRCFGPVTVPERSMLVMGDHRSNSADSVYQCRGLTAEQAGDC +AHFVRDEDVVGRVFSTVWPPSNWSGH +>PROKKA_00500 +MAERVEPAHGDDVDGGAVAAPQPHRPRLPFWASLLLNVVVALAVVAVVQALWVKVYSVPS +GSMENTLEVGDRMLVNRTAYPDGAADSQDVVVFTANEDWAHPMPPEGAVENAVRTFGDLT +GIGRSHEQALVKRVVGTAGQTVECCTAEGAVTVDGEPLDEPYIHNDLPFIRDELDCESEV +MSARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQVGDCARFVTREDIVGEVFVT +VWPPTHWGGH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000521.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000521.fa new file mode 100644 index 0000000000000000000000000000000000000000..d4f52b786b101f33211f93b217778269151a0a6e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000521.fa @@ -0,0 +1,40 @@ +>PROKKA_00506 +MTDAPLFWRSEDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALTRRRSTGDDAPRLLL +PAGDVHTLVALESFGPTQLAALASPVAALATARPEAAAGVGWVLPAGDAPALPGAVGHRE +HAATADVVTDRLPGLRRVLVAGEYLPSGRAAVRWARQRGARVGVVQHGLLAVSTPPVPRD +ATLYAFTSADADWWTQGRADVEAVAVGSALLEQARRAAPAPSDTAGDGPGVFLGQLHGAE +LPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQHAAWRRAGVRIDDAGAPLVATRGPV +AAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWRRYGMTRWRPGRTPEPTPPLASPTADP +AAAIAEHVWKESA +>PROKKA_00226 +MTDAPLFWRSGDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALARRGSTGDDVPRLLL +PPGDVHTLVALESFGPTQLAALASPVAALATARPEAAAGVGWVLPAGDAPALPGAAGHRE +HAATADVVTDRLSGLRRVLVAGEYLPSGRAAVRWARQRGARVGVVQHGLLAVSTPPVPQD +ATLYAFTSADADWWTQGRADVEAVPVGSALLEQARRTAPALSGAGDDGPGVFLGQLHGAE +LPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQHAAWRRAGVRIDDAGAPLVATRGPV +AAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWRRYGMTRWRPGRVPEPTPPLASPTTDP +AAAIAEHVWKESA +>PROKKA_02444 +MSGVGSGDVPLFWRPEDLPAWQRWQRAQWPASRRLADTARRLARAGRGALAAGRGAAPAP +ESGLRLVLPAGDVHTLVGVESAAPTQRAALVEPVRALAEGRAGHAAADAARTAAGVGWVV +PADVVAAQLPDLPGSDALSVHAVDDVMVAERLGGLRCVLVAGEYLPAGRAAVRWARERGA +RVGVVQHGLLAVSTPPVPRDVALYAFTDHDAHWWTQGRTDVQAVAVGSALLEAARRMASH +AVADAVPRAAGPGVFLGQLHGAELPRTDFARAAQEYVRATGAAYRPHPAERDRLSLAQHE +AWRKAGMRIDATAGPLASTAGPVAAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWERYG +MTRWRPGVETEPTPPLASPSADPAAAIAAHLWKETA +>PROKKA_02328 +MTRAVAQPPLFWRAEQLDAWRRWQRTQWPLARRAADLVRGGVARSRGAVQAPDAGLRLLL +PAGDVHTLIAVESAGPTQRAALVEPTRALAEGRTGLDAAARTRLLGGVAWVVPADVAGAL +LPDLPAAAQLTGHAADPDTVGTRLAGLERVLVAGEYLPAGRAAVRWAHERGASVHVVQHG +LLAVSTPPVPRDATLYAFTARDADWWTQGRADVRAVPVGSALLEAARRGAASADPTATGS +TGPGPGLFLGQLHGAELPRAQFAAAAEQYVRTTGAVYRPHPAERDRLSRAQHARWEGAGI +AVDRSGAPLTQTAGPVAAVFSTGILEAAQTGRPAWAVHPDPPRWLVEFWDRYGITRWMPG +ADPTPTPALVAPTADPAAAIARDLWKEHA +>PROKKA_00505 +MTDAPLFWRSEDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALTRRRSTGDDAPRLYL +PAGDVHTLVALESFGPTQLAALASPVAALATARPEAAAGVGWVLPAGDAPALPGAVGHRE +HAATADVVTDRLSGLRRVLVAGEYLPSGRAAVRWARQRGARIGVVQHGLLAVSTPPVPQD +ATLYAFTSADADWWTQGRADVEAVPVGSVLLEQARRTAPALSGAGDDGPGVFLGQLHGAE +LPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQHAAWRRAGVRIDDAGAPLVATRGPV +AAVFSTGILEAAQAGRPAWAVHPEPPAWLEGFWRRYGMTRWRPGRTPEPTPPLASPTADP +AAAIAEHVWKESA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000570.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000570.fa new file mode 100644 index 0000000000000000000000000000000000000000..bcd83a4dac1f6273be5505926cb9db81499a0187 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000570.fa @@ -0,0 +1,50 @@ +>PROKKA_00580 +MPTAPAPSEAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALP +DPAEARWSVAGDGLDVLGEEQGRVPSPGPRLVRHDDPADPDRAWAGLAAAAAPRPVVGGE +GLPLRGGLVGWLGYELGLADLGVTPPSRRAEDPAPLPAQFWVRPSRYVVADHAAGVLHCC +VVSLDPTTAEAGADRWAADVRRALAAARRALETAAGDAVVPPPQDAVPGPRADEEAPGTW +REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVDPLVLFHELAAHQPAPYAAL +LEHGTGSRRWAVVSASPERFLSGREGRYSTKPIKGTAARLADPAGDAEAARALAADPKTR +AENLMIVDLLRNDLSRVCEPGSVQVPSLMAVESYASVHQLVSTVTGTARAGIEPVDVVRS +LFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVLAGGRWS +VGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGLPTTAPDIA +>PROKKA_00313 +MPTAPAPSVAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALP +DPAEARWSVAGDGLDVLGEEQGRTPSPGPRLVRHDDPADPDRAWADLAAAAAPRPVVGGE +GLPLRGGLVGWLGYELGLADLGVTPPSPRPGDPASLPAQFWVRPSRYVVADHAAGVLHCC +VVSLAPTAAETGADRWAADVRRALAAARRALETASGDVVVPPPRDAGPGPQADEEAPGTW +REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVDPLVLFHELAAHQPAPYAAL +LEHGTGARRWAVVSASPERFLAGRAGRYSTKPIKGTAARLADPVADAEAARALAADPKTR +AENLMIVDLLRNDLSRVCEPGSVEVPSLMAVESYASVHQLVSTVTGTARAGVEPVDVVRS +LFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVLAGGRWS +VGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGVPTTAPDVA +>PROKKA_02353 +MAAVYAHAVQRGAGSFWLDSALPDPAEARWSVAGDGLDVLGEEQGRVPSPGPRLVRHADP +ADPERAWSDLAAAAAPRRVVGGEGLPLRGGLVGWLGYELGLADLGVRPPSRRAGDPAALP +AQFWVRPSRYAVADHAAGTLSCCVVALDAAAAEAAADRWAADVRRALDAARRATQAAADD +AAASEVRADVAPEAGTGEAAGAWREDRAAYDEHIARCHAALHAGDSYELCLTTRFDADPA +LRVDPLALFLELAAHQPAPYAALMEHGTGPRGWAVVSASPERFLAGRDGRYSTKPIKGTA +ARLPDPAADAEAARALAADPKTRAENLMIVDLLRNDLSRVCEPGSVQVPSLMAVESYATV +HQLVSTVTGTARAGVAPVDVVRSLFPGGSMTGAPKRRSVELLAQWEDSPRGVYSGALGLL +GADGAVSLSIVIRTAVLAAGRWGIGAGGAIVADSTAEAEHEEVLLKARGLRRALARADGT +ARTTTAPPRSR +>PROKKA_02247 +MPTAPGRPDASPAPLHVAVRTLDIATLAAVGHTAATAAGAVYAHAVQRGTASFWLDSALP +DGGEARWSMVGDGVDVLGEEEGRIPSPGLRLIRHGDPADPDRAWADLAAAAAPREVHGGE +GLPLRGGLVGWLGYELGLADLGVTPPPPRPGDPAALPAQFWVRPSRYAVADHVAGALSCC +VVSLDADAAEAAADRWEADVRRALEAARTSTEEVEVDVDAPEAPGVWREDGAAYAEQIAR +CRAALHAGDSYELCLTTRFDADPALRVDPLALFRDLAAHQPAPYAALMEHGTGAERWAVV +SASPERFLSGRDGRYSTKPIKGTAARLPDPTEDAAAAAALAADPKTRAENLMIVDLLRND +LSRVCEPGTVQVPALMAVESYATVHQLVSTVTGVARAGVAPVDVVRSLFPGGSMTGAPKR +RTVELLAAWEGSPRGVYSGALGMLGADGTVELSIVIRTAVLSPTTPDAPARWSVGAGGAI +VADSDAHAEHEEVLLKARGLRRALTRAAGTA +>PROKKA_00581 +MPTAPAPSEAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALP +DPAEARWSVAGDGLDVLGEEQGRVPSPGPRLVRHDDPADPDRAWADLGAAAAPRSVVGGE +GLPLRGGLVGWLGYELGMADLGVSPPSRRPEDPAPLPAQFWVRPSRYAVADHAAGVLHCC +VVSLDPTAAEAGADRWAADVRRALAAARRDLETAAGDAVVPPPEDAGPEPRADEEAPGTW +REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVNPLVLFHELAAHQPAPYAAL +LEHGTGARRWAVVSASPERFLAGREGRYSTKPIKGTAARLPDPAADAAAARALADDPKTR +AENLMIVDLLRNDLSRVCEPGSVEVPSLMAVESYASVHQLVSTVTGTARAGVEPVEVVRS +LFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVLAGGRWS +VGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGVPTTAPDIA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000601.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000601.fa new file mode 100644 index 0000000000000000000000000000000000000000..cf672f22d0384f53d25cf0dafeab43c3b48d652d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000601.fa @@ -0,0 +1,34 @@ +>PROKKA_00673 +MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL +AGPRGGAAGTLFLGIDDDAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA +AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPHVVQAQP +HDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHTGRVFIDPGPRDAGGPLRFKA +DIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY +ERVGFERRGTFATVLY +>PROKKA_00410 +MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL +AGPRGGAAGTLFLGIDDDAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA +AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPHVVQAQP +HDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHAGRVFIDPGPRDAGGPLRFKA +DIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY +ERVGFERRGTFATVLY +>PROKKA_02289 +MTRLPPVPRWSPSTDRQVRAATGGRVRLLTDADTPALAALSARAPVSNVFVDSLLEAGRL +AGPRGGAAGTLFLGIDAGEGRDDDGAPVAGLRAALWVGSNVVPVAAAETPDAGWAPGDAE +ALGAAAVALRRRYGSLYGPAEPVLAVGSALAAAGHRARSVREDQPLLVLGADGAAETSPH +VVQAHPRDFERVLPASAAMFEEELGFSPFLGGAAQYRDRVERLIRAGRVFIDPGPADAGG +PLRFKADIGLLSSRCAQIQGVWMAPAARGRGLAAAAMAAVVEYVRLQAPVVSLYVNAYNT +PALRTYERVGFERRGTFATVLY +>PROKKA_02151 +MDLAAASDGRVRVLTDADTPALTALAAADPVANVHAASLLEAGRLAGPRGGRADGTLFLG +VEDPDRPGALRSACWVGSTVVPLAGHDDDVPALAASVAALRRRFASVYGPAVTVLAVGRT +LRDAGHRPRAVREEQPLMVHARTPGDLVPDPAVRAAAPGEWESVVPASAAMFEEELGFSP +FLTGAAQYRDRVRRLVADGRVFTAPGEPVVDDPTSGVRFKADIGLLSASCVQVQGVWLHP +SRRGRGEAAPAMAAAVALMARRAPAVSLYVNGFNTPALRTYERVGFERVGTFATVLY +>PROKKA_00643 +MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL +AGPRGGAAGTLFLGIDDDAPGAGGLRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA +AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPSVVQAQP +RDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIQAGRVFIDPGPRDAGGPLRFKA +DIGLLSSRCAQIQGVWMAPAARGRGLAVSAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY +ERVGFERRGTFATVLY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000639.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000639.fa new file mode 100644 index 0000000000000000000000000000000000000000..dcbffdf1c730331ceab76cfe3584dd899b94cac3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000639.fa @@ -0,0 +1,25 @@ +>PROKKA_00720 +MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA +YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE +LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH +HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL +>PROKKA_00451 +MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA +YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE +LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH +HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL +>PROKKA_02238 +MARPTSVPGVRPSVAVLDYGSGNVHSAVRALERAGADVELTRDPEAVQSADGLLVPGVGA +FASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERAEGMGEWPGVVEA +LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLRWEFDQTISAMRPPQVTWAH +HGADFVAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL +>PROKKA_02110 +MASPTSVPGVRPTVAVLDYGSGNVHSAVRAVEHAGARVELTKDPDAVLGADGLVVPGVGA +FASVMEALRSSGGTRWIGRRVAGGRPVLGICVGHQVLFEAGVEHGVRTEGMGEWPGVVEP +LPAATVPHMGWNTVRPAEGSALFAGIEDERFYFVHSYAVQSWEFDQGNEAMRPPQVTWSH +HGADFIAAVENGPLSATQFHPEKSGDAGQALLRNWLETL +>PROKKA_00684 +MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA +YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE +LPAEVLPHMGWNTVRPAEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH +HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000676.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000676.fa new file mode 100644 index 0000000000000000000000000000000000000000..006d32f6c6e071b1f2a51c14beb55f3061e1da42 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000676.fa @@ -0,0 +1,36 @@ +>PROKKA_00764 +MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQARVVPAPTAAPSSSHDAGGDPDADTDGV +DPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPEGPAYAQPGRCRPNRVILLDVRFRATAG +GPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEGDTIVV +YDDDHGLSAARAWWLLRHAGLRDSMLLDGGLEAWRAAGLPLQPGEVIPVPGTARPSWGRM +PVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNVPTAESIAEDGRLRP +AAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWVQDPSN +AVAVGPEPDGASGRD +>PROKKA_00494 +MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQGRVVPAPTAAPSSSHDAGGDPDADIDGV +DPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPGGPAYAQPGRCRPNRVILLDVRFRATGG +GPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEGDTIVV +YDDDHGLSAARAWWLLRHAGLRDSVLLDGGLEAWRAAGLPLQPGEVIPVPGTARPSWGRM +PVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNVPTAESIAEDGRLRP +AAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWVQDPSN +AVAVGPEPDGASGRD +>PROKKA_02165 +MWGIDDGDTVVVYDDDRGLSAARAWWLLRHAGLRDSMLLDGGLAAWRAGGLPLQPGEVIP +MPGSARTSWGRMPVVDTAGAEAMASGGLLLDARAAERYRGETEPIDPVTGHIPGARSLPT +AGSLAEDGRLRPAEELAARFDAVGVDDETPVAVYCGSGVTAAHAVLTLAVAGRPGVALYP +GSWSAWIQDPSNAVAVGPDPHGEPGRD +>PROKKA_02061 +MKDSTEGRPPSPASSPAADAPTDQTPLAELAEDATAPDPAAAEPPSLVDVGVLAGWLGLT +PAEPVPAPPPGPVFDRRVDPGRVILLDVRYAVAGAGGSGHDAYLRGHLPGAVFVSLPNQL +AGHAGPRQGRHPLPDPVQFAHSLRMWGIDDGDTVVVYDDDRSLAAARAWWLLRHAGLRDS +VLLDGGLGAWRAAGLPLQPGEVIPQPGSVHPSWGRMPVVDTDGAEAIAAGGLLLDARSAE +RYRGEEEPLDPVAGHIPGARSLPTSGNVAADGRLLDPAALAARFEDAGLSDEVPAAVYCG +SGVTAAHQVLALAVAGRHGVALYPGSWSAWIQDPDRPVATGPRPEGD +>PROKKA_00728 +MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQGRVVPAPTAAPSSSHDAGGDPDADIDGV +DPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPGGPAYAQPGRCRPNRVILLDVRFRATGG +GPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEGDTIVV +YDDDHGLSAARAWWLLRHAGLRDSVLLDGGLEAWRAAGLPLQPGEVIPVPGTARPSWGRM +PVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNAPTAESIAEDGRLRP +AAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWVQDPSN +AVAVGPEPYGASGRE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000691.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000691.fa new file mode 100644 index 0000000000000000000000000000000000000000..086af3a97aa8a684bc560e0e6e12a5cbe9ffa959 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000691.fa @@ -0,0 +1,45 @@ +>PROKKA_00782 +MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW +QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL +YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD +FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED +NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN +AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV +VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE +ALAALDVVHEVASVLRVEGN +>PROKKA_00513 +MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW +QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL +YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD +FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED +NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN +AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV +VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE +ALAALDVVHEVASVLRVEGN +>PROKKA_02148 +MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRNTGATRDW +QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL +YAAAAATGAQLSFEAAVAGAIPILRPLRDSLAGDRVTRVMGIANGTTNYILDKMDSEGAG +FDEALAEAQRLGYAEADPTADVEGHDAAAKAAILATLAFGAPYTLDQVAVSGITAITAED +NEAAADAGYVIKLLAIAERARAADSAEGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN +AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVAELPALDPAEAVTSCLV +VLRVADEPGVLRRVAGVFEEQGVSIETLRQVQSDRDDAPGASLRLITHRARQRDLDATVE +ALAALDAVHEVASVLRVEGN +>PROKKA_02042 +MAEPTASAAQTAPAPARDALRVALLGGGTVGSQAARILTEDAAVLADRVGVRLELTGIAV +RDTAAVRDWQADPSLYTTDAEALVDGADLVIELMGGIEPARSLIRRALQVGTSVVTGNKA +LLAEHGEELYRLASETGAQLSFEAAVAGAIPILRPLRDSLSGDTVNRVMGIANGTTNFIL +DRMDTEGASFADALAEAQRLGYAEADPTADVGGFDAAAKAAILATLAFGSSYTLDQVSVE +GITEVTAEDNAAAADAGYVIKLLAIAERDTARDGTAGAILRVHPTLIPREHPLGSVRGAY +NAVFVEAENAGQLMFYGPGAGGAPTASAVMGDAVAIGQRIVRGGPARLRTPVAALPALDV +SEARTSCMVVLRVADQPGVLRRVAGVFEEHGVSIETLRQVQGADDAAGASLRLITHRARQ +RDLDDVVAELTTLDAVHEVASVLRVEGN +>PROKKA_00749 +MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW +QADPALYTTDAEALVDGADVVIELMGGVEPARTLILRALAAGTSVVTGNKALLAQHGEEL +YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD +FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED +NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN +AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV +VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE +ALAALDVVHEVASVLRVEGN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000719.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000719.fa new file mode 100644 index 0000000000000000000000000000000000000000..129fcea83195f6f4825936aa50ec2709a2e84288 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000719.fa @@ -0,0 +1,30 @@ +>PROKKA_00812 +MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD +TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL +PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAPAFGRALNDV +RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG +ADESAPGAGDAEDEQ +>PROKKA_00544 +MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD +TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL +PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHNQAPAFGRALNDV +RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG +SDESAPGAGDAEGEQ +>PROKKA_02118 +MAERFRWTRRGYTAQLEKPEVRLLRGLVKDVITLLEGRRRNVLSEADDLPADAPGAPEPS +ADVAPVPQGPEAGAGPAAGLDEADAAFWELVSGLHLSQDRVPHRAAPADPAVARLLPEAM +PQADAQERGAHRALTEDALSEGKLADARLALELLRSTRVEVPHHQAPAFGRALNDVRLVL +AARLGVETEEDAERVHAVDDWRSAEDVESTMALLYNFTTWLLETLMTEMLSELPEGADED +APGADEAGDDA +>PROKKA_02009 +MAQRFRWTRRGYVAELEDAELRLLRGLVKDVVTLLENRQDEVAPPGSDAGTAEDAPEAGA +EPVADARPGDAVGPGEETPHDAAFWALVGGLDLVADPVAERSAPEDPAVARLLPDAMPHA +EPAERARQRALTEDALTAAKLADARRALEALRSVRVTVPHEHAVSFGRALNDVRLVLAAR +LGIETEQDAARVHAVDDWRDAQDVEATMALLYNFTTWLQETLMAEMLSELPLEGAAGPDE +EERA +>PROKKA_00781 +MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD +TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL +PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAPAFGRALNDV +RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG +SDESAPGAGDAEGEQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000733.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000733.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a2827acb6a8cd203cf19d0c0b4e109736466854 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000733.fa @@ -0,0 +1,55 @@ +>PROKKA_00828 +MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG +IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE +VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG +TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS +LPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNA +VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE +GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK +SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI +KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL +VDEAELAARRESWEPVEPKFTTGVLGKYAKLVHSAAEGAYLG +>PROKKA_00560 +MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG +IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE +VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG +TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS +LPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNA +VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE +GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK +SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI +KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL +VDEAELAARRESWEPVEPKFTTGVLGKYAKLVHSAAEGAYLG +>PROKKA_02094 +MDTAASTPRTPSAAPDMKPRSRDVTDGMERAASRGMLRAVGLGDADFAKPQIGIASSWNE +ITPCNLSLDRLAQAAKEGVHADGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVE +TVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSTMPGHARLSDGTEKQVTI +IDAFEAVGACARGLMSEEDLLRIEKAIVPTEGACGGMYTANTMASVGEALGMSLPGSATP +PSPDRRRDDFARRSGAAVVNLLRQGITARDIMTKEAFENAIAVTMAFGGSTNAVLHLLAI +AREAGVDLSLEDFNRVGDRTPHIADLKPFGRYVMTDVDRVGGVPVVMKALLDEGLLHGDA +LTVTGRTVAENLAELAPDPVDGDVIRTMDRPMHPNGGIAILHGSLAPEGAVVKSAGFDAD +VFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPRGGPGMREMLAITGAIKGAGLGK +DVLLLTDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIAGRTLDVQVAEEELE +ARRREWTPVPPKFTTGVLGKYAKLVHSAAEGAYLG +>PROKKA_01993 +MDTSAADRTPQDVVTAPDMKPRSRDVTDGMERTAARGMLRAVGLGDEDFAKPQIGIASSW +NEITPCNLSLDRLAQASKDGVHAAGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADS +VETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDGTEKQV +TIIDAFEAVGACARGLMSEEDLLRIEKAIAPGEGACGGMYTANTMASIGEALGMSLPGSA +AAPSADRRRDAFARRSGEAVVNMLRLGITARDVMTKPAFENAIAVTMAFGGSTNAVLHLL +AIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRVGGVPVVMKALLDEGLLHG +DTLTVTGKTLAENLAALDPDPVDGTVIRTMENALHPNGGIAILHGSLAPEGAVVKSAGFD +ADVFEGTARVFDRERAAMDALEEGVIQAGDVVVIRYEGPKGGPGMREMLAITGAIKGAGL +GKDVLLITDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIASRTLDLLVEEAE +LEARRTSWQPVPPKFTTGVLGKYAKLVHSAAEGAYLG +>PROKKA_00797 +MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG +IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE +VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG +TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS +LPGSAAAPSADRRRDAFARRSGEAVVKMIRQGITARDIMTKPAFENAIAVTMAFGGSTNA +VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE +GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK +SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI +KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL +VDEAELAARRESWKPVEPKFTTGVLGKYAKLVHSAAEGAYLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000748.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000748.fa new file mode 100644 index 0000000000000000000000000000000000000000..55421a619edbb15e07a4a6e233dc0eee264aaee8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000748.fa @@ -0,0 +1,50 @@ +>PROKKA_00861 +MTETTAPAAPAEQEAAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLARGEV +PFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVDAAV +ASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGFAVR +DTLTPDRLVIGMHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISF +INAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGL +DRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRIRRAEASGPAPTPASVQVLNGTRI +AVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDSLEAA +VDGAELTLLLTEWRQFREMDPDTVGARVASRLLIDGRNVLDVAAWREHGWDVIGLGHRFD +PERLLRAA +>PROKKA_00583 +MTETTAPAAPAEQEAAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLARGEV +PFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVDAAV +ASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGFAVR +DTLTPDRLVIGTHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISF +INAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGL +DRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRIRRAEASGPAPTPASVQVLNGTRI +AVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDSLEAA +VDGAELTLLLTEWRQFREMDPDTVGARVASRLLIDGRNVLDVAAWREHGWDVIGLGHRFD +PERLLRAA +>PROKKA_02074 +MTHPSAPAEQDRAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPEKIARLSRGEVPFH +EPGLPELLRTHVESGRLRFTTDVAEAARWADVHFVGVGTPQKVGESGADLRYVDAAVASL +AAAIDRDALIVGKSTVPVGTARRLAAMVRRVRAEAGLPGEVELAWNPEFLREGFAVKDTL +TPDRLVIGTDGPRAEQVLRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISFINA +FSEITEAVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGLDRT +MRFLAEVDDINLRRRDRVVDLAVQVLSAARDAGRGEAAAYGGKTTASGVEVLRGARIAVL +GVTFKPDSDDVRDSPALDVANRLYTAGADVRVHDPEGNANAAARFPRLDYVDSLEEAVEG +AELTLLLTEWQAFREMDPAAVGALVDARLLIDGRNVLDLAAWAEHGWTVVGLGHRFDPAA +LGA +>PROKKA_01968 +MTETAVVPAAAESEEAPARPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLAR +GEVPFHEPGLPELLRAHVASGRLRFTTDVAEAASWADVHFIGVGTPQKVGEAAADLTYVD +AAVESLARAIDRDALIVGKSTVPVGTARRLAARVAEIRAAEGLPGEVELAWNPEFLREGY +AVKDTLTPDRLVIGTHGPRAELLLRTVYATPLAAGTPWISTDLETAELVKVAANAFLATK +ISFINAFSEITETVGGDIGTLADAIGHDGRIGRRFLNAGVGFGGGCLPKDIRALQARVSE +LGLDRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARQGVVRSAPGGARTAPTPAGVQVLN +GTRIAVLGVTFKPYSDDVRDSPALDVANRLFTAGAEVAVYDPEGNANAAARFPRLGYVDS +LDAALQGAELVLLLTEWDEFRQMDPAAAGELVAQRILIDGRNVLDVDAWGEHGWTVLGLG +HRFDPAALNGGRPGDDAQA +>PROKKA_00820 +MTETTAPAAPAEQEAAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLARGEV +PFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVDAAV +ASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGFAVR +DTLTPDRLVIGTHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISF +INAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGL +DRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRVRRADASGTAPTPASVQVLNGTRI +AVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDSLEAA +VDGAELTLLLTEWRQFREMDPDAVGARVASRLLIDGRNVLDAAAWREHGWDVIGLGHRFD +PERLLRAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000758.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000758.fa new file mode 100644 index 0000000000000000000000000000000000000000..88472308d67222ed7744b0ee633d53370292f406 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000758.fa @@ -0,0 +1,35 @@ +>PROKKA_00871 +MGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACPAQDDAGAVLAHAGAAALDSA +RGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADRAARQALSDPREGTILTVLSAA +ARSLARSSTQAPDTPAVAGDADPAVRLGPAVTLMLADCVQAVEETESLLAPLTRAHVVDA +GAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGAHAAEAEPAAAAEAPAEGAVEVMGT +LALTPLAAAELRRRLTEVGDAVILAPLGTARDGQGRVPWRVHVHVPRAEDAIGPLRAAGD +VEGLTVTDLAGPSHGDDAAPDGCHGR +>PROKKA_00593 +MSTPSRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACP +AQDDAGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADRA +ARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTVMLADCVQ +AVEETESLLAPLTGAQVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGVHAAE +GEPAAAAEAPAEGAVEVMGTLTLTPLAAAELRRRLADVGDAVILAPLGTARDGQGRVPWR +VHVHVPRAEDAIGPLRAAGDVEGLTVTDLAGPSHGDDAAPDGCHGR +>PROKKA_02064 +MSTPPRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACP +AQDDAGAVLARAGAAALDLARGNSGTLLAVALAGMAEPLRGRARADAFALAAAFGAADRA +ARQALSDPREGTILTVLSAASRSLARSATQAPDSPAVAADVDPAVRLGPAVTAMMADCLR +AVEQTESQLAPLAQARVVDAGAVGLLWVLEALRAAVTDTAPDEELATALHGYVEGVRPGP +EPAGEDAVEVMGTLALTPLAAADLRRRLAETGDSVILAPVGTERDEHGRVPWRVHVHVPR +AADAVELMRAAGEVQGLAVTELSGDAAGPDADGCHGR +>PROKKA_01958 +MIRARLRGALAWLRGAEAALAQAAPRLDALNLFPVPDADTGSNMLATVRAARQAAERSAG +TDMSAVLRDAGAAALDSARGNSGTLLAVALVGLAAPLTPDAPLTTAELAAGARAADRAAR +AALSDPREGTILTVLREAATVLEAAAAGGREPAEALGSVVEAARRAVEDTEGQLAPLTRA +RVVDAGAVGLLLVLEALRAEVTRTPFDEGVVAALHGWADGPGAAGEDPQADGREAPGVEV +MCSIDLTPVDAAGLRRGLEEAGDSVILAPLSRAVDGAGRLRWRVHVHVARAEDAVALLEA +AGAPEEVAVTDLWDPAHRHPDDPAEGDAASPAPDGHGR +>PROKKA_00830 +MSTPSRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACP +AQDDVGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADRA +ARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTVMLADCVQ +AVEETESLLAPLTRAHVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGVHAAE +GEPAAAAETPAEGAVEVMGTLALTPLAAAELRRRLADVGDAVILAPVGTARDGQGRVPWR +VHVHVPRAEDAIGPLRAAGDVEGLAVTDLAGPSHGDAAPDGCHGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000763.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000763.fa new file mode 100644 index 0000000000000000000000000000000000000000..78d39a8a38c8f24172d2306e8d97559a1e02e72a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000763.fa @@ -0,0 +1,35 @@ +>PROKKA_00876 +MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV +LMITGRNKRALEDHFDRHPALEAALEHKGDTKRLAQIHESDLVGDIHYVRQGEALGLGHA +VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA +AVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL +TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAWLREF +TAGL +>PROKKA_00598 +MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV +LMITGRNKRALEDHFDRHPALEAALEHKGDAKRLAQIHESDLVGDIHYVRQGEALGLGHA +VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA +AVEAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL +TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGARHEDLGADLRAWLREF +TAGL +>PROKKA_02059 +MTVPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEARRAGLQDVLM +ITGRNKRALEDHFDRHPALEATLERKGDATRLAQIRESDLVGDIHYVRQGEALGLGHAVN +CARRHVGDEPFAVLLGDDIIGDGEALLARMIDVQQRLGGSVVALMEVPEEAVSAYGVAAV +EAVPGEGEDVVRVTGLVEKPAREDAPSTLAVIGRYVLASQVFDVLDRTPPGRGGEIQLTD +ALQTLADDDGEGGGVHAVVFDGRRYDTGDKLGYLQAVVEFGTRHEELGGDLRAWLKAFAA +GL +>PROKKA_01953 +MTEQSTAASPTRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEAVSAG +LGDVLMITGRNKRALEDHFDRHPALEQVLEAKGDTKRIDLIRASDLVGDIHYVRQGEALG +LGHAVGCARRHVGDEPFAVLLGDDLIGEDEGLLARMIDVQHRLGGSVIALMEVPEDAVSA +YGVAAVAPVDGEDDDVVAVTSLVEKPARGDAPSNLAIIGRYVLAPQVFEVLERTAPGRGG +EIQLTDALQTLAAGEGEGFGVHAVVFRGRRYDTGDKLGYLQAVVELGVRHPELGGDLREW +LKGFAAGL +>PROKKA_00835 +MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV +LMITGRNKRALEDHFDRHPALEAALEHKGDATRLAQIHESDLVGDIHYVRQGEALGLGHA +VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA +AVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL +TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAWLREF +TAGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000783.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000783.fa new file mode 100644 index 0000000000000000000000000000000000000000..e91b42507628f9a597ce7ba3fa03d424b50fef80 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000783.fa @@ -0,0 +1,29 @@ +>PROKKA_00910 +MRTSEPRDPRRSRGSVASGAGSSPGTTAAPASGASRWWAWLGLTVVAAVVVAAVLRALTG +PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLERGLE +DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEPAAA +GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTVD +APSGDTP +>PROKKA_00629 +MRTSEPRDPRRSRGSVASGAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRALTG +PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLERGLE +DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLRNGEPLDEPYLGRPVTADEPAAA +GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTMD +APSGDTP +>PROKKA_02032 +MSHPEPRDPRRSRGSAVSRSVAPGSGRGTTPARGSGGTAWWAWIGLTVAAAVGAAAVLRA +LTGPVYLIPSGSMEPTLHPGDRVRVDASAAGGEGVRRGDVVVFDGAGSLAPYRSVGSLER +GLEDVARSWGLGASGDAFVKRVLALPGDRLECCAPDGRLLRDGAPVDEPYLGRPVTAQDP +AADGSWTFEVPEGRMVVLGDNRSASRDSRALLGGAGGGLIPLKRVEGRAAEVVWPLDRRG +PVDASAPEAAPGAAP +>PROKKA_01930 +MRAQEPRDRNRSRGSRASGEAGRPWWALVLLTLAGAVVAAALLRAFTGPVYLVPSGSMEP +TLLPGDRVHVDTAAADGAGLEHGDVVVFDGAGSLAPYRSRTALDRGLEDVAAFWGVGAAQ +DVYVKRVLALPGDTLSCCTADGRLERNGAPLDESYLGRTVDAAAPASRSTWAFEVPEGRM +VVLGDNRDVSRDSRALLGAPGGGLIPVEKVIGRVDSVAWPLDRRGDVPAGAQDGSRG +>PROKKA_00858 +MRTSEPRDPRRSRGSVASGAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRALTG +PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLQRGDVVVFDGAGSLAPYRSAGSLERGLE +DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEPAAA +GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTVD +APSGDTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000848.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000848.fa new file mode 100644 index 0000000000000000000000000000000000000000..3e4d8b39008fb6651db9e760a1be0ef96dba28cb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000848.fa @@ -0,0 +1,96 @@ +>PROKKA_00999 +MAANNEDTTRADERVEETAEQAVTQTAADTADGAEPERTAASDDAADPAEEPSAPTLQVD +PTDPFAVPANLIEVLRTETTSRQRSEDEDAGESEDRAEGAVVSRRRRRRRRGEVDMELDG +GEAGDPEHTVTRVRAPRQAVGTASDTVQSVKGSTRLEAKRQRRRDSRSGGRRRTVITEAE +FLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM +EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARL +TSQVSLPGRYLVYVPGGSMTGISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQ +ELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQGEAT +WDNIEAYVTYVAPHLLGRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI +DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVL +EANRDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGI +LIQDTPVERGRSGGEQRGEAEGRRRRRRRGDGEGEHAHAAAATTTGAEHADSEDERQRRE +RAEAARVALHSIAKASGKVAEDEAPAQESAPAEQAADAAEDSAAEAVEAASAGPAEAGQP +AGTDEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEE +EAAEPAAAAAPEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAEQDDRPRRSRRRRGGRG +RSRRGGEAASTEADADAEDHGAERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPVP +AEDAPAPRRRRSRRASSDGVVRPAAGADASAERTADRTDAAPVEATEPSPEESTDATEVH +EQPAAPAAVEEAVMVEPAATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRR +AVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQGAAPVMLGVGVKAADLARRGR +>PROKKA_00713 +MAANNEDTTRADERVEETAEQAVTQTAADTADGAEPERTAASDDAADPAEEPSAPTLQVD +PTDPFAVPANLIEVLRTETTSRQRSEDEDAGESEDRAEGAVVSRRRRRRRRGEVDMELDG +GEAGDPEHTVTRVRAPRQAVGTASDTVQSVKGSTRLEAKRQRRRDSRSGGRRRTVITEAE +FLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM +EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARL +TSQVSLPGRYLVYVPGGSMTGISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQ +ELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQGEAT +WDNIEAYVTYVAPHLLGRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI +DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVL +EANRDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGI +LIQDTPVERGRSGGEQRGEAEGRRRRRRRGDGEGEHAHAAAATTTGAEHADSEDERQRRE +RAEAARVALHSIAKASGKVAEDEAPAQESAPAEQAADAAEDSAAEAVEAASAGPAEAGQP +AGTDEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEE +EAAEPAAAAAPEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAEQDDRPRRSRRRRGGRG +RSRRGGEAASTEADADAEDHGAERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPVP +AEDAPAPRRRRSRRASSDGVVRPAAGADASAERTADRTDAAPVEATEPSPEESTDATEVH +EQPAAPAAVEEAVMVEPAATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRR +AVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQGAAPVMLGVGVKAADLARRGR +>PROKKA_01891 +MAANEDTTGAEERAEQTEQTTAETSAAVAGQAAAESPVEDGGTVTQAQADAAEGADAPER +TAEAADIEDEAETDTAAEPEPDEAPGAPALQFDPTDPFAVPANVMEILRTEKSERRPARD +ERPARGAEDEEEAPGRSRRRRRPSRDRDQAETEAGAEDEAVETAEGEQDAETAERGEGAV +VSRRRRRRRRGDVDMELDGGEDGDPENTVTRVRAPRQALSTGSDAVQGVKGSTRLEAKRQ +RRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQREHRIQIAVLEDGVLAEHFVSNTTQ +DSLIGNVYVGKVQNVLPSMEAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPKKIENALKSG +DTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMTGISRKLPDVERSRLKKILKDH +LPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASSTKVLAPELLYAEPDLTIKT +VRDVFNEDFSAVLVQGEATWDNIEAYVTYVAPHLLDRLHHWVPQDHDGEDLYATHRVDEQ +LHKALERKVYLPSGGSLVIDRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEVVRQ +LRLRDIGGIIVIDFIDMVLEANQDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMG +TGLVEVFSETCEHCAGRGILIHDTPVERGRSGGEPRGEGEGRRRRRRKGAGEGEQAQPAE +STTTAGGEEVDAEDERQRRERAEAARAALHSIAKASGKVSEDEDPAEQAAPAEQAADAAE +DQAAEAVEAARQDAAEETGEAGAQDGEGAEDEDEAPRRRRRRGRRRGRGRSEEAAEAAEA +ASEDGSRDADAAPAGQAPAADEEEAPAADPVAQAEAAVTAVAEAEADAESGGEEREAEPA +GDEEGARPRRARRRRGGRGRSRRGADREASTADADDEAAQPAQEPAQADAGAAGDRARAS +RAGRVGAARAARVRPGRGRGGRRAASRPAPPPFAPRFERRCRAPGRGPGRRPGVVRPGDP +VPRGGGRRRGDRAHRGAVHGRHRGARAPGRPRPGGGGRDGRAGGGRPRPGRAGRARPAAR +PELRARRPPSPGAVGPVARCPRTACACRSRTPPGRHGADASRRPPPSPRPPPSRAPRRP +>PROKKA_01819 +MAADESTTQDTHETAEGSTTPVEATEEETAAEVAESPAGEAAEATAAPDVRFDPTNPFAV +PEGLLPLIEAETVERRRRRPAADPVPEGAADDAHADDEDDEDRPAVSRRRRRRRRGTVDM +ELAGGEDGDPEDTVTRVRAPRRALSTGPEAVQGVKGSTRLEAKRQRRRESRSGGRRRTVI +TEAEFLARRESVDRKMLVRQREHRIQIAVLEDGVLAEHFVSNTTQDSMIGNVYLGKVQNV +LPSMEAAFVDIGRGRNAVLYAGEVDWDAAQLDGKAKKIENALKSGDTVLVQVTKDPVGHK +GARLTSQISLPGRYLVYVPGGTMTGISRKLPDVERARLKKILKDHLPQDAGVIVRTAAEG +TSEQELQNDINRLRVQWEGIQEKASSTKTLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQ +GEATWDSIEAYVTYVAPHLLDRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGG +SLVIDRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEVVRQLRLRDIGGIIVIDFI +DMVLESNQDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMGTGLVEVFSEVCEHCG +GRGILIQDTPVERNRWGHEHRAEPEARRRNKRRRGTESGEGGPAEPTAAELTEEERLRAE +RAAAARTALMSIAKASGKAADEEPSEEAAPRAEDAPEEAADEVRPSPAGDAEEQGESESG +GRRRKRRGRRRGRGRGGDDAARSAEEQDAPAEHPAEAAGEPAPAEAGAPDPAETATEDAD +ADSASDAPAAQAEADEDGRSGGRRRSRRRGGRRAESPQGSGAPASAPEASVEAEQDPEEP +AGAAEAEEALAAEEAPASPEPAAVVTFDGEPVAVPRRRRSRRATSDGVSAPRPSGMDALE +AAVDRRAEDAAAAAQRSPATPAATPTAAPEPAPAPVAGEGPAAAAPRRRSRRAVSADGAT +VQVQEGAAAGGGRFTAQAAQAAPAGETAAPVMLGVGVKAADIVRGE +>PROKKA_00942 +MAANNEDTTRADERVEETAEQAVTQTAADTAAGAVQPERTPASDDAADAPEEPSAPTLQV +DPTDPFAVPANLIEVLRTETTSRQRSEDEDDPDTSGRSRRRRRPSREDDRAEEGAADASA +DAEDREDASESEDRAEGAVVSRRRRRRRRGEVDMELDGGEAGDPEHTVTRVRAPRQAVST +ASDTVQSVKGSTRLEAKRQRRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQRDQRIQ +IAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSMEAAFVDIGRGRNAVLYAGEVNW +DAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMTGI +SRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASG +TKVLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQGEATWDNIEAYVTYVAPHLLDRLHHW +VPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVIDRTEAMTVVDVNTGKFTGSGGN +LEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVLEANRDLVLRRLVECLGRDRTKH +QVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGIIIKDTPVERGRSGGEQRGEAEG +RRRRRRRGNGEGEHAHAAAATTTGAEHADSEDERQRRERAEAARVALHSIAKASGKVAED +ETPAQEPAPAEQAADAAEDSVAEAVEAASTGPAEAGQPAAADEEETPRRRRRRGRRRSRG +RAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEEEAAEPAAAAAPEHQDPVVQAEE +AVAAVAEAEADAEAESPEDAAEQGDRPRRSRRRRGGRGRSRRGGEAASTEADADAEDHGA +ERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPVPAEDAPAPRRRRSRRASSDGVVR +PAAGADASAERTADRTDAAPVEATEPSPEESTDATEVHEQPAAPAAVEEAVMVEPAATEP +TAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRRAVSSDGVHVQVQAAPGGAQGGR +FTAAVAEASTPAEPQGAAPVMLGVGVKAADLARRGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000859.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000859.fa new file mode 100644 index 0000000000000000000000000000000000000000..c637182f0ed8e85bca73d82942f70ec7e52c8599 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000859.fa @@ -0,0 +1,16 @@ +>PROKKA_01017 +MYPTPMTFDVARAGRALAQVSARTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALLK +YGVGLVPEDEFGGAGVRRIFSAEKSRRIKAMENEGGPAYEDDI +>PROKKA_00731 +MYPTPITFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALLK +YGVGLVPEDEFGGTGVRRIFTAEKSRRIEAMENEGGPAYEDDI +>PROKKA_01870 +MYPTPMTFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALRK +YGVGLVPEDEFGGTGVRRIFTAEKSRRLEAMENEGGPAYEDDI +>PROKKA_00705 +MESQHISNGDMTRAARILVKVSAQYIAREANVTKEELRDFEKGRHDLSEKKQERVRAALE +ELGAEFLPDGPNGGYGIRLKFGRSRIYSLERCEGEGGPRLTTESDRRTQAHVPFSEPDSN +LPFHLEDRTTASLRILVPLRLGRLWPSHLASVPGMEARAR +>PROKKA_00961 +MYPTPMTFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALRK +YGVGLVPEDEFGGAGVRRIFTAEKSRRLEVLENEGGPAYEDDI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000865.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000865.fa new file mode 100644 index 0000000000000000000000000000000000000000..0988a3e3bf10c2104abed2f9a5b84ac872e88797 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000865.fa @@ -0,0 +1,15 @@ +>PROKKA_01023 +MSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRGHAAALTAG +AVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR +>PROKKA_00738 +MSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRGHAAALTAG +AVEDIETNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR +>PROKKA_01865 +MTARDAAGGPAVTRNDAESRYELHDGGTLLAVLDYRDNGTAVALTRAFTIPVHRGHGHAA +TLTAGAVEDIEARGGAAGGRQIVPLCWYVAQWLEEHPEKAHLVAPR +>PROKKA_01758 +MDASDSPTTFTRNDAASRYELHDASGELLAALDYRDNGTAVSLTRAFTVPVHRRQGHAAT +LTAGAVADIEARGGAAGGTTVVPMCWYVARWFEEHPEKAGLLDAR +>PROKKA_00967 +MTTGGCPGMSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRG +HAAALTAGAVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000894.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000894.fa new file mode 100644 index 0000000000000000000000000000000000000000..c217e64d1f4a4dbc154a41e2d30a3a7f0bbd78d2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000894.fa @@ -0,0 +1,15 @@ +>PROKKA_01078 +MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE +EISQLLYHVQTMMIARGISLEDVYRHL +>PROKKA_00797 +MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE +EISQLLYHVQTMMIARGISLEDVYRHL +>PROKKA_01820 +MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE +EISQLLYHVQTMMIARGIALEDVYRHL +>PROKKA_01707 +MKTFEELFAELTRKVAERPEGSGTVAQIDAGVHAIGKKIVEEAAEVWMAAEYESHDAAAE +EISQLLYHVQTMMIAKGIGLKDVYRHL +>PROKKA_01027 +MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE +EISQLLYHVQTMMIARGISLEDVYRHL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000911.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000911.fa new file mode 100644 index 0000000000000000000000000000000000000000..b0aa9c8f8fd67fe133e10fedca5c9dce36785c93 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000911.fa @@ -0,0 +1,55 @@ +>PROKKA_01096 +MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGS +VLATSLGGWPGGIGIGFAADMLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILI +GGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL +LVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST +SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVR +AVLSWQMVSGIGGILVGLGLSTRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLA +DLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVSAGLDAGRGVTAALVLGASLV +SLWVLLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPSPSGRGSSTDHERTESWA +SQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAA +QGLMDPSRYIEAVLNP +>PROKKA_00815 +MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGS +VLATSLGGWPGGIGIGFAADMLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILI +GGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL +LVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST +SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVR +AVLSWQMVSGIGGILVGLGLSTRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLA +DLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVSAGLDAGRGVTAALVLGASLV +SLWALLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPSPSGRGSSTDHERTESWA +SQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAA +QGLMDPSRYIEAVLNP +>PROKKA_01799 +MSPEALGQLLPLFVAVPLITAGLLTLAGDRPRVHRLVVALVLCLTAGAGALIVARSLDGD +VLATSVGGWPGGIGIGFAADMLTGLMLLLTSLLTLVGVNLAHGTRVVNSLYFGPLMLVLM +AGVNGALLTADLFNLFVFIEVMLLPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL +VVAVGFLYALTGTVNLAVMAGAAARDERVAIAGGLVLFALSIKASVVPLHGWLARAYPST +SPAVTAIFAALHTKVAVYALYRVFSVLFDNDARFLPLLLALAGLTLAVGALASVGVHGVR +LVLSWQMVSGIGGILVGLGLSTQLGLSAGLFYLVHHMVAMGCLLAATAAVEVRYGTGRLA +DLRGLARREPLIAVVFFVGLLSIVGIPPFSGFVGKLMLVTAGVEAGRLVTVAVVLVGSLV +SLWALLRVWDAWFWGEPGTPHGLRERLATAALPVVGRGAERTGPSGRGSSTDHERTESWT +STQTIDPPTGVLPVTFAADEDVTRSRIPVRLAMPGVVLAAATLVLGLAGQALWTLTDVAA +QGLLDPARYIEAVLAP +>PROKKA_01689 +MSDHAVGLLLPLFVAVPLLSAGLLVVAGSRPRLHRAVLAAVLAGGTVGGGLLMARAADGS +VAAAGVGGWPDGIAIAFAADMLTGLMVALTAGLTLVGAWFAYGSRVANSAHFAPFMLVLM +AGVHGALLTADLFNLFVFIEVMLLPSYGLYVLSANRREPLRRVDGARMYVTLNLLTSTIL +VTGVGFVYALTGSVNMAVLAGAARGDVRVALAAGLVLFALSIKASMLPMHGWLARAYPST +SPAVTAIFAALHTKVAVYAMYRIYMVVYDGDPRLLGLILTLCLATLMVGAVASVGEHGAR +AVLSWQMVSGIGGIMVGLGLATQAGLSAGLFYLVHHMVVMACLLTATGAIEVRYGSGRLA +DLQGLAVREPLIAAAFFVGMLSLVGIPPFSGFAGKLALVLAGVAAGRTVTVVLVLVASLI +SLWALLRIWDAWFWGRPRAPHGHRERLDTAALPLVHGDGVMPAAGAPVHPAGRGSSTDSE +RAEAWASTETLDTPTGVLPVVVDPDEDHTASRIPLRLAGPAALMAAATLALGLGAEGLWS +VTDQAARGLADPTAYIEAVLGR +>PROKKA_01045 +MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGS +VLATSLGGWPGGIGIGFAADMLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILI +GGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL +LVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST +SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVR +AVLSWQMVSGIGGILVGLGLSTRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLA +DLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVSAGLDAGRGVTAALVLGASLV +SLWALLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPSPSGRGSSTDHERTESWA +SQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAA +QGLMDPSRYIEAVLNP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000928.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000928.fa new file mode 100644 index 0000000000000000000000000000000000000000..ed65360a55bbef223c34d4c3cbb431f0d1b93186 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000928.fa @@ -0,0 +1,60 @@ +>PROKKA_01119 +MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTR +TMVFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQ +VMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGK +CSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA +ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEP +EMVAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKAD +LMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEITEPLLRIECYDISHSQGTNV +VGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE +ADDQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEF +PVVLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHF +GSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES +>PROKKA_00838 +MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTRAM +VFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVM +RGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGKCS +APCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIAAL +RRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEPEM +VAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKADLM +ETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEVTEPLLRIECYDISHSQGTNVVG +SMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVEGD +DQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLAELGLDDLPVVGLAKRLEEVWLPGDEFPV +VLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHFGS +VAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES +>PROKKA_01774 +MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLGSYFQDPARLTTKTRTM +VFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVM +RGDRRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGKCS +APCVGRISPAEHRELAQDFCDFMAGDAQRFIRELERAMQGAVEELRYEDAARLRDDIAAL +RRVFERNAVVLPESTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVSEPEM +VTHLLQQVYGDLAGEDRIPHEILVPAEPDDAAQLVEWLSGLRGARVNVRVPRRGTKADLM +ETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEIAEPLLRIECYDISHSQGTNVVG +SMVVMEDGLPKKKDYRRFNVTGEAARDDTASMKDVLSRRFARLAEERAEGAPLSGQLEGE +EEGRDRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEFPV +VLPRTSEALYLLQRIRDESHRFAIAGHRGRRAKAMTASALDGISGLGPAKRTALLNHFGS +VAQIRAAGVERLTEVAGIGPTLAQTVHAALAPAEPTDTVEP +>PROKKA_01667 +MADPRTYRPAPGEISTSPGVYRFRDPDGRVIYVGKAKNLRARLSSYFQDPARLATKTRTM +VFTASAVEWTVVASELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNERFPRVQVM +RGDKRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRAQAQDRPCLLGYIGKCS +APCVGRISPDEHRALAQDFCDFMAGDADRFVRELEKAMAGAVEELRFEDAARLRDDIAAL +RRVFERNAVVLAESTEADVFALHSDELETAVQVFHVRQGRIRGQRGWIMERVEDVGEDEA +VAELLTQVYGDVPDTERIPHEVLVPVLPAGAEQVTEWLSGLRGARVQVRVPQRGPKADLM +GTVRENAEMALKLHKTRRSGDLTTRSAALRELQDALEIDEPLLRIECYDISHSQGTNVVG +SMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARMAEDRREGGVLTGQIDAE +EAEGERRRFAYPPSLVVVDGGPPQVAAAAEVLAELGLDDLPVVGLAKRLEEVWLPGDEFP +VVLPRTSEGLFLLQRIRDESHRFAIAGHRSRRTKAMTASALDDVPGLGPTRRRALLTHFG +SVERMRQAGPAGLTEVAGIGPALAEAVHAALTASDGGDTVAP +>PROKKA_01069 +MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTR +TMVFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQ +VMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGK +CSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA +ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEP +EMVAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKAD +LMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEITEPLLRIECYDISHSQGTNV +VGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE +GDDQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEF +PVVLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHF +GSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001022.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001022.fa new file mode 100644 index 0000000000000000000000000000000000000000..2bfc9dcbac56836cf7d0ce96fb400919503e66a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001022.fa @@ -0,0 +1,20 @@ +>PROKKA_01222 +MNTRAQPDAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY +RDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALTWAAMAVYGVMGA +SHVSKGRPFRYPFNLRILR +>PROKKA_00941 +MNTRAQPDAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY +RDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALTWAAMAVYGVMGA +SHVSKGRPFRYPFNLRILR +>PROKKA_01666 +MNPSAQPDAGRPGHEPPAWLASAGGRATPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY +RDRGPFTSQESKEALNFSGPPTLITTLFFFLALLPVIGAIFAILGALSWAVMAVYGVMGA +SNVSKGRPFRYPFNLRILR +>PROKKA_01563 +MATTPSTTPAGETATPRRAAGGSAAHEAPAWLRDAAGGRAPLTAKQDRDRAALSHLSLAC +GLPGPLVMWLLYRDRGPFTAQESREALNFSLAPTLLIVLLFLLGGVPLLGGLLAILGALL +WIALALYGVMGASQVAKGRPFRYPFSPRLLR +>PROKKA_01180 +MNTRAQPDAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY +RDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALTWAAMAAYGVMGA +SHVSKGRPFRYPFNLRILR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001047.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001047.fa new file mode 100644 index 0000000000000000000000000000000000000000..cb795493a95ac5ad6ada4d2586eb9fa5395e3996 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001047.fa @@ -0,0 +1,40 @@ +>PROKKA_01249 +MTDREPDITEQETPGAAPAAAPAAPEDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLPDL +LGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVLGQ +NDFTRSDAIVSVGGGAVSDLAGFVAATWLRGIRVVHMPTTLLGMVDAAVGGKTGINTAEG +KNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQNP +HSPRLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVSVG +LVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQLRF +VLLDGLAQPTTVDIPDASLLFAAYQEIAE +>PROKKA_00968 +MTDREPDITEQETPGAAPAAAPAAPEDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLPDM +LGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVLGQ +NDFTRSDAIVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTAEG +KNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQNP +HSARLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVSVG +LVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQLRF +VLLDGLAQPTTVDIPDASLLFAAYQEIAE +>PROKKA_01639 +MTDRHPDPAEPEIPGEPPAAEPAAAGQEDVTVIPVSGGQEAAAHGGYDVVVGRGLLARLP +EMLGPGVQRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVL +GQNDFTRSDAVVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTS +EGKNLVGAFHPPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEQDPAQSQ +NPHSARLRELIERSIRVKADIVSRDLRESGEREALNYGHTMGHAIELAERYQWRHGAAVS +VGLVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQL +RFVLLDGLAQPSTVDIPDPSLLFAAYQEIAE +>PROKKA_01536 +MTEHQPDQSDPIAEHSAAAPEQDVTVIPVAGGPENRAGGGYDVVVGRGLLGRLPAVLGPQ +VRRVLVIHPRALRATGDVVKNDLEAAGLVSLTAEIPDAEEGKHLQVAGFCWQVLGQNDFT +RSDAIVSVGGGAVSDLAGFVAATWLRGIRVVHMPTTLLGMVDAAVGGKTGINTAEGKNLV +GAFHPPAGVLADLDTLLTLPSNELVSGLAEVVKCGFIADPRILELIEEAPEQAQNPHSAV +LRELIERAVRVKAEVVSGDLREAGPREALNYGHTLGHAIEHAERYQWRHGAAVSVGLVFA +AELARSLGRLDDATADRHWSVLQSLGLPVSYRGDRWQTLLEGIKRDKKNRGDQLRFVLLD +GLARPTTVDIPDASLLFAAYQEIAE +>PROKKA_01207 +MTDREPDITEQETPGAAPAAAPAAPEDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLPDM +LGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVLGQ +NDFTRSDAIVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTAEG +KNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQNP +HSARLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVSVG +LVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQLRF +VLLDGLAQPTTVDIPDASLLFAAYQEIAE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001094.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001094.fa new file mode 100644 index 0000000000000000000000000000000000000000..66d0dbbfcc687e6c77d072fc5a68d2e720beb001 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001094.fa @@ -0,0 +1,40 @@ +>PROKKA_01307 +MTGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDGLGRSLLKR +FGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPDRDVVIN +QLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGGRFVAGRTL +IARAQAAERALKDARVPTLVYFYVNELDRAGHRDGVGSDRWLHALEEIDAAVRRLVDRVP +AGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADAALLEGVAHTAGEPRLVQLHFRSDA +GPDVRARVRRAWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVAVHGDLALY +DGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR +>PROKKA_01030 +MTGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDGLGRSLLKR +FGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPDRDVVIN +QLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGGRFVAGRTL +IARAQAAERVMKDARVPTLVYFYVNELDKAGHRDGVGSERWLHALEEIDAAVRRLVDRVP +AGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADPALLEGIAHTAGEPRLVQLHFRSDA +GPDVRARVRRTWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVAVHGDLALY +DGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR +>PROKKA_01585 +MSGPAVPVGVVPPERALRSVLTSAAAALGVPGCENALGVPASRRVVVALVDGLGRSVLKR +FGGHAPTLRAAMADGGRVLQAAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPERDAVVN +QLGGWDEATDPVAWQPRPTVFERAGAAGVDAVTVSLPAFEHSGLTRAGLRGGRFVAGRGL +LARAQAAERVLKDAREPTLVYFYVNELDKAGHRDGVGSDRWLHALEEIDGALRRLVDRVP +AGTVVLATGDHGMVDVPPTRRVDYAAADESGALADPALLEGIAHTAGEPRLVQLHFRPDA +DADVRARVRRAWEDRFGAHAWVLTRDEAVAAGWFGTVVEERVRGRIGELLVAVHGDLALY +DGRRVAPHAFEMVGQHGSPTRAEREVPLLTWRR +>PROKKA_01481 +MTGPDAAAPAGPGLPPGPVPPERALRSVLTSAAAALGVPGCANALGVPVTRRVVVALVDG +LGRGVLKRFSGHAPTLRAAMADGGRVLTAATPTTTAASLTSLGTGLDVGEHGVAGYDVLD +PDRGVVVNMLGGWDEATDPLAWQPHPTVFERAVEAGVDAVTVSLPEFEHSALTRAGLRGG +RFVGGRGLLARAGHAERVLADACVPTLVYFYVNELDKAGHRDGVGSRSWLHALEEVDAAL +RRLVSRVPAGTVVLATGDHGMVDVAESRRVDYAALGDDGAPVRPGLLAGVAHTAGEPRLV +QLHFAPTATPAEREGTRRAWEDAYGDQAWILTRDEAVAAGWFGERVADRVLPRIGDLLVA +CHGELALYDGRRVSPRAFAMVGQHGSPTRAEREVPLLTWRR +>PROKKA_01265 +MTGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDGLGRSLLKR +FGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPDRDVVIN +QLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGGRFVAGRTL +IARAQAAERVMKDARVPTLVYFYVNELDKAGHRDGVGSERWLHALEEIDAAVRRLVDRVP +AGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADPALLEGIAHTAGEPRLVQLHFRSDA +GPDVRARVRRTWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVAVHGDLALY +DGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001096.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001096.fa new file mode 100644 index 0000000000000000000000000000000000000000..90cd840ee6be239f353aad8331e013e7b629425f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001096.fa @@ -0,0 +1,85 @@ +>PROKKA_01309 +MGETEADRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKS +ELSAKDLDRFTHVDHRDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG +SILMEHLAAAARENGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA +RWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGTVHAVN +RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAG +AEGLEAQRRLVSLARAHGMRVIGPASTGLVRTDPAIRLNASPSPGLAQRGPVSLFSQSGA +VGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFS +RIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD +ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPADTL +VSAVRDAVCHEQADAVVVLARLGLHQADDEPERLAHALADATREARIPVLGCLTDVVSPR +YRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMAVLGALADYVHWRHQEVGEPLEPTG +LHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSVRFETAEEAVAAAERL +GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAG +QACMLTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGT +GGVPPVDLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAPERVTVLQAEVHVANAARRTD +SARRALRGR +>PROKKA_01032 +MGETEAVRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKS +ELSAKDLDRFTHVDHRDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG +SILMEHLAVAARENGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA +RWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGAVHAVN +RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAG +AEGLEAQRRLVSLARAHGMRVIGPASAGLVRTDPAIRLNASPSPGLAQRGPVGLFSQSGA +VGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFS +RIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD +ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPAETL +VSAVRDAVRHEQADAVVVLARLGLHQADDEPERLAHALADATRDARIPVLGCLTDVVSPR +YRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMTVLGALADYVHWRRQEVGEPLEPTG +LHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSARFETADEAVAAAERL +GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAG +QACMLTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGT +GGVPSVNLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAPEGVTVLQAEVHVANAARRTD +SARRALRGR +>PROKKA_01583 +MGDTEPVRDYPSHWEADVVLRDGATARLRPITPEDADELQRMHAGQSENSIYLRYFTYKS +ELSAKDLDRFTHVDHKDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG +SILMEHLAVAAREHGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA +RWRAVVESREHRAEARSVAELVAPESVAVVGASRDPQAVGSMVLRHILEGGFAGPVHAVN +RAAGEVQGLTAHASLAEIGEEVELVVVAVPVDQVEALVPEAAAAGAAGLLVLTSGYADAG +AEGLEAQRRLVSLARAHGMRVIGPASAGLVRTDPAVRLNASPSPGLAQRGPVGLFSQSGA +VGAMVSAGAKRRGVGVSTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFT +RITRRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGAVDSMLDQTGVLEVHTHEAMLD +LLMAVASQPLPTGRRVVLVADSLAVDRLARDAAAEAGLDVVATVGLAGSEQGVAPPAETL +VASVREAVAHEQADAVVVVGRLGLHQEDDDPETVARALAEATAGARMPVLVCLTDVVSPR +YAGATLGASGPVADDAEPGSLQPGVPFYPSPQQAMSVLGALADYVRWRGEEAGEPLEPAD +VRLHAAEDLVEAAAARAEGTELVRLSAAETEELLGHYGIAVLPSARFETADEAVAAAERL +GFPVAVKAVDPHLRHRLDLGGVRLNVVDAASLRRNVEQMRRVLAPFGVTELEVQAMAPAG +QACMVTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAAKLEGR +GGVPAVDLAALEDLVGRVSVLKDDLPQVARLRFSPVLASPEGVTVLQAEVDVANAAGRTD +SARRALRGS +>PROKKA_01479 +MAEPDTETAYPSQWEADVVLRDGATARLRPIREDDVDGLRALHAGQSESSIYLRYFTFKS +ELSAKELERFTHVDHRDRVALVIERGGRILGVGRYDRYGDSDAAEVAFNISDAAQGQGLG +SILMEHLAVAAREQGIRRFTAEVLPENRKMLSVFQDSGFEVARHFEDGVVAVEFPIDPTA +RWRAVVESREHRAEARSVAELVEPESVAVVGASRDPHAVGSIVLRHILEAGFTGRVHAVN +RAAEDVQGLTAHASLKDIGEPVDLVVVAVPVAEVDAVVAEAAEAGAQGLLVLTSGYADAG +EDGLRAQRRLVARARARGMRVIGPASAGLVRTAPDVRLNASPSPGLASRGPVGVFSQSGA +VGAMITAGMKRRGVGMSTSLSAGNRADVSGNDAMQFFEDDPHTAAVGVYLESFGNPRKFS +RIARRLSRTKPVVVVRSDVTGRALPPGHETRTTQAPEGAVDSMLEQTGVLEAATHEDMLD +LLMAVATQPLPTGRRVTLVADSLALDRLGRDAAAVAGLEVVATHGLGGSEQGIAPTADDV +VASVEAALAAGDTDAVVVVTRLGLHQDEDAAHEVAQALARVAEGATVPVLGCLTDVVSAR +YGGARVGGAAAPAADAEPGALQPGLPLYPSPRKAMTVLGRLCDYVAWRREDAGEPIELTD +VDVRAAEALVDRALERALGTELIRLTGAETEELLRIYGIGVLRSRRFTTPDEAVAAAEEL +GFPVAVKAVDPYLRHRLDLGGVRLNLEDAESLRQNVRQMRAVLAPFGVTELEVQSMAPSG +QPCMVTALEDPLLGPVVSFGMAGDATDLLGDWVHRVPPLTDQDVRRMVRSPRAAVKLDGV +GGVPAVDLDALEDLLARVSCLKDDLPAVARLRFAPVLAAPTGTTVLSAEVDVANAAGRTD +SARRALRAS +>PROKKA_01267 +MGETEAVRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKS +ELSAKDLDRFTHVDHRDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG +SILMEHLAVAARENGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA +RWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGAVHAVN +RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAG +AEGLEAQRRLVSLARAHGMRVIGPASAGLVRTDPAIRLNASPSPGLAQRGPVGLFSQSGA +VGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFS +RIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD +ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPAETL +VSAVRDAVRHEQADAVVVLARLGLHQADDEPERLAHALADATRDARIPVLGCLTDVVSPR +YRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMTVLGALADYVHWRRQEVGEPLEPTG +LHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSARFETADEAVAAAERL +GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAG +QACMLTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGT +GGVPSVNLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAPEGVTVLQAEVHVANAARRTD +SARRALRGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001107.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001107.fa new file mode 100644 index 0000000000000000000000000000000000000000..eaba508297817e7a73a4e08cdabd3cffd51cd63f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001107.fa @@ -0,0 +1,33 @@ +>PROKKA_01322 +MEAPTSLDVPVLPARGPEDLLAYVGHALGRLPEGSLVLLTLRDGRLRAVVRVDLPPEEVD +VGAWACAVAEVCRRDAAADATLCLALPDGARATLARPGWAAALDDALASAGRPLTAAWTC +ARGRARPWWGSGVAEEGPLDPRAAPLSLHLMTRGSVWDRAAVPDPVPRRGPAAARADDAR +WRPPEQDAPAARRAWLAQWESVLTGAARDRGAPAPAVLGSPLTRPAWRDGLLLHAAAPSG +AATGDPGDEERILTAASGRAPAWDRLDALRAGLRALVPVATPAVAAQALALAGWVGWARG +HGSDADAHLTAAAALSPDDPFVSVLRRIVAAGCVAGWATDPATAWRPDGGRP +>PROKKA_01043 +MEAPTSLDAPVLPARGPEDLLAYVGHALGRLPEDSLVLLTLHDGRLRAVVRVDLPPEEVD +VDAWACAVAEVCRRDAAADATLCLALPDGARATLTRPGWAAALDDALASAGRPLAAAWTC +AHGRARPWWGSSIAEEGTLDPRAAPLSLHLMTRGSVWDRAAVSDPVPRRGPAAARPDDAR +WRPPEQDAPPARRAWLAQWEPVLTGTARGRGAPAPAVLGSPLTRPAWRDGLLLHAAAPSG +AATGDPGDEERILTAASRRAPAWDRLDALRAGLRALVPVATPAVAAQALALAGWVGWARG +HGSDADAHLTAAAALSPGDPFVSVLRRIVAAGCVAGWATDPATAWRPDGGRP +>PROKKA_01569 +MWLSQWESVLAGERGAAGPVTAEGTAPVSGTEEHPSADAAVLGAPLTLPSWRDALVLHAA +VRPGDPPPEPAERERFLIAGSEQAPPWERLDRLRAGLRRLVPAAPPPAAAQALALAGWVG +WARGQGSDAAAHLAAAAELAPDDPFVTLMRRVVDTGCVAGWAAHPDTAWRPGA +>PROKKA_01465 +MRPRTLEGMDHPPAVPSAVPAGVTPPHLPVLRARGVDDLLGYAFHVLGTEPRESILLVTL +ARARLRAVVRVDRPGRETPPAARHWAEAVAAVARRDAAADAVVCVSLTGRAGGLEPPGWW +PPLVRALRDRGIPAREGWGVVAGHAARWPVEPGAGPGPLEEVDPRHSDLSLHLIGAGSVW +GLRAGHRSVPTPAALDPAAPDRPHWTAARARPEAPGPWLAAWERVLDGGGLPERPAGRAR +LGAGLEHPARRDALLIAAAGAAADELPAAERAALLTGTRDPGPDWRRLDRLWDALRALAA +DAPAPCAAPALALAAWICWARGEGTAAGAHLDVARRLAPRDPLVGVLRRILDAGAVCAWA +ADPRRAWTPWDPQDPASGMRG +>PROKKA_01278 +MEAPTSLDVPVLPARGPEDLLAYVGHALGRLPEGSLVLLTLRDGRLRAVVRVDLPPEEVD +VGAWACAVAEVCRRDAAADATLCLALPDGARATLARPGWAAALDDALASAGRPLTAAWTC +ARGRARPWWGSGVAEEGPLDPRAAPLSLHLMTRGSVWDRAAVPDPVPRRGPAAARADDAR +WRPPEQDAPAARRAWLAQWESVLTGAARDRGAPAPAVLGSPLTRPAWRDGLLLHAAAPSG +AATGEPGDEERILTAATGRAPAWDRLDALRAGLCALVPAATPAVAAQALALAGWVGWARG +HGSDADAHLTAAAALNPGDPFVSVLRRIVAAGCVAGWATDPATAWRPDGGGP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001115.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001115.fa new file mode 100644 index 0000000000000000000000000000000000000000..4be4f7d43ebf8a4f9ea23a6d68d4e2e6e8fd7616 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001115.fa @@ -0,0 +1,35 @@ +>PROKKA_01330 +MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC +PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV +TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN +LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG +CDIITITQYVRPSKLHHPIDRWVKPQEFVQWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA +QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS +>PROKKA_01051 +MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC +PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV +TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN +LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG +CDIITITQYVRPSKLHHPIDRWVKPQEFVHWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA +QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS +>PROKKA_01561 +MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC +PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMDEPQKVAENIREMDLRYATV +TGVARDDQKDGAAWLYAETIRRIHAFNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN +LETVPRIFKRIRPAFTYEKSLKVLSMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG +CDIITVTQYVRPSKLHHPIDRWVKPQEFVEWSRRAEEIGFQGVMAGPLVRSSYRAGKLYA +QAMQRLGRTLPENLEHLAGEKTARQEASAVVAQMS +>PROKKA_01457 +MTTAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNTVKGSGLHTVCEEAGC +PNIFECWEDREATFLIGGDICTRRCDFCDIASGRPLPLDMDEPQKVAENIREMDLRYATV +TGVARDDQKDGAAWLYAETIRRIHELNPSTGVEILPPDFGAVPELVQQVFDARPEVFAHN +LETVPRIFKRIRPAFTYEKSLRVLTMAKEQELVTKSNLILGMGETDEEIDQALVDLHEAG +CDIITITQYVRPSKLHHPIDRWVKPQEFVAWSQRAEEIGFAGVMAGPLVRSSYRAGKLYA +QAMERLGREVPEHLAHLRGERTARQEAAAVVARMS +>PROKKA_01286 +MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC +PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV +TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN +LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG +CDIITITQYVRPSKLHHPIDRWVKPQEFVQWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA +QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001131.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001131.fa new file mode 100644 index 0000000000000000000000000000000000000000..c89d6faf131f924b2e303b2888346c3e9c81bd07 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001131.fa @@ -0,0 +1,30 @@ +>PROKKA_01349 +MTAPATAGPTPTDPRAREIADALAAVHARIADAARDAGREAEPALVVVTKTHPAEDVVRL +AALGVTDVGENRDQEARPKAEAVAAALGADAPRWHFVGQLQTNKAKYVVRYASVVESVDR +PELAEALSRALVLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGARPEDVPAL +ADVIAGLPGLRLGGLMCVAPRGLDPEHAFRRLAALGARLRQTHPEATALSMGMSADLEAA +VRAGATQVRIGSDVLGARDAVG +>PROKKA_01069 +MTAPATAGPTPTDPRTREIADALAAVRARLADAARDAGREAEPALVVVTKTHPAEDVVRL +AALGVTDVGENRDQEARPKAEAVAAALGADAPRWHFVGQLQTNKAKYVVRYASVVESVDR +PELAEALSRALLLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGARPEDVPAL +TDAIAGLPGLRLGGLMCVAPRGLDPEDAFRRLAALGAHLRQTHPEATALSMGMSADLEAA +VRAGATQVRIGSDVLGARDAVG +>PROKKA_01543 +MSTPEQHPTPHDAAAETRTREIAAGLAAVRERIARAAREAGRADEPALVVVTKTHPAEDV +VRLAGLGVAAVGENRDQEARPKAAAVAEALGDAAPRWHFIGQLQTNKAKHAARYASVVES +VDRTELAEALSRALVLRREREPGVEVPDLECLVQVDVDDRADEDRPEGIGPRGGAAPEDV +PALAAAIAALPGLRLGGLMCVAPRGLDPEASFRRLAALGEELRSAHPDASTLSMGMSADL +ESAVRAGATQVRIGSDVLGARPAVG +>PROKKA_01439 +MAEPLQDDPRVAEIAAGLDGVRRRIADAAAAAGRADLPELIVVSKTHPAEDVVALAGLGV +RQVGENRDQEARPKAAAVAEALGGAGVPAPAWHFIGQLQTNKAKHVARYASAVHSVDRLD +LVDALSRAVVLRREREGADAVSALDCLVQVDVDDRADEDRPEGIGPRGGAAPEDVPELAR +AIAAADGLRLRGLMCVAPRAADPAAAFARLAALSARVRAEHPDADALSMGMSGDLEAAVA +AGATHVRVGSDILGARGAVG +>PROKKA_01304 +MTAPATAGPTPTDPRAREIADALAAVRARIADAARDTGRAAEPALVVVTKTHPAEDVVRL +AALGVTDVGENRDQEARPKAEAVAAALGADAPRWHFVGQLQTNKAKYVVRYASVVESVDR +PELAEALSRALLLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGARPEDVPAL +ADVIAGLPGLRLGGLMCVAPRGLDPEDAFRRLAALGAGLRQTHPEATALSMGMSADLEAA +VRAGATQVRIGSDVLGARDAVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001136.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001136.fa new file mode 100644 index 0000000000000000000000000000000000000000..df87517607f838f8b927414dbbcc1bbc61c250b1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001136.fa @@ -0,0 +1,40 @@ +>PROKKA_01354 +MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEGDGGGPVECTMVGTASGMETRLVPE +AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRATHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAARRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL +TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAQEGARR +>PROKKA_01074 +MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEGDGGGPVECTMVGTASGMETRLVPE +AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRAAHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAARRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL +TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAQEGARR +>PROKKA_01538 +MPQTPDPARELRVVLAGGGTAGHISPMLAIARALESDDAGPVRCTMVGTASGMETRLVPE +AGYELDLIERVPMPRRPSMDVVHFPARMRAAVAAAGRILAERRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRAAHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAQRRAARAALGLDPERTTVVVTGGSSGALAVNRTVRDSLDDLLGAGLQVFHLTGRDKAL +TEADGTPLRREGYVQREYLDGMEQAYAAADLLVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALTVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAEEGARR +>PROKKA_01434 +MTTPNDASRPLRVVLAGGGTAGHISPMLAIARALGRQDPSTVCTMVGTDSGMETRLVPQA +GYELDFVERVPMPRRPSMDVVRFPGRFQASVRQAGEILRRRGADVLVGVGGYVSTPMYLA +ASRAGVPVVVHEANARPGLANRVGALRAARVGTALPDTRLPKAQWVGMPMRPEISGLDRA +AARDAARAELGLDPERTTVVVTGGSSGALNVNRTVRESLDDLLGAGLQVFHLTGRGKELT +DEAGQRVTRPGYVQREYLDGMEKAYAAADLIVARSGAGTVCEIAAVGLPAVFVPLPVGNG +EQALNARPVVDAGGALLVRDETFRADWVRRELIPLATDPQRLAAMGEAAARLGVRDADVR +TADLVREAAREGARR +>PROKKA_01309 +MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEDDGGGPVECTMVGTASGMETRLVPE +AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRATHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAAGRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL +TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAQEGARR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001143.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001143.fa new file mode 100644 index 0000000000000000000000000000000000000000..bd8e80de1a2f5bbc79545f255407dc921910d0c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001143.fa @@ -0,0 +1,35 @@ +>PROKKA_01362 +MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH +LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR +AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE +KPTEEEISENRRASSARVRAVEKIRTSRTTA +>PROKKA_01082 +MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH +LRVIGIDRDVHAQAMAAERLGPLADRLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR +AIVRARAEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE +KPTEEEISENRRASSAKVRAVEKIRTSRTTA +>PROKKA_01531 +MDADQLRPEDRHVPVMRDRVVDLLAPAVQAALDAGRAPVAVDGTLGMGGHTEAMLTRFPE +LTVIGIDRDAHAQALAAERLGPLAERLVPFHGTYDLVPEAMAAAGVEKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEHELRRIIRRDGEERFAGPIAR +AIVRARAEAPIETTGRLVEVIRTAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRIAKRHLSAWAASTAPPGFPVVLEEHEPVVRTLTRGTE +KPTEEEILENRRASSAKVRAVEKIRTSRTPA +>PROKKA_01426 +MDPTQPLPRDRHVPVMRDRVVDLLAPAVEAAAAAGRTPVAVDGTLGMGGHTEVLLRRFPT +LRVVGIDRDPNALAMAQERLGPLAERLVPFHGTYDQVPEALAAAGAERMDAALYDLGVSS +YQLDARERGFAYSYDAPLDMRMDTTAPVTAADLVAELDEQSLRRIIRRDGEDRFAGPIAR +AIVRAREEEPILTTGRLVDVIRAVVPVSAGNKGGHPAKRTFQALRIAVNEELDILDAAVP +AVLDALEVGGRLVVMSYHSLEDRIAKRHLQEWAASTAPPGFPVELPEHRPLVKVLTRGTE +KPTEEEIEENRRASSAKVRAVEKIRTSRTTA +>PROKKA_01317 +MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH +LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR +AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE +KPTEEEISENRRASSARVRAVEKIRTSRTTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001149.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001149.fa new file mode 100644 index 0000000000000000000000000000000000000000..cddeaac0be7fb38cd8acdd0cf967f1dea0d4e250 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001149.fa @@ -0,0 +1,40 @@ +>PROKKA_01368 +MPRSAVPHTPVRSRCLRSVLTGGAVPLLLLTGLPAQAHAQEAAVHTVRPGDSLTRISAAR +GVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAAGTYTVQPNDGWWVIARRTGVSAA +QLQRLNGMSASSMLHPGMVLTTQRTAAAPKAPASPAPTTTPATAPASTTPTAAGGTVRYT +VVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDGTLEVEPVSAVQAVGDT +FLGRTYAPHVTASANENLRLLRAVPQPTPEQMQQIVRETAERMGVDPRLALGHAYTESRF +RMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAGVAFIKYVQDRTPTLDE +GIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF +>PROKKA_01088 +MPRSAVSHTPVRSRRLRSVLTGGAVPLLLLTGLPAQAHAQEAAVHTVRPGDTLTRISAAR +GVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAVGTYTVQPNDGWWIIARRTGVSAA +QLQRLNGMSASSMLHPGMVLTTQRTAAAPKTPASTAPATTPASAPASTAPAAAGGTVRYT +VVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDGTLEVEPVSAVQAVGDT +FLGRTYAPHVTASANENLRLLRSVPQPTPEQMQQIIRETAERMGVDPRLALGHAYTESRF +RMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAGIAFIKYVQDRTPTLDQ +GIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF +>PROKKA_01525 +MPRSSVSHTPSRRLRHALAGGAVPLLLLTGLPAQAQAQEAPVHTVRPGDTLTAISAAHGV +PLVDLFRLNGLDHESIIYPGDAIRLTGEAAPAAAAGTYTVQPDDGWWIIARRTGVSAAEL +QRLNGMSASTMLHPGMVLTTAGKAAAPAPTPAPPRCSLAPATRDVVRYAVVSGDSMWGIS +QRFEMSIPRLRELNGLTRSSMLHPGQVLVISDGTLEVEPVSDVQPIGDTFLGRTYPAHVT +ASANENLRLLQSVPQPSPEQMREIVRETAVRMDVDPRLALGHAYTESRFRMASVSPANAI +GAMQVIPITGEFASELVGRELNLLDPYDNAVAGVAYIKYVQDRTPTLDTGIGAYYQGLGG +VLQGGLSAEGRTYVATVRAAMAMF +>PROKKA_01420 +MPPARKVTPLMPQPAAPRASATTARRSLGLVAGGVVPLLMTGALPVAAQAAEAAHAAPRT +HTVRAGENPYRIAEAEGVRLSDLLRLNGLRADSVIYTGQVLALTGAPAPAAAPGTVEVER +GEGWWQVSRRAGVDAAVLQRINGLGARSMLHPGQILLTEAPARPTTPATPVAAAPAPVRQ +AAPTTYTVRNGDSMWSISQRVEVSIPRLRELNGLTWRSVLHTGDVLVIADGTEQAPVIDG +PVGSTFLSTTYAPHVTASANDNLRALQAVPQPSPAEVQALVRQTALELGVDPALALGHAY +TESRFQHASVSPGNAIGAMQVIPITGEFASQLVGRELNVLDVRDNVTAGVVLIKYLQEHT +DTVDQGISAYFTGLGGSDDPVKQQEARNYVARVKAAAAMF +>PROKKA_01323 +MPRSAVPHTPVRSHRLRSVLTGGAVPLLLLTGLPAQAHAQEAAVHTVRPGDSLTRISAAR +GVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAAGTYTVQPNDGWWVIARRTGVSAA +QLQRLNGMSASSMLHPGMVLTTQRTAAAPKAPASPAPTTTPATAPASTAPTAAGGTVRYT +VVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDGTLEVEPVSAVQAVGDT +FLGRTYAPHVTASANENLRLLRSVPQPTPEQMQQIVRETAERMGVDPRLALGHAYTESRF +RMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAGVAFIKYVQDRTPTLDE +GIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001176.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001176.fa new file mode 100644 index 0000000000000000000000000000000000000000..017b6ec82455cf65ce19ef55a047ea1286b7185c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001176.fa @@ -0,0 +1,30 @@ +>PROKKA_01423 +MSTTFFDGHDGLLCDLDGVVYAGDGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE +HLRTLGVPAEAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA +QCPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR +ATGTAPVAAGKPEPRLFRTAADALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR +ETAAAAPGPDRPTWVRAHLPALLAGGAEASADPRRG +>PROKKA_01154 +MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE +HLRTLGVPAQAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA +QRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR +ATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR +ETAAAAPGPDRPTWVRAHLPALLAGGAEAFADPRRG +>PROKKA_01476 +MSPTLPRGHDGLLCDLDGVVYAGGGAVPGAVETLTALAERGVPVGFVTNNASRAPESVAE +HLRSLGVPARPEQVFGSAPAGVDLLEETLGARTGRVLVVGSDYLRQVVRDRGFEVVAASQ +DRPDAVIQGFDPGVGWAELAQAAYAVNAGAAWVATNLDASIPRAEGIAPGNGALVGAVGQ +ATGTAPAAAGKPEPLLFRTAARALGLTRPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR +ENAGSAPEADRPTWIVEDLPALLSEPDGQAGTADGRRG +>PROKKA_01384 +MTDPAASTFFGGHDGLLCDLDGVVYAGGEAIPGAVETVSALAERGVPVGFVTNNASRPPE +AVAEQLRRFGLEVSPSHVFGSAPVGVDLLEERLTAAGHEGPARVLVVGSVHLADLVAARG +HHVVETAAERPDAVLQGFDPRVDWSRLAEAAYAVNAGAAWVATNLDLSIPRAEGVAPGNG +ALALAVTQATGVIPVAAGKPEPRLFHTAAAALGLQAPLMVGDRLDTDIRGGNAAGMETVL +VLTGVGSRHAAGEAPEEDRPTWIVDDMTALLGEPAEAARG +>PROKKA_01373 +MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE +HLRTLGVPAQAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA +QRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR +ATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR +ETAAAAPGPDRPTWVRAHLPALLAGGAEAFADPRRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001192.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001192.fa new file mode 100644 index 0000000000000000000000000000000000000000..7c56784ccdb0bf4778bea183a407ac57485a2444 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001192.fa @@ -0,0 +1,80 @@ +>PROKKA_01443 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEP +QKNGKTINWCSVRVVPEGAAQPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVALPGAVLPG +DFRISPRKTYGHVSAGMIASSTELGMGDDGTDGIIVLGDLGLDPEPGTDARDVLDLHGEA +AEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE +PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDAD +TLSGEIVVRRARAGETLTTLDGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTT +IVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTAEP +GVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVAEAAADVAPRLTV +TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGL +TEVLAYPFVSEEQNRRFGADSDAQGQALAMVALANPIASQYRYLRLSLLPGLVETARRNL +GRGFRDLALYEMGLVFLPGAQLGSATIPPRAVHPSAEVLADLEAGIPAQPWHVAGLYAGH +DSAPGPDHDPRPVDWQDAIAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGDR +VVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPEIVVAAPLSTFPVSTQDVALVVD +EAVVAGDVRATLAEGAGELLEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEVS +EARAAATALAAQRHGAVQR +>PROKKA_01175 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEP +QKNGKTINWCSVRVVPEGAAQPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVTLPGAVLPG +DFRISPRKTYGHVSAGMIASSTELGVGDDGTDGIIVLGDLGLDPEPGTDARDVLDLHGEA +AEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE +PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDAD +TLSGEIVVRRARAGETLTTLDGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTT +IVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTAEP +GVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVAEAAADVAPRLTV +TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGL +TEVLAYPFVSEEQNRRFGADSDAQGQALAMVALANPIASQYRYLRLSLLPGLVETARRNL +GRGFRDLALYEMGLVFLPGAQLGSATIPPRAVHPSAEVLADLEAGIPAQPWHVAGLYAGH +DSAPGPDHDPRPVDWQDAIAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGDR +VVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPEIVVAAPLSTFPVSTQDVALVVD +EAVVAGDVRATLAEGAGELLEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEVS +EARAAATALAAQRHGAVQR +>PROKKA_01455 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPSDELRGPIVVGQVLSKEPEP +QKNGKTINWCTVRVVPEGAEQTLTGEGIDPSGVQGVVCGAHNFEVGDKVVVTLPGAVLPG +DFRISPRKTYGHVSAGMIASVRELGIGDDHDGILVLSTLGLDPEPGTDALEVLDLQGEAA +EINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAALTPPAADDAGHPVRIADDAPIYGAP +GATRFVARTVSGVDASRPTPPWMAARLRLAGIRSISLPVDISNYVMWELGQPLHFYDAQK +LAGEIVVRRARAGETLRTLDDKERTLDPEDLLITDDSGPIGLAGVMGGLATEVTDATTTI +VIESANFDPISIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTAEPG +VTDVGTRPELAVVEMAADFPTALVGVEYTADEVAETLRALGAQVEAAEAADGAAPRLRVT +APSWRTDLRIPEDLVEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGHT +EVLAYPFVSAEQNRRFGVDSEEQGEALEMVALANPISSQYRYMRLSLLPGLVEIARRNLG +RGFRDLALYEAGLVFLPGTQLGSASIPPRAAHPAPEVLADLEAGIPAQPWRVAGLYAGHD +SAPGPDHAPRPVDWQDAVSGALAVADVLGVELAVRQGRHHAFHPGRVAELVVLGERGDQV +VGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPPAVVAVPLSTYPMSTQDVALVVEE +AVVAGDVRASLAEGAGELLESVELFDVYRGPGVPEGSKSLAFSLRFRAPDRTLTAEEASE +ARAAATALAAQRHGAVQR +>PROKKA_01363 +MRIPLDWLREFAQVPADATAEDVLADLVTVGLEEEDVHRPSDELTGPLVVGQVLTREPEP +QKNGKTINWCSVRVVPEGAEQTLTGEGIDPSGVQGIVCGAHNFEVGDKVVVCLPGAVLPG +DFRISPRSTYGHVSAGMMASARELGLGDDHDGIIVLGDMGLDPEVGTDVVDLFHLREEAA +EVNVTPDRSYAFSIRGIAREYAHATGTAFTDPAAAVTAPEANDAGPAVTLADGAGIYGVP +GCDRFVARVVEGIDPAAATPPWMAARLRLAGIRPHSLAVDVSNYVMWELGQPLHFYDADR +LTGGITVRRAAAGETLRTLDDKERTLDPEDLVIADESGAIGLAGVMGGAATEVSEGTTRV +LIESAHFDAVSIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTPAQG +VTDVGTRPEPVVVELDPEYPARRIGVDYPRERVVELLTGLGASVEDAGDLLQVTAPTWRH +DLRIPEDLVEEVARLDGYANIPSTLPVAPPGRGLTRAQVHRRRVADTLAAAGLTEVLDYP +FVSEGQNRLFGSATPEEGAAQRMVRLANPISSEFGWMRTTLLPNLLETVRRNVSRGFKDV +ALFEVGAVFLPGDGALGSPSNEPIGVKPSAETLAELDAGIPAQPRHVAGAFAGHEAAPGA +GFAPRAFDWQDPIAAALAVGRAVGVELTVVQGTHQAFHPGRTATLSLPDGTAVGVAGELL +PAWLEDADMPARTGAFELDLDAVLAAAADRVVARPLSTYPASQQDVALVVADDVVAGDVR +ATLAEGAGELLEEVALFDVYAGKGVPEGHKSLAFSLRFRAPDRTLTADEASEAREAATAL +AAERHGAVQR +>PROKKA_01393 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEP +QKNGKTINWCSVRVVPEGAAQPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVTLPGAVLPG +DFRISPRKTYGHVSAGMIASSTELGMGDDGTDGIIVLGDLGLDPEPGTDARDVLDLHGEA +AEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE +PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDAD +TLSGEIVVRRARAGETLTTLDGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTT +IVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEVADEAAERAVQMLVELAGGTAEP +GVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVTEAADGAAPRLTV +TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGL +TEVLAYPFVSEEQNRRFGADSDAQGQVPAMVALANPIASQYRHLRLSLLPGLVETARRNL +GRGFRDLALYEMGLVFLPGAQLGSATIPPRAVHPSPEVLADLEAGIPAQPWHVAGLYAGH +DSAPGPDHAPRPVDWQDAVAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGDR +VVGVAGELHPQWLEAEDLPARMSVWELDLDALCAAAPETVVAAPLSTFPVSTQDVALVVD +EAVVAGDVRATLAEGAGELLEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEAS +EARAAATALAAQRHGAVQR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001196.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001196.fa new file mode 100644 index 0000000000000000000000000000000000000000..478d4e99f71d90206a700a140801f1c906cefdd9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001196.fa @@ -0,0 +1,37 @@ +>PROKKA_01448 +MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV +PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ +AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL +TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA +YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF +>PROKKA_01180 +MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV +PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ +AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL +TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA +YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF +>PROKKA_01451 +MRWEAQTLRSESGAQRAAAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNAV +PAASAMPFRWTVNPYRGCTHACRYCYARSTHAFLDLDAGEDFDRQIVVKVNVAQVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYSLMPGIIEALADSGTPFSVLTKGTLLARDVPLLQ +AASRSVPVQVSLSLAMLDPAVAAAVEPGTPSPAARLRLIERLAAAGADVTVMAMPLLPWL +TDGDRDLDALMRALAAAGAARVMPGALHLRPGAKEWYLRWIRQEHPDLLAGYEQMYARSA +YAPESYRRTLARAAGEAAARHGLTRGGAHGIRREDGPVARPVPRSTPVAVPAPAAPAQPA +LF +>PROKKA_01355 +MRWEAQTLRTGGGAQRPGAGTPAGSPATLPLPGLQRIVSPPEFAGVTFHEVLARSALNKV +PASSAMPFRWTVNPYRGCTHACVYCYARGTHRYLDLGPGEDFDRQIVVKTNAPEVLRAEL +SRPGWTREPVALGTNTDPYQRAEGRYRLMPGIITALADTGTPFSILTKGTLLGRDAPALQ +AAAAQTSVQVGLSLALLDPSLAAAVEPGTPSPAARLRLISRLAEAGVEVSVMAMPLLPWL +TDSDRQLDRLMAALADAGAHSVLAGTLHLRPGAREWFLGWIDREHPHLAADYRRMYARSA +YAPQAYRRVVSQAAREAAARHGLRHGGAHTITREDGPGPRGGASAPLSAPAGTTGAEQAD +TAADAVRPVIAQPTLF +>PROKKA_01398 +MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV +PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ +AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL +TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA +YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001205.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001205.fa new file mode 100644 index 0000000000000000000000000000000000000000..fad2f705c0efd9ae51254316cda526745bc89020 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001205.fa @@ -0,0 +1,50 @@ +>PROKKA_01459 +MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVAL +AQVRPFTAPTLFHRDIVGSRARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVV +RAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQHGRWPAPEEPSGLWAGGTPR +VGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV +LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIRE +IHHRVKNNLQTVGSLLRMQARRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVD +GLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLALVLNELAANAVEHGTAPGGG +CVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGESPRAGEGSGLGLRIVHSLVEGDLR +GTLRWERSDDGGTRVVLRLPLT +>PROKKA_01191 +MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVAL +AQVRPFTAPTLFHRDIVGSRARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVV +RAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQHGRWPAPEEPSGLWAGGTPR +VGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV +LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIRE +IHHRVKNNLQTVGSLLRMQARRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVD +GLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLALVLNELAANAVEHGTAPGGG +CVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGESPRAGEGSGLGLRIVHSLVEGDLR +GTLRWERSDDGGTRVVLRLPLT +>PROKKA_01441 +MVSSLAQDPLTSHPDLADEDRSWLQLLVGDWQLVADLALADLVLWCPAPRPDPAEGFVAV +AQVRPFTAPTLFHRDIVGSRARADLRAVVASTWSGGERPEGAGPVETPDGTLQVRLWPVV +RRGRVVAVLSAHGDPNGRPSRSVIEENYIRTADSLLDMMQHGRWPAPEESAGLWAGGTPR +VGDGLVVLGPDSVARFTSPNAVSALRRLGIGATLEGHRLTDVLAGTDAARQPSEEGTWAV +LTGLRAGRREVQSRGASLTVRSVPLLGPDGWHGALLLLRDVTELRRQEQRLVSKDATIRE +IHHRVKNNLQTVGSLLRMQARRTSSPEADRALRQAMRRVDTIALVHQTLSEEIDGQVPVD +DLLKRQFRLAVEVSGDGRPLEAAASGEFGELPSHVTTPLALVLNELAANAVEHGTAPAGG +RVELHAERELTPAGSVLVVSVTDGGSGVQDGWSPGEFQPAADGAGLGLRIVQTMVEGDLR +GTLRWERLPDGGTRVVLRIPTA +>PROKKA_01344 +MVSTIASDPLNTHPDLGAEDRAWLQQLVGDWQLIADLALADLVLWCPLPVEVDGTGHLAM +AQVRPFTAPTLFHRDIVGSRARADLRALVDRVWAAGAPADGTGPLVEPGATLKVRLWPVV +RAGRVVGVVSAHEDPRTRPARSAVEDNYRTSADTLLDMVQHGRWPNPEDPPAYWIGGTPR +VGDGLVVLGDDSRATFTSPNAVSALRRLGLPTTLAGHSLTELLGGTEAARRPVEEGSWAM +LNGQRAGRTEVQANGATLTVRSVPLRNRDGWCGALIMLRDVTELRRQEQRLISKDATIRE +IHHRVKNNLQTVGSLLRMQARRSDSPETGRALRQAMQRVDTIALVHQTLSEQIDAQLSVD +ALMARQFRLAVEVAGDGRPLGTRVEGTFGELASHVVTSVALVLNELATNAVEHGTGEEGG +VVSLQAHREDTPAGDVLVFSVTDGASVEDGPGEGFVPQPAPNGLGLRIVHSLVEGDLRGS +IQWRRMPDGGTRVTVRLPVE +>PROKKA_01409 +MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVAL +AQVRPFTAPTLFHRDIVGSRARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVV +RAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQHGRWPAPEEPSGLWAGGTPR +VGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV +LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIRE +IHHRVKNNLQTVGSLLRMQARRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVD +GLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLALVLNELAANAVEHGTAPGGG +CVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGESPRAGEGSGLGLRIVHSLVEGDLR +GTLRWERSDDGGTRVVLRLPLT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001234.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001234.fa new file mode 100644 index 0000000000000000000000000000000000000000..3cd12ff1fd169acd360c7008eafd96af03f8cf80 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001234.fa @@ -0,0 +1,30 @@ +>PROKKA_01516 +MRTVAETVTTVPHDAAASALEPGAWAPPTDVHVAGLDAVGAAIAHALAGAGALRLALWDP +RPVDAADLGTGLLPGDLGRPRAGALARRLGDVAPGLRLYAHHGPVPVLVGQATVAVGSVL +DADLAAHALAADHPLLPVTVGPRAVTVGPWCAPVVRGCPLCRWPADPAGVPGAPTAPGPS +AHRGQVDGLAALRAAVLTVDALRTGPAPGVLRADRVTGRTRRVKVRPRPGCACDPDALGW +AF +>PROKKA_01225 +MRTVAETVTTVPHDAAASALEPGAWAPPTDVHVAGLDAVGAAIAHALAGAGALRLALWDP +RPVDAADLGTGLLPGDLGRPRAGALARRLGDVAPGLRLYAHHGPVPVLVGQATVAVGSVL +DADLAAHALAADHPLLPVTVGPRAVTVGPWCAPGVRGCPLCRWPADPAGVPGAPTAPGPS +AHRGQVDGLAALRAAVLTVDALRTGPAPGVLRADRVTGRTRRVKVRPRPGCACDPDALGW +AF +>PROKKA_01409 +MPAAPSSALSDALSSAEPGAVRPEVEPGPPGAGWEPPVDVHVAGLDAVGVAVAHALAGAG +AHRMALWDPRPVDAADLGTGLLPGDLGRPRARALERRLLDVAPGLRVYAHHGPLPVLVGQ +ASVAVGDVLDADLAAQALAADHPLLPVHVGPRAVTVGPWCAPDVVGCPLCSLPADPVGPP +GRRSARGRATSSGESGAAAVDALTAQRAAVLVADALRAGPSAGVVRADRASGRTRRARVR +PRAGCACDPDALAWGT +>PROKKA_01308 +MATTDAHGPRESGLLADPAGIQVAGLGPAGGALAAALAAGGVAALALWDPTPVGASDLGL +GLLPADLGRPRDRAWEARLSRTWPALPVYAGAGTRPGALGAATVAVDLPGLPDLAARAIA +AQHPLLPVRTDLHGVSAGPWTGGGAPGCVLCTEDVPGTALTAPPAAPPRRDPGAAREPGH +ALRAVVLALDVLTGRRDATSAVLRVDAATGRLTRIPVRTRPGCGCADLLAGDGTGDDWAA +ALAAVEESLDGALADARP +>PROKKA_01443 +MRTVAETVTTVPHDAAASALEPGAWAPPTDVHVAGLDAVGAAIAHALAGAGALRLALWDP +RPVDAADLGTGLLPGDLGRPRAGALERRLGDVAPGLRVFAHHGPVPVLVGQATVAVGSVL +DADLAAQALAADHPLLPVTVGPRAVTVGPWCAPGVRGCPLCRWPADPAGVPGVPTAPGPS +AHRGQVDGLAALRAAVLTVDALRTGPAPGVLRADRVTGRTRRVKVRPRPGCACDPDALGW +AF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001255.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001255.fa new file mode 100644 index 0000000000000000000000000000000000000000..6fce951474d4faa2b0784f21f3a313f587f402a1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001255.fa @@ -0,0 +1,15 @@ +>PROKKA_01537 +MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVSDGTPLVLADAKGRQVVVPGDRIGFVE +IGAKKSGPLGFAAS +>PROKKA_01247 +MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVADGTPLVLADAKGRQVVVPGDRIGFVE +IGAKKSGPLGFAAS +>PROKKA_01388 +MEIRIGVQHVGREVVIESEQPAEEVRSLVDAAVADGSTLVLADAKGRQVVVPGDRIGFVE +INAKKSGPLGFAAS +>PROKKA_01279 +MEIRIGVQHVGREVVLESDHTAQEVRALVDAALADGTTLALTDTKGRQVIVPADRIGFVE +IGAKKSAPLGFAAV +>PROKKA_01464 +MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVADGTPLVLTDAKGRQVVVPGDRIGFVE +IGAKKSGPLGFAAS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001256.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001256.fa new file mode 100644 index 0000000000000000000000000000000000000000..6b1861e4050da35ea9000d3a880939f6181182e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001256.fa @@ -0,0 +1,50 @@ +>PROKKA_01538 +MTPHALGLRGPADPTLLERLAALRTELELPPAFPAPVLAEAEAAAREVHAGLTGSPDHAD +RTALPFVTVDPAGSTDLDQALLLTPADDDGILVRYAIADVPAFVTPGGAVDGEARRRGQT +VYLPDGRVPLHPEVLSEDAASLLPDREHPAFVWTFLLDAAGAVVETGLERARIRSRAQLT +YGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR +GGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM +PAPDTDAVAAFRERTRALGAPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA +FDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHAIGAPAPAWVRS +ALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA +VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR +>PROKKA_01248 +MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHAD +RTALPFVTVDPAGATDLDQALLLTPSDDDGILVRYAIADVPAFVAPGGAVDAEARRRGQT +VYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDAAGAVVETGLERARVRSRAQLT +YGQVQAFLDARPGAQAPATPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR +GGASLNLPDQEVLVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM +PAPDADAVAAFRERTRALGVPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA +FDAQAEDPALRTPPAEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHASGAPAPAWVRS +ALPELPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA +VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWSHSSR +>PROKKA_01387 +MPHRAVALRGRPDPALIERLAALRTELELPAGFPPEVLEEADAAARDVLAALASDPAYAD +RTDVPFVTVDPAGSTDLDQALYLEAADGDAITVRYAIADVPAFVAPGGAVDVEARRRGQT +VYLPDGRVPLHPEALSEDAASLLPDRERPAFVWTFVLDAAGAVVDTSLERARIRSRAQLT +YAQVQAFLDALPDAKAPAAPRPGLDEADHAAHRGWDAPLRDSLALLPEVGRRRAAQEAAR +GGASLNLPDQEVHVAEDGRHCLVQRAPLPAEDHNAQLSLMTGMAAARLMLEAGVGILRTM +PAPDAEAVAAFRSRTRALGAPWEEGQDYGAYLRTLDPADPGHLAVLHEATSLFRGAGYTA +FDAHAEDPELRTPPSEPEQAALAAPYAHATAPLRRLVDRFVLALCHAHATGAPAPEWARA +ALPEVPALMTESSRRTSAADRAATDLVEAAALQDHVCAELEGIAVRRVKGGAEVWLLDPA +VTLRVPGEAEPGTRVRVRIEGVDRASGEVTASGVDWPHSSR +>PROKKA_01278 +MPHHALEVRGGPDAALAARLRALRAELDVPGEFPADVLTEAERAAAEVPGRVAADPDRAD +LTAVPFVTVDPAGSTDLDQALHLQAGPGRDELTVRYAIADVPGFVAPEGAVDAEARRRGQ +TVYLPDGRVPLHPEVLSEDAASLLPEVERPTFVWTFVLDAEGAVASTDLVRARIRSRAQL +AYPQVQALLDDDAAPEAADWPAEVRASLALLPEVGARRTAQEAARGGASLSMPDQEISVV +DGAYTLVQRVPLAAEDHNAQLSLMTGMAAARIMLEAGVGILRTMPAPDPDAVDAFRARTR +ALGLPWGEELDYGAYLRTVDPTDPRGLAVMHAATTLFRGAGYTAFDRGSVDPALRALPED +PEQAALAAPYAHTTAPLRRLVDRFVLVLCHAHVAGEPVPDWVRRALPDLPALMAESGRRA +SAADRAATDLVEAALLAARVGSVLEGTAVRTSEKGTDVQLTDPAVSLRVPGRAEPGTVVR +VRVDAVDVAAGKVTASGVDWPHSAR +>PROKKA_01465 +MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHAD +RTALPFVTVDPAGATDLDQALLLTPSDDDGILVRYAIADVPAFVAPGGAVDAEARRRGQT +VYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDAAGAVVETGLERARIRSRAQLT +YGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR +GGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM +PAPDTDAVAAFRERTRALGAPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA +FDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHAIGAPAPAWVRS +ALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA +VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001270.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001270.fa new file mode 100644 index 0000000000000000000000000000000000000000..52d4c78998560ae5ee8a9fe7728204bb9857f681 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001270.fa @@ -0,0 +1,30 @@ +>PROKKA_01554 +MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGESLRIGIKFD +QPGLGYREGSAQPTGFDTDVARYVADKLGVAEQDIEWVQTPSANRENALENGEVDMIFAT +YSITDARKERVAFAGPYFVAGQDLLVRADDTAITGPESLDGKNLCSVTGSTSAQKIKDQF +ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG +VGLPKDSERCEDINEAIKEMKDSGEWEKALESNTEGTGYTYDETLNSGEDAEFEPCA +>PROKKA_01264 +MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGERLRIGIKFD +QPGLGYREGSAQPTGFDTDVARYVADKLGVAEKDIEWVQTPSANRENALENGEVDMIFAT +YSITDARKERVDFAGPYFVAGQDLLVRADDTAITGPESLEGKNLCSVTGSTSAQKIKDQF +ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG +VGLPKDSERCEDINEAIKEMKDSGEWEKALESNTEGTGYTYDETLNSGEDAEFEPCA +>PROKKA_01371 +MFRKKLLTLSAVTAAAALSLTACSPSAQQGGGEGSGSASAGGSQSAGSGEGLRIGIKFDQ +PGLGFREGSGAPTGFDTDVARYVADKLGVAEGDIEWVQTPSANRENALENGEVDMIFATY +SITDARKERVDFAGPYFVAGQDLLVRADDTEITGPDALDGKNLCSVTGSTSAQKIKDQFA +SGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAATDANKGKFKVVGNTFTTERYGV +GIAKGDDRCEDINDAIKEMKDSGAWKESLDANTEGTGYEYDEALNSGADAEFESCS +>PROKKA_01262 +MARSRILSVAAVAAAAALSLSACSPSSSGGSGSASSASGSTAAQSGSSDTLRIGIKYDQP +GLGFREGQNAPTGFDTDVARYVAGKLGVAEDKIEWVQTPSANRENALENGEVDMIFATYS +ITDARKQRVDFAGPYFVAGQDLLVRQDDTSITGPDSLNGKNLCSVTGSTSAQKIKDNYAS +GVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAATDANKGKFKVVGQPFTTERYGVG +LQKGSDKCKDINEAIKAMKDSGEWEKSLKANTEGTGYEYSEDKNSGADAEFEPCA +>PROKKA_01481 +MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGESLRIGIKFD +QPGLGYREGSAQPTGFDTDVARYVADKLGVAEQDIEWVQTPSANRENALENGEVDMIFAT +YSITDARKERVAFAGPYFVAGQDLLVRADDTAITGPESLDGKNLCSVTGSTSAQKIKDQF +ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG +VGLPKDSERCEDINEAIKEMKDSGEWKKALESNTEGTGYTYDETLNSGEDAEFEPCA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001271.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001271.fa new file mode 100644 index 0000000000000000000000000000000000000000..349de6fd145d3f670d51136a7a6bebb0051cc06e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001271.fa @@ -0,0 +1,25 @@ +>PROKKA_01555 +MESISSLLADYGADIPLAFWMNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN +VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT +VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG +LMKRMIEFSPDVMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR +>PROKKA_01265 +MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN +VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT +VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG +LMKRMIEFSPDLMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR +>PROKKA_01370 +MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRAIGTAYVN +VVRNTPLTIVMLLGVLAVWGQLKITFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT +VPLGQAEAARAIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG +LMKRMIEFSPDVMVAIFLTFAIGFCLIVIPIGLLTTWASDKWAVAR +>PROKKA_01261 +MESLSTLVEQYGAAVPQAFWMNIRLAALATLGAFVLGVLLALCRISPVPSLRAVGAGYVH +IVRNTPLTIIMLIGVLAVWGQLKVTFAPDFKVNFFVYAVLALSLYHAAFMCEAIRSGVNT +VPLGQAEAARAIGLGFLPAARLVILPQALRGAITPIGNTVIALTKNTTVAAAASVAEASG +LMKTMIEFRPDAMVAIFLTIAIGFCLIVIPIGLLTTWASDKWAVSR +>PROKKA_01482 +MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN +VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT +VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG +LMKRMIEFSPDLMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001272.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001272.fa new file mode 100644 index 0000000000000000000000000000000000000000..0be6435d706ed15bb10ce1ccf11a2c3536c6ad17 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001272.fa @@ -0,0 +1,30 @@ +>PROKKA_01556 +MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN +AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV +MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA +AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGNG +NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG +>PROKKA_01266 +MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN +AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV +MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA +AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLHYARQLGSGNG +NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG +>PROKKA_01369 +MSSQASVLFDAPGPLARRRILIANLVALAAVLALAVAVLMRMADADQLEARRWTAALDAN +AWTNYYLPGLQFTVQAAAIAVLTSVVFGLVLGFLRLAPFAPVRGAAGLVVEFFRAVPVLI +MMVFFYQVFAQVARTGVIAPADGPYYAVIVALTLYNGSVIAELVRSGVRSLPKGQREAAA +AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGQG +NILQSLVVAALIFIVINFLLTWVATRLSRRLSSRTAGDAGAPTTPVVGAPTDKPA +>PROKKA_01260 +MSAQASVLFDAPGPATRRRILIVNLVALALVLAVAVVVGMALQDRGQLEPRRWLAALDAN +AWTNYYLPGLQFTLQSAGIAVVTSVVFGLVFGFLRLAPVAPVRWLAAVVVEFLRAVPVLV +MMVFFYQAFALAARGGAINAADSPYYAVIVGLTLYNGSVIAELVRSGVTGLPKGQREAAA +AIGMTPNQSLRLVEVPQALVAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGQG +NILQTLVVAAVIFILINMLLTWLATLLSRRLSSRTSGRTKPHAGSTAVTIGKD +>PROKKA_01483 +MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN +AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV +MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA +AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGNG +NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001273.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001273.fa new file mode 100644 index 0000000000000000000000000000000000000000..4261d12c179081cb5d7e614ac284bac3b1a832d9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001273.fa @@ -0,0 +1,40 @@ +>PROKKA_01557 +MSLTPNTLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEQALRALGGLEVRRFGDA +VVARTALGRSTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQLA +LAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDGVV +EGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYREGL +HAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRAVLEGAGVDWDAQVRIDDAS +PAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDEHV +SREAVHACLAALTAWLAG +>PROKKA_01267 +MSLTPVSLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEHALRALGGLEVRRFGDA +VVARTALGRPTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQLA +LAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDGVV +EGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYREGL +HAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRAVLEGAGVDWDAQVRIDDAS +PAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDEHV +SREAVHACLAALTAWLAG +>PROKKA_01368 +MTETSAPALPDLADPGLDVAELTAVLLDVPSVSGDEGPLADAVETALRALGGLEVRRFGD +AVVARTDLGRDTRVILAGHLDTVPLPTVPGSRGTVPSAWEGDVLYGRGAVDMKSGVAVQL +ALAGRYGRADGPAPAHDVTWVFYDHEEVASDLSGLARVARQAPELLEGDFAVLLEPTDGV +VEGGCNGTCRYRVSFSGVAAHSGRAWRGENAIHKLGAVLTALAAHEPATVTVEGLDYREG +LNAIRVAGGVAGNVIPDAAHVDVNYRFAPDKTLEQAHARVREVLEGAGVDWDAQVRIDDA +SPAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSELGVPAVNFGPGDALLAHTDDEH +VHRAAVHACLDALDAWLAG +>PROKKA_01259 +MTDAVAPVLPDLAAADLDVAALTATLLDAPSVSDDEGPLADAVEAALARLPRLGVRRFGD +AIVARTELGLPGRVILAGHLDTVPLPTAPGARGTVPSAWEGDVLYGRGAVDMKSGVAVQL +ALAGLFGRADGPDPVHDVTWVFYDHEEVDSARSGLARIARQAPELLEGDFAVLLEPTDGV +VEGGCNGTCRYRVRFEGVAAHSGRAWRGDNAIHKLGALLSALAAYEPATVTVEGLDYREG +LNAIRVSGGVAGNVIPDAAATEVNYRFAPDKTLEQAHAHVREVFAAAGVDWDAQVEVTDA +SPAARPGLDRPAAAAFVAAVGGEPMPKYGWTDVARFSELGVPAVNFGPGDALLAHTDDEH +VERAAVERCRDALEAWLRG +>PROKKA_01484 +MSLTPVSLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEQALRALGGLEVRRFGDA +VVARTALGRSTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQLA +LAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDGVV +EGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYREGL +HAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRTVLEGAGVDWDAQVRIDDAS +PAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDEHV +HREAVHACLAALAAWLAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001324.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001324.fa new file mode 100644 index 0000000000000000000000000000000000000000..8cb9e66dd0419eea08e681324db0b4df70b8c8de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001324.fa @@ -0,0 +1,33 @@ +>PROKKA_01643 +MDETTAPTRAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF +MHRLQSSPAVRALTARFSGRLSAAADAARAARGRTGLHIRWGRTALFLAALVALLVFLVA +GLAAAFGAGTLALAGWSLLFAVAGLAGLRALAVRDRTRRARPAAVVVPERPAAPAAEERQ +APPADPERDRRVLETVLAFETEAPRPAAAPAAPRVEPVVVTASAAAPAADRVVTIPAVPR +PTYLDAPEMARPLPAPLETPAPTGADTRLTDAARTADDQISAAAEQDIAALDLDNVLARR +RAC +>PROKKA_01348 +MDETTPPTTAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF +MHRLQSSPAVRALTARFSGRLGAAADAARAARGQTGLHIRWGRTALFLAALAALFVFLVA +GLAAAFGAGTLSLAGWSLLFAVAGLAGLRALAVRDRTRRARPAADVVPARPAAPAAEERQ +APPADPERDRRVLETVLAFETEAPRPAAAPAASRVEPVVVTASAAAPAADRAVTIPAVPR +PTYLDAPEMARPLPAPLETPAPTGADTRLQDAASTADDRISAAAEQDIAALDLDNVLARR +RAC +>PROKKA_01250 +MEDTTAPASAGRAALDALADARVSASFVILALVAYFAWRLVVRRRRVESAPARPTMLRST +MHRLQSSPAVRALTERLSGRVSGLADSARAAGRRTAGLQVRWGRTALFLAALAALAVALV +AGVAAAFGAGTAGLAGACLLFAVAAVAGLRALAVRDRARRAPAAVVEAPAEAAPHAAPEA +PRVDPERDRRVFETVLGLEDEAARVSAAAPAAPAAAPTVVAASAVRAPEATDTVTLPVVP +RPTYLDAPEMLRPAPAPLTAPEAAGSDVRLKDAARAAEHEEALSATAEQDVAALDLDHVL +ARRRAS +>PROKKA_01161 +MTETPSPREDARLDAEPGHADSGFHVHWDRASLFLVGVGALAVALVTALCALAGLPTAGL +AGWSLLVTVGAVVGLRVLAARDQREHHDDLADDADEPNLAEEDLDTHELPVVPDPERDRR +VLAAALSLTDEAEDEEPAAEPVPVVVDALQRRRAPRIPLGGIVIPEVPRPTYLDAPEAPA +AEAQAEYPAEDDAVATRPEAEEQAASAEVVEIPEPAARAVVLDLDGVLARRRAS +>PROKKA_01573 +MDETTAPTRAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF +MHRLQSSPAVRALTARFSGRLSAAADAARTARGRTGLHIRWGRTALFLAALVALLVFLVA +GLAAAFGAGTLSLAGWSLLFAVAGLAGLRALAVRDRTRRARPAAVVVPERPTAPAAEERQ +APPADPERDRRVLETVLAFETEAPRPAAAPAAPRVEPVVVTASAAAPAADRAVTIPTVPR +PTYLDAPEMARPLPAPLETPAPTGADTRLTDAARTADDQISAAAEQDIAALDLDNVLARR +RAC diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001372.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001372.fa new file mode 100644 index 0000000000000000000000000000000000000000..e9fe1e5763888729b791469a79ff29859633ff5c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001372.fa @@ -0,0 +1,25 @@ +>PROKKA_01699 +MTRMLLMGPPGSGKGTQATRIADKLGIVPISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV +PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAEAGLSLSAVVELEVPDEE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE +RLLQAVYSVRAATGSLPVIQPGAES +>PROKKA_01406 +MTRMLLMGPPGSGKGTQAARIADKLGIVPISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV +PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAESGQSLSAVVELEVPDEE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE +RLLQAVYSVRAATGSLPVIQPGAES +>PROKKA_01179 +MTRMLLMGPPGSGKGTQATRIADKLGIVAISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV +PDDVTNRMVADRIAQPDAEHGFLLDGYPRTKGQVEALDAMLTEAGLALSAVVELEVPDAE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETEAVIQEYVERGIVARVDGTGQIDDVTE +RLLQSVYAVRAATGSLPVIAPDTES +>PROKKA_01109 +MTRMLLMGPPGSGKGTQATRIADKLGIVAVSTGDIFRHNVKNMTELGKEAKRYMDAGDFV +PDEVTNRMVADRLSQSDAETGFLLDGYPRTAGQVDALDAMLKDTGQALSAVVELEVPDAE +LVARLLKRAEIEGRADDTEEVIQHRLDLYHRETESVIESYAERGIVARVDGTGQIDDVTE +RVLQSVYSVRAATGTLPIITPDTQA +>PROKKA_01628 +MTRMLLMGPPGSGKGTQAARIADKLGIVPISTGDIFRHNVKSMTPLGVEAKRYIDNGDFV +PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAEAGQSLSAVVELEVPDEE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE +RLLQAVYSVRAATGSLPVIQPGAES diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001383.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001383.fa new file mode 100644 index 0000000000000000000000000000000000000000..772a4102cb7dcd24531bc1430821c91e13057820 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001383.fa @@ -0,0 +1,15 @@ +>PROKKA_01710 +MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED +NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK +>PROKKA_01417 +MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED +NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK +>PROKKA_01168 +MTEQTPAVSEERGYRKALRGVVVSDKMDKTIVVEVEDRKKHSLYGKVMKTSKRVKAHDED +NTAGIGDRVRIAETRPLSASKRWRLVEIVERAK +>PROKKA_01098 +MTEQTAAPVEERNYRKSLRGVVVSDKMDKTIVVEVEDRKKHALYGKVMKTSKRVKAHDED +NTAGVGDRVLIVETRPLSADKHFRLVEIVERAK +>PROKKA_01639 +MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED +NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001396.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001396.fa new file mode 100644 index 0000000000000000000000000000000000000000..30bb7f5e4eedf73b10876053f3a26c8fecdac533 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001396.fa @@ -0,0 +1,40 @@ +>PROKKA_01723 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA +LEGDAQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK +>PROKKA_01430 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA +LEGDPQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK +>PROKKA_01155 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQEFDGDDAPVIRTSGLKA +LEGDAQWVKSVEDLMDAVDEYIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLA +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVAPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MTVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK +>PROKKA_01085 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEKRDFASIDSAPEERQ +RGITINISHVEYQTDKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQEFDGDEAPVIRTSGLKA +LEGDAQWVKSVEDLMDAVDEYIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLA +INSEVEIVGIRPVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVQPGS +ITPHTDFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKINK +>PROKKA_01652 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA +LEGDAQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001435.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001435.fa new file mode 100644 index 0000000000000000000000000000000000000000..8d54921ac9d6a7412b762920bdfb66cd1d0aa401 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001435.fa @@ -0,0 +1,20 @@ +>PROKKA_01765 +MTTAFEPRPHTAAAPREPDPHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWITAF +EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLADGTWRLRD +ADPRAWSTTYRATILGAAPEAVCTIWDVFPLPAA +>PROKKA_01472 +MTTAFEPRPHAAAAPREPDPHGPGTAGSLRPGARGSVLIVTRHPDPDEAMRHAMAWITAF +EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWRLRD +ADPRAWSTTYRATILGAAPEAVCTIWDVFPLPAA +>PROKKA_01112 +MTTAFEPRPHTGLAPREPEPHGPGTPGPLRPGVRGSVLIVSEHADPDTAMRHAMAWITAF +EDDCGLVLDADGTELYAVGLAGELGASLRRSPGVAEDGTPTDTSEFVDAILTGGVWRLRE +PDARAWSTAYRAAILGAAPHAVCTVWDVLPLPAA +>PROKKA_01037 +MTAQHAEPTRTDRAEPHGPGTPATLRPGERGSVLVLSPAGPPEAAMGHAVAWITAFEDDC +GLVLDRDATSLYAVSPADGLRREGDVPSDGGIAEHLDFVLAGDVWHHRGTCPPAPAGSDV +DGWALLVHRLQREAPRGALGTVWDVFPLPAAG +>PROKKA_01694 +MTTAFEPRPHTAAAPREPDPHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWITAF +EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWRLRD +ADPREWSTTYRAAILGAAPEAVCTIWDVFPLPAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001438.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001438.fa new file mode 100644 index 0000000000000000000000000000000000000000..faf48c440e21b955a5a2c3fd49c8ad982b36e045 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001438.fa @@ -0,0 +1,45 @@ +>PROKKA_01770 +MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL +VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGFESVPVLYALVALHSG +ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID +VVTFLAALYAVWRLPSLPPQQAEAAAASGTRGGLASVVEGLRFLGSRPNLRMTFLADIVA +MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI +LVWGGAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT +PDHLRGRLQGVFVVVVAGGPRLGELITGGASVVLGEGPTLLAGGVLCMLGVSALMRWQPG +FLRYDARNPTP +>PROKKA_01477 +MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL +VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGLESVPVLYALVALHSG +ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID +VVTFLAALYAVWRLPSLPPQRAETATASGTRWGLASVVEGLRFLGSRPNLRMTFLADIVA +MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI +LVWGAAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT +PDHLRGRLQGVFVVVVAGGPRLGELLTGGASVGLGEGPTLLAGGVLCMLGVTALMRWQPG +FLRYDARNPTP +>PROKKA_01107 +MARLLVDLTPLKVSPAYRRLWVGNTLSFVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL +VPLVVAGLYGGAVADRHDRRTVALASSAVMWLTTVGIAAHAWAGIESVPLLYALVALHSG +ASGINQPTRGAIIPALVGMKLVPAANALNMMTFSVAMMAGPVLGGVLVASVGYAWTYSID +VVTFLAALYAVWRLPSLPPQRAEGEAAPTGRVGVRSVVEGLRFLGSRPNLRMTFLADIVA +MATAFPRALLPAVGGVVLGGGEAAVGVLLAAMAAGAFLAGLFSGPFTRLHAQGWGVYVSI +LVWGASVAAFGGVVWWAQGLPDGDPRLTGAFVAAALCLAVGGAADSISGVFRTTILQSAT +PDHLRGRLQGVFVVVVAGGPRVGELLTGGASVAVGEGLTLLLGGLACVLGVSLLMRRQPE +FLKYDARSPTP +>PROKKA_01033 +MPRLLVDLAPLEASPAYRRLWLGNALAFVGTQLTLVAVSLEVFALTGSSFAVGMLGLAAL +IPLVVAGLYGGAVADRHDRRTVALASGAVMWAATALIAAHAWAGVESVGVLYGLVALHSA +ASGINQPTRGAIIPALVGPALLPAANALNMLTFSTAMMAGPLLGGVLVASVGYAWTYTVD +VVTFLAALWAVWRLPSLPPDRSAAPDDAGRGGLSSVLDGFRFLGTRRNVRMTFVADIVAM +ATAFPRALLPAVGGTILGGGEAAVGVLLASMAAGTFLAGLFSGTFTRVHRQGRGVAVAIA +AWGLSVAAFGAVVLWAAPLPDGDPRLGPALAACAACLVVAGAADSVSAVFRTTILQSATP +DHLRGRLQGVFVVVVAGGPRVGEMIQGTASAALGEGATLVLGGVLCVAGIALLMRVQPGF +LHYDARRPTP +>PROKKA_01699 +MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL +VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGLESVPVLYALVALHSG +ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID +VVTFLAALYAVWRLPSLPPQRGEAAAASGTRGGLASVVEGLRFLGSRPNLRMTFLADIVA +MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI +LVWGAAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT +PDHLRGRLQGVFVVVVAGGPRLGELLTGGASVGLGEGPTLLAGGVLCMLGVSALMRWQPG +FLRYDARNPTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001472.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001472.fa new file mode 100644 index 0000000000000000000000000000000000000000..b7efdb6c6295eb47c1c553252742e2d105b0d57d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001472.fa @@ -0,0 +1,79 @@ +>PROKKA_01823 +MTGHLPEHDPWADPAGGWGPPGTADAAPPVDDAAPDSSGPEPQPVGEVVADVVAGLSVTA +PGDLCPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGV +ERPWLHQVRAAALAGAGTHTVLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALA +ADQLTSWRALERDGAPGLRSAPYDGDTAPQDRIWAREHASVLMTNPDMLHVGILPHHERW +ATFFRNLAFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA +GHFARLIGAPAAAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLA +LQQVRTLAFIRSRRGAEAIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSG +RLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPL +DTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVRALL +DVLVDQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQ +AHPGAVYVHQDRTYLVEELDEDAHAVVVTRAWPDFTTQARDVTEVEIVAVHRRLDAREGT +LRWCLGDVQVRTQVVSFQRKALASGEVLGEEPLDLPARDLFTSAVWFQAASDELIAAGLT +TDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAGFAE +RGFEQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADH +LVPADASTDGSGGGASGGSSGGATDAAPGA +>PROKKA_01520 +MTGHLPEHDPWADPAGGWGPPGTADSAPPVDDAAPDFSGPEPQPVGAVLADVVAGLSVTA +PGDLRPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGV +ERPWLHQVRAAALAGAGTHTVLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALA +ADQLTSWRALERDGAPGLRAAPYDGDTAPQDRIWAREHATVLMTNPDMLHVGILPHHERW +AAFFRNLTFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA +GHFARLIGAPATAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLA +LQQVRTLAFIRSRRGAEAIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSG +RLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPL +DTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVRALL +DVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQ +AHPGAVYVHQDRTYLVEELDEDAHAVVVTRAWPDFTTQARDVTEIEIVAVHRRLDAREGT +LRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLDLPARDLFTSAVWFQAASDELIAAGLT +TDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAGFAE +RGFEQARRWVEATAGAIAACECTEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADH +LVPADASTDGSGGGASGGSADPAPGA +>PROKKA_01046 +MSTPPPEPAAAGVAFDPWADPAAGWGAPDDGPSDRRDAPADVDETDHPGDEAHPWDEPAP +LADAVADVVAGLSVSRPGDPVAGGEAADVLRGALGRHGLPEQIRHVVTLPAREARHADWP +SEAPEALVGAFAGRGIERPWAHQVRAATVAGAGTHTVVATGTASGKSLAYQLAAGIRLSG +DPHATVLHLSPTKALAADQLLAWRALERDGATWLRAAPYDGDTAPPDRIWAREHANVLMT +NPDMLHVGILPHHERWARFFRHLAFVVVDESHSYRGVFGSQVGILLRRLRRVAAHWRGDR +PEPVFIGASATSADPAGHFSRLIGAPATAVAEDASPHGAVTVAFWEPELTDRRGENGAPV +RRSAMAASADLLTDLALQQVRTLAFIRSRRGAEAIASAARRQLEELEAGLGSRIAAYRSG +YLPEERRALEADLRSGRLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGR +GGQDALAFFVASDDPLDTYVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPLTP +EAFERFGDPERVRALLDVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAE +SGTLLGTMDSPQTHYQAHPGAVYVHQDRTYLVEELDEDAHAVIVTRAWPDFTTQARDVTE +IEIVDVHRRLDAREGTLRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLELPARDLFTSA +VWFQASSEELIAAGLTMDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSP +AVFVYDGRPGGAGFAERGFAQARRWVEATAGAIAACECEAGCPSCVQSPKCGNRNSPLDK +AGALTVLRFLLGQADHLVPVVAEGSGETDGGTDDGVGVDGEDASGSGSSGTA +>PROKKA_00985 +MTGGPVPWPDDDPWAARGPAEDRSARDVPTPAPGGPGWEPPQELATGDPEARAAFAAALG +RRSLPAQIRHVTTIPARTPRSAPWPAGTPAGLVRAFAARGVQAPWEHQARGTAAALAGRH +TVLATGTASGKSLAYQLAVGATLAADPRATVLYLAPTKALAADQLASWRALERDGAAWLR +AAPYDGDTAPQDRIWAREHANVLLTNPDMLHVGILPHHERWAVFFRNLAYVVLDESHTYR +GVFGSQVGILLRRLRRVVAHYRGERPETVFIGASATSAAPAEHLATLIGAAPGEVEAVTE +DASPHGAVHVAFWEPELTDRRGENGAPVRRSATATAADLLTDLALQQVRTLAFIKSRRGA +ETIAGAAKRQLEEVEAGLGSRIAAYRSGYLPEERRALEEALRSGRLLGMASTPALEMGID +VAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPLDTFVVEHPGAVFDLGV +EDTVLDPANPHLLGPQLCAAAAELPLRPEDLPWFGGPERVRELLDVLVEQGLLRRRPAGW +FWTHTEHAASLVSLRDDGGGPMDIIDVESGALLGTMDSPQTHYQAHPGAVYVHQDRTFLV +EDLDEDAHAVLVQRAWPDFTTQARDVTEIEIVAVHRRLDAAGSSLRWCLGDVQVTTQVIS +FQRKALLSGEVLGEEPLDLPARDLFTSAVWFQAASEELVAAGLTMDRLPGALHAAEHAMI +GMMPLVASNDRWDIGGVSMVLHPDTGVPTVFVYDGRPGGAGFAERGFAQARRWVEATAGA +IAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLAERFDGLIEVPAHLPDVTA +>PROKKA_01744 +MTGHLPEHDPWADPAGGWGPPGTADAAPPVDDAAPDSSGPEPQPVGEVVADVVAGLSVTA +PGDLRPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGV +ERPWLHQVRAAALAGAGTHTVLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALA +ADQLTSWRALERDGAPGLRSAPYDGDTAPQDRVWAREHASVLMTNPDMLHVGILPHHERW +AAFFRNLAFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA +GHFARLIGAPARAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLA +LQQVRTLAFIRSRRGAEAIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSG +RLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPL +DTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVRALL +DVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQ +AHPGAVYVHQDRTYLVEELDEDAHAVVVTRAWPDFTTQARDVTEIEIVAVHRRLDARAGT +LRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLDLPARDLFTSAVWFQAASDELIAAGLT +TDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAGFAE +RGFEQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADH +LVPADASSDGSGGASGGATDAAPGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001499.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001499.fa new file mode 100644 index 0000000000000000000000000000000000000000..770d88dddcebfc6b6e978307fe1ef048050e5561 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001499.fa @@ -0,0 +1,50 @@ +>PROKKA_01856 +MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG +IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA +DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE +TALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRL +ALEQPVEADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR +LKLNVESTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI +DFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA +DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRTPL +>PROKKA_01552 +MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG +IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA +DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE +TALELLPKIRGAYCFVFMDERTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDAAIAGRSVYESRVEMGRRL +ALEQPVDADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR +LKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI +DFATRAELIANGAAVDQIAASIGADSLAYISEKGMIEATGQPRERLCTACFTGDYPIPLA +DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRIPL +>PROKKA_01008 +MIASRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG +IAASDGKRIGVYKDIGLVSQVFDESTLATFTGHIAVGHCRYSTTGANKWANAQPTLGATA +GGDTVALAHNGNLVNSGELLRMVQARDGLQLRGEMKQGNTTDTALVTALLHGEEGRKLEE +TALELLPKVRGAYCFVFMDEHTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDASIAGRSVYESRVDMGRRL +ALEGPVDADVVIPVPESGTPAAVGYAEASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR +LKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGAAEVHVKISSPPVKWPCFYGI +DFASRAELIANGAGVAEIASSIGADSLGYISEEAMIAATGQPRERLCTACFTGTYPIELA +DESERGKSVLETDAGSAAVTVMAPDGDATTVASTGCEPGPDADDEKLLTETDRTPL +>PROKKA_00952 +MISARTRRGDGRLTAALDPQEAGPQDECGVFGVWAPGEEVAKLTYYGLYALQHRGQESAG +IAASDGKRIAVYKDMGLVSQVFDEPTLAALTGHVAVGHCRYSTTGVNKWANAQPTLGATA +DDGTVALAHNGNLVNSAELLRMVESKEGAHTLGEIKQGNTTDTALVTALLHGEKGVSVEE +TALELLPKVRGAYCFVFMTERTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDAAINGRSVYESRVEMGRRL +AQEHPVDADVVIPVPESGTPAAVGYADASGIPFRQGFVKNAYVGRTFIQPSQTLRQLGIR +LKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGAAEVHVKISSPPVKWPCFYGI +DFATRAELIANGAGVQEIASSIGADSLAYISEEGMIAATEQPRERLCTACFTGTYPIELA +DEKERGKAVLENGTPTAEATDVVSEDGTVTTVASTGCEPGPDSEDEKLLTQTDRTPL +>PROKKA_01776 +MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG +IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA +DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE +TALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRL +ALEQPVDADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR +LKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI +DFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA +DEGERGKGLLEPVAVSPASTVVLDVDGETTTVTATGCEPGPDADDEKLLTETDRTPL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001532.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001532.fa new file mode 100644 index 0000000000000000000000000000000000000000..36619b2f9a1c2ff9d4de15010bcc2ef30c21181c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001532.fa @@ -0,0 +1,35 @@ +>PROKKA_01896 +MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV +LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG +DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTTAGRRRAVRRSPGRAVADQVRHTV +TNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR +RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL +RVSKDTILVTTIVAIPAMIAVALLLA +>PROKKA_01592 +MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV +LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG +DAALAAPALIFQLAIYTPLYVAAMDAATAREVRRRTTAGRRRAVRRSPGRAVADQVRHTV +TNPLILGSVAGLVFSLTGWSLPGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR +RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL +RVSKDTILVTTIVAIPAMIAVALLLA +>PROKKA_00962 +MTQVLSGFVVVWVIIAVGFLVGRSGVLGEDARTVLSRTAFYIGSPALLFVTLSGADVAAV +LGPQLWVATLSALAAAALFLAISIPVFKQRPASERIMAALSASMVNSANLGIPIAAYVLG +DAALAAPVLIFQLAIYTPLYVAAMDVATTSEARARAAGGRPAVRRSRGQALAAQLRQTGT +NPMILGSAAGLLFSLNDWTLPGPLMQSVELIGGLSIPAMLLAFGMSLVGSRPLERAGGRR +ADVLLASGVKLLVHPLIAWVLAQFVLGLDAREVFVAVVLASLPTAQNVFVSAVRYDAGLR +VAKDTILITTIVAIPAMIAVALLLA +>PROKKA_00901 +MIEVLSGFSVVWVIILVGLLLGRTGVLGDEAREVLSRTAFFVGNPALLFVTLSRADVGAV +LGPQLWVACLSAFAAAVVFLGLSIPLLKGRPASERVMSGLSASLVNSANLGIPIATYVLG +DAALAAPALIFQLAIYTPVYVAVMDWATTHEAAARASSAGAAHDAGAPAPRTVRPRNPVL +AQLRQTATNPMILGAFGGLLLSFTGWTLPGPLMTSVELIGGLSIPAMLIAFGMSLAGSRP +LARDSGRRADVLLASAVKLVVHPLVAWMIAQFVFGLDARRVFVAVVLASLPTAQNVYVSA +VRYRAGETVSKDTILVTTIVAIPAMIAVALLLA +>PROKKA_01816 +MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV +LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG +DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTTAGRRRAVRRSPGRAVADQVRHTV +TNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR +RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL +RVSKDTILVTTIVAIPAMIAVALLLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001543.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001543.fa new file mode 100644 index 0000000000000000000000000000000000000000..4a6564d52e9d63430f347d9e9a9dc274575fac8e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001543.fa @@ -0,0 +1,10 @@ +>PROKKA_01909 +MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER +>PROKKA_01605 +MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER +>PROKKA_00949 +MAKDKDVRPIIKLKSTAGTGYTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER +>PROKKA_00889 +MAKDKDVRPIIKLKSTAGTGYTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER +>PROKKA_01829 +MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001546.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001546.fa new file mode 100644 index 0000000000000000000000000000000000000000..ca48669ca88256a023bddb15a6d5383472e3ff09 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001546.fa @@ -0,0 +1,40 @@ +>PROKKA_01918 +MENQQTGQAADRGTIDTREGFTGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEEGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMSALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGERVDPEHTPLR +>PROKKA_01614 +MENQQTGQAADRGTIDTREGFTGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWTAMDWLEERLSTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMPALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGERVDPEHTPLR +>PROKKA_00942 +MENQQTGQAADRGTIDTREGLKGNYVQSGAEFTRDTNYITDRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRAIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERLQENYFARFPDYPRGITVPAVVDVPTGDVVTNDYPQMTLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIKRVFTEVNNGVYRCGFAGSQEAYDAAYDR +LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMPALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGEEVEPAHTPLR +>PROKKA_00877 +MEDQQTGQAADRGTIDTREALTGNYVQSGAEFTRDTDYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDAGGKDPVLGTERLQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWAAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNKLTEMPALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPDLSGWTTEHGRADLGGDPW +GGGTAPGPVRDDERVDPEHTPLR +>PROKKA_01838 +MENQQTGQAADRGTIDSREGLKGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNKLTEMPALWG +YARDLFQTPGFGDTIDFVQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGERVDPEHTPLR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001556.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001556.fa new file mode 100644 index 0000000000000000000000000000000000000000..8729e905fff7d27467fb5772d687c7dab111e67f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001556.fa @@ -0,0 +1,25 @@ +>PROKKA_01930 +MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDAM +VRTGLWDEIRRRGWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDGD +VAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSARTP +LPHTWDLDTVRRG +>PROKKA_01626 +MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDAM +VRTGLWDEIRRRGWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDGD +VAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSARTP +LPHTWDLDTVRRG +>PROKKA_00928 +MHLIPRTLWVLARARRRPPLSIWDSASLPMRALPTDVDIAGHVNNGQYFGLFDLGRFDLM +ARSGLMRAVRRRGWLPVVQAEQIAFRRSVTLGTAFTLETRIIGLDERAVWFEQRVVVAGD +VAVRGYVCTRLRGRDGTPVGNDEVRALAVELGHDPAAEPELPGWLHDWREQVALPSARTP +LPHAWGR +>PROKKA_00862 +MLHLLPRTALVVVRARRRPRLGIWEASTLPLRALPTDVDFAGHINNGQYFGLFDLGRFDL +MVRAGVWDGAKRRGWLPVVQAEQIAFRRSVTLGTRFTVESRIIGLDERAVWFEQRAVVDG +DVAVRAFICTRLRAKDGTPVSNEDVRDLARELGHDLAAEPVLPEWLHGWRSDIALPSART +PLPHAWGTPAPAGV +>PROKKA_01849 +MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDAM +VRTGLWDEIRRRHWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDGD +VAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSARTP +LPHTWDLDTVRRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001558.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001558.fa new file mode 100644 index 0000000000000000000000000000000000000000..26ef3796da187f456e7a6a353571969bee4ec48d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001558.fa @@ -0,0 +1,45 @@ +>PROKKA_01933 +MSAAQPAGVTPPPASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP +VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK +YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSAVTGTAVSAITKIATNVYAVFGLL +VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD +VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAVLGLAAGGWSDFLWVVVSYSVL +NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN +ARWINALIASDLKGMERRQSSLLERLRPAAWRSDAHGKDEDRAPTDGGDDDGPATDEVTG +GAGAAPGR +>PROKKA_01629 +MSAAQPAGVTPPSASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP +VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK +YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSAVTGTAVSAITKIATNVYAVFGLL +VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD +VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAILGLAAGGWSDFLWVVVSYSVL +NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN +ARWINALIASDLKGMERRQSSLLERLRPAAWRSDAHGGDEDRASADGGDDDGPATDEVTG +EAGAAPGR +>PROKKA_00926 +MSAAQPVGAAPTPSAAGPVSDWDIRRPHRMWPRMLVIVLTLAGLVLLVQFFQGIASIAAP +VFLGLNLVIVAYPLQAWLIRRGVHPVLGAAASVVVVVAVLGAFVGMIVWSGLELVAELPK +YSGQFQQIVLDVSNWLNARGVTPDMVSQQLASIDVSAVTSAAVSALTKIATNLYAVLGLL +VTVVMGMFFLAMDSMDVERRVRLLSTARLELGEALIDFAHGVRRYWVVTTVFGLIVAALD +VIALVLIGVPLALVWGVLSFLTNYIPNVGFIIGLIPPAILGLAAGGWTSFLWVVVSYSVL +NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN +SRWVNSLIASDLKGMERRQHSLLERLRVGRRGEGRAGKADAEAVAGADVAAAGVEAALDV +DDAAAGARRPEAAPTGSTLTEPARTEPGPAAPADAADGPGLTGGAAPAPGR +>PROKKA_00860 +MSASAPPAVTGTSTPATEWDNRRPHRMWPRMLVIVLTLAGLVVLVQFFQGIASIAAPVFL +GLNLVIVAYPLQAWLIRRGLHPVLGAATTVVVVCAVIAAFLGMIAWSGMELLTELPKYAG +QFQQIMHDASQWLSDHGVTPDMVNQQLASVDMSAVTGAAVSALTTIASNLYAVLGLLITV +IMGMFFLAMDSMAVERRVRLLSTARHELGQALIDFADGVRRYWIVTTVFGLIVAVLDMVA +LVIIGVPLALVWGVLSFLTNYIPNVGFIIGLVPPAILGLAAGGWPAFLWVVVSYSVLNFV +LQSIIQPKVAGDAVGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLVKAVLIDADPNSRW +VNSLIASDLKGMERRQSSMLERLRLPRELIRHGGSTASHATAADVQGDDDVAPERTAEDA +APAQDRRRVRAAAQEARLEGPPPSTLRAPRVDLPGEPEPATADGSAPPEAGAAPGR +>PROKKA_01852 +MSAAQPAGVTPPPASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP +VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK +YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSTVTGTAVSAITKIATNVYAVFGLL +VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD +VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAVLGLAAGGWSDFLWVVVSYSVL +NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN +ARWINALIASDLKGMERRQSSLLERLRPAAWRSDAHGGDEDRASADGGDDEGPAADEVTG +EAGAAPGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001583.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001583.fa new file mode 100644 index 0000000000000000000000000000000000000000..512c4735d8944a97d101b4150e8e6f0380a3ce34 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001583.fa @@ -0,0 +1,30 @@ +>PROKKA_01982 +MTAAPAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR +ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD +PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG +YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQAGRVPA +GG +>PROKKA_01676 +MTAAPAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR +ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD +PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG +YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQAGRVPA +GG +>PROKKA_00876 +MTARPPTPPAEPEPGRRRAPGHAVILDWLEGELRSGRIQVGDKLPSERTLAERFGMSRSS +VREAGRVMDAMGLVRSATGSGPRAGAIVVSEPSAALAWALRMHVATRALPVADLVTTRVL +LETEAALEAAEHDVPGRGAILATAHAHLDRMDVPDFPAREFHRLDAEFHVLLSTLSGNVV +LETILRSLREATIGYVEEAMAGVEDWGAVRDELQRQHRDILAAAVERDGPRAAQAVREHI +HWFSRFTTAGPDAAGG +>PROKKA_00811 +MTAAPAYTIVLDWLEAELRSGAVAVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR +ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD +PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG +YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQTGRVPA +AG +>PROKKA_01908 +MTAAPAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR +ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD +PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG +YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQAGRVPA +GG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001589.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001589.fa new file mode 100644 index 0000000000000000000000000000000000000000..788c815fc8ec3b9b46ab197d6ec981027ed71fc4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001589.fa @@ -0,0 +1,46 @@ +>PROKKA_01991 +MTQSTPEPTPTVTEHDFTVRENRPGKVLAVHLNYPSRIAQRGRPPQAPGYFLKAGTSLAR +SGDTIERPAGTELLAYEGEIALIIGRTARRVSPEEGWSHVSGITAANDWGLYDLRHADKG +SNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIVQDDTTEGLVFPFGRLVADLS +QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVDSEHALAPF +GAQPQVDDVQREEAWGSREAAGLAPQAEAASSSAVDENGHWVASAPQPDRSLLTPELRAK +IDAIAVATLTAQLQKRGVQNATIDGPRPVHRGRRVLGYAKTLRYVPKREDLAKEFGGGFN +AQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDSAAVAEVG +LQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSLLQEVVDD +AYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA +>PROKKA_01685 +MTQSTPDPTPTVTEHDFTVRENRPGKVLAVHLNYPSRIAQRGRSPQAPGYFLKAGTSLAG +SGDTIERPAGTELLAYEGEIALIIGRTARRVSPEEGWSHVSGITAANDWGLYDLRHADKG +SNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIVQDDTTEGLVFPFGQLVADLS +QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVDSEHSLAPF +GAQPQVDDVQREEAWGSREAAGLAPQAAAPSSSAVDENGHWVASAPQPDRSLLTPELRAK +IDAIAVATLTAQLQKRGVQNATIDGPRPIHRGRRVLGYAKTLRYIPKREDLAKEFGGGFN +AQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDSAAVAEVG +LQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSLLQEVVDD +AYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA +>PROKKA_00866 +MDENGHWVASAPQPDRSLLTPELRAKIDAVAVATLTAQLQKRGIQNATIDGPRPIHQGRR +VLGYAKTLRYVPKREDLFKEFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLAL +RAQVNGANAVITDGGIRDSAAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQ +PGDVIVGDDDGVVVIPPSLLQEVVDDAYEQELQDAWAYEQVKAGHPVDGMFPPNAEWKAT +FDEYRKTLPDAPAPEGDA +>PROKKA_00804 +MTQNTSPATPSVTEHDFTVRQNRPGKVLALHLNYPSRIAQRGRSPQFPGYFIKAGTSIAR +SGDAVERPAGTELLAYEGEIALIIGRTARRVRPEEGWSYVSGITAANDWGLYDLRHADKG +SNVKNKSGDGYTPLGPAVIAAANLDPAALRVRTWVNGALVQDDTTEGLVFPFGQLVADLS +QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPTAPGAPSTGRLITHVTDSDIPMADY +GHGPRVDDLQREEAWGSREAAGLAPVEDAPAQDDAAPASTAVDENGHWVASAPQPDRSLL +TPELRAKIDAIAVATLTAQLQKRGIQNATIDGPRPIHQGRRVLGYAKTLRYIPKREDLFK +EFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDS +AAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVVPPSL +LQEVVDDAYEQELQDAWAYEQVKAGHPVDGMFPPNAEWKAKFDEYRKTLPDAPAPEGDA +>PROKKA_01917 +MTQSTPDPTPTVTEHDFTARENRPGKVLAVHLNYPSRIAQRGRSPQAPGYFLKAGTSLAR +TGDTIERPAGTELLAYEGEIALIIGRTARRVSPKEGWSHVSGITAANDWGLYDLRHADKG +SNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIVQDDTTEGLVFPFGQLVADLS +QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVESEHALAPF +GAQPQVDDVQREEAWGSREAAGLAPQAAAPSSSAVDENGHWVASAPQPDRSLLTPELRAK +IDAIAVATLTAQLQKRGVQNATIDGPRPIHQGRRVLGYAKTLRYIPKREDLAKEFGGGFN +AQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDSAAVAEVG +LQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSLLREVVDD +AYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001622.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001622.fa new file mode 100644 index 0000000000000000000000000000000000000000..abd4535e1bc09a29a250c8ddc39dce184ff616d2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001622.fa @@ -0,0 +1,36 @@ +>PROKKA_02036 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLARLRRLATQAQEAAARRV +ERTLERRLRSPGAPAFPDDDADGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL +DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPEDEKG +>PROKKA_01743 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV +ERTLERRLRSPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL +DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPADPRD +>PROKKA_00780 +MDVQQFFADLSDVPWLLTTLDLIGIFFFATSGALLASRKEFDLVGSMALALLAGLGGGFT +RDILLDRGLPASLENPIYLAPPVLVSLLVYVKALHPNRLNLTITLFDAGGLALFTVSGVL +IAHSMDVHPVSTVVVAMVAALGGGVLRDIVANEVPSIFDPRGVYVMPTFVGATVATIAAM +NGVLNAFTGFLIAFLIFAVRMLAYRYQWRLFGADISQDKESLDRLRRLATQAQDAAARRV +ERARERRLRSASGPGGMDVGEAEAIADRAVHHPPAPAGYHYDAVEDAYTRDHAFDDDGEP +GSASYGPRQEYEDQVRVDEYDPETQTITVIDPASRQQVRLDPATGVMDVTDLRTGRTRSY +DDPEHDWIADDAEDDARG +>PROKKA_00747 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPVLVSLLVYVKLIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV +ERTLERRLRAPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL +DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPEDSRD +>PROKKA_01971 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV +ERTLERRLRSPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL +DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPADPRD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001655.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001655.fa new file mode 100644 index 0000000000000000000000000000000000000000..393d0c178cc937d8fa80fad56fa3d0a011c6852a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001655.fa @@ -0,0 +1,15 @@ +>PROKKA_02117 +MSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREVVADLKRGARI +TTFLPALAEREATRRLQAATPAHEAMAVAA +>PROKKA_01825 +MSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREVVADLKRGARI +TTFLPALAEREATRRLQATTPAHEAMAVAA +>PROKKA_00663 +MSINTVHHLPAAPSPLMQRHVLKRVEETLARRFEGVATAEAVRATVREVASELKRSARMT +MFLPALTEREAARRLQAGAPAHEPLAAAA +>PROKKA_00580 +MTATLTTQHHMPVHPDTTMQQRVLERIAGTLIRRFDGSVPAADVRTTVAEVTAELEAEAR +LTTYLPALTEREALNRLEAMAAAPAHMTITHARHAA +>PROKKA_02055 +MVRQPKEVLTVSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREV +VADLKRGARITTFLPALAEREATRRLQAATPAHEAMAVAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001666.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001666.fa new file mode 100644 index 0000000000000000000000000000000000000000..6ed25bc91bb22ff991a7ca948c63bb08b6e85108 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001666.fa @@ -0,0 +1,48 @@ +>PROKKA_02130 +MSSTLATGAYRRAVDRAHESLDSVRLSLAPSSSTAPTGADQGLRAALQGLRREVRESWLR +SLGALTPAGSALDAGASAAAPAVPGQTDPATLADDDLAAARREQRLAVALPVVRRMLIQP +AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP +TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLLSTVDAVH +AAWRDLPAPSRGRPRGTVPTPGPSAPPSASPGPSPAGAPHRHDEAAGLLRVTGHLPPTLD +GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRSAPGDAPARAISLRAEVHRL +RRALRDVGAPVELLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAVGPVLPRSASPGV +ASIRAELGEALREAVAQDADVDQLWAYLGRPEARDDVELWGAALRLLPTDSPRRALAVAT +LERIERDLA +>PROKKA_01838 +MSSTLATGAYRRAVDRAHESLAAVRLSLAPSSPTAPAGADQGLRAALQGLRREVRESWLR +SLGALTPAVPGQTDPATLSDDDLAAARRDQRLAVALPVVRRMLIHPAAEAGMLAAIGNAR +GHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAPTQVSRGEHLSPRVH +PWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVHAAWRDLPAPSRGRP +RGTAPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLDGVELTGRHAEILTL +LAWHGPGLTGAELEVALYPEETAGPRPAPGDSPARAISLRAEVHRLRRALRDVGAPVALL +SRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSTSPGVASIRAELGEALREA +VAQDADVDQLWAYLGRPEARDDVELWGAALRLLPTDSPRRALAVATLERIERDLA +>PROKKA_00650 +MSSTLATGAYRRAVDRAHESLDSVRLSLAPSSPTAPTGADQGLRTALQGLRREVRESWLR +SLGALTPAGSALDAEAAATAPAVPGQTDPATLADDDLAAARREQRLAVALPVVRRMLIHP +AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP +TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVH +AAWRDLPAPSRGRPRGTVPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD +GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRSAPSDAPARAISLRAEVHRL +RRALQDAGAPVELLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSVSPGV +ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGVALRLLPADSPRRALAVAT +LERIERDLA +>PROKKA_00566 +MSSTLATGAYRRAVDRAHESLAAVRLSLAPSSPTAPTGADQGLRAALQGLRREVRESWLR +SLGVLTPAGSALDAGASATAPAVPGQTDPATLSDDDLAAARREQRLAVALPVVRRMLIQP +AAEAGMLAAIGNARGHLLWVEGDRTAVRHAEALGFVAGADWSEASMGTSAPGIVLATGAP +TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQTTVDAVH +AAWRDLPAPSRGRSRGTVPTPGPSAPPSVSPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD +GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETVGPRSAPGDAPARAISLRAEVHRL +RRALRDVGARVELLSRPYRLVGAVHADLLCAREALRAGDLDRALHAAAGPVLPRSASPGV +ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGAALRLLPADSPRRALAVAT +LERIERDLT +>PROKKA_02068 +MSSTLATSAYRRAVDRAHESLAAVRLSLAPSSPTAPAGADQGLRAALQGLRREVRESWLR +SLGALTPAVPGQTDPATLSDDDLAAARRDQRLAVALPVVRRMLIHPAAEAGMLAAIGNAR +GHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAPTQVSRGEHLSPRVH +PWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVHAAWRDLPAPSRGRP +RGTAPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLDGVELTGRHAEILTL +LAWHGPGLTGAELEVALYPEETAGPRPAPGDSPARAISLRAEVHRLRRALRDVGAPVALL +SRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSASPGVASIRAELGEALREA +VAQDADVEQLWAYLGRPEARDDVELWGAALRLLPADSPRRALAVATLERIERDLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001683.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001683.fa new file mode 100644 index 0000000000000000000000000000000000000000..213f0a09eba7fa0793410ff6520882c440159edf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001683.fa @@ -0,0 +1,43 @@ +>PROKKA_02149 +MRRPSLPSLSRLPVRRLLRGAAVAAGVGLVGLPLTVAAGLTGVDMVKRGGRVRRPAPNPG +VFDAHVEGSELRIFTSGEDLYKEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRAAA +RGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMVVD +DEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPDTW +DPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGVDV +QVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANVDR +LSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPLRP +LL +>PROKKA_01862 +MAAGVGLVGLPLTVAAGLTGVDMVKRGGRVRRPAPNPGVFDAHVEGSELRIFTSGEDLYK +EMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRAAARGVEVYVSYDGFGNLVVPPRFY +RQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMVVDDEVGFAGGFNIGDDYARLWRDT +HVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPDTWDPRVTVAANQPPLLVYPIRLSY +LDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGVDVQVMVPEDSNHIVADWASRGFFG +KMLEAGITILLYRASMIHAKTATVDGIWSTVGSANVDRLSLGFNYESNVVVVDRDFAARM +EEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPLRPLL +>PROKKA_00613 +MSPLPASPLHRIPVRRIVRGAALAAGTGLVGVPMAVAAGLTGVDMVKRRGRRRRPAHNPG +VFDAPVKDCHLRIFTSGEDLYEEMLAAIDSAERIVKFETYIWKADPTGQRFIEAFNRAAA +RGVEVYVSYDGFGNLVVPRAFYRQLDPRIRVFRLPAFARPFWRGPVRNTGFNHSKIMVVD +DEIGFVGGFNIGDDYATFWRDTHVCERGPAVWALDQSISIKWNAHHREGEQMSWRPPESW +DPRVTVSANQPPLLVYPIRLTYLEAIQRAQHRILINTPYFIPDQQVLQALLHAARRGVDV +QVMVPRDSNHIVADWASRGFYAGMLEAGITILLYEASMIHAKTATVDGIWSTVGTANIDR +LSLGFNYESNVVVVDRDFAARMEEIFAIDAEQSERVESPRWQDRHGVARMVERLLVPLRP +LL +>PROKKA_00537 +MGYALRRAAVAGTTAFVGVPLATAVAVSAYDAFKHRGRKLRPAERPGTFQAQVGPDALTI +YTAGDDVYDAMIQAIDDARETVKFETFIWKDDATGQRFVDALNRAAARGVQVWASYDGFG +NLLIPPSFYRQFDPRVRVFRLPAFARPLWRGVVRYSGFNHSKILTVDGRVGFVGGYNVGD +LYAAHWRDTHLRVEGPAVWGLEHSLSVLWNEGYTDMAEMPWTRPEEWEERTVVAANLPTQ +LVYPIRNTYLNAIARAQDHIYISTPYFVPDRQVLDALKEAARRGVDVQVLVPKDSNHVVA +DWVSRGFYSEMLDAGITILLYAAGMIHAKTATIDGRWATVGTANIDRLSLSFNYETNVSV +VDRDFAARMEDVFRADAARSERIQSPRWKDRHGLARVVEKLLVPLRPLM +>PROKKA_02092 +MHRPPLPSLSRLPVRRLLRGAAVAAGVGLVGLPLTVAAGLTGVDMVKRRGRVRRPAPNPG +VFDAHVKGSELRIFTSGEDLYEEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRAAA +RGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMVVD +DEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPDTW +DPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGVDV +QVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANVDR +LSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPLRP +LL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001684.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001684.fa new file mode 100644 index 0000000000000000000000000000000000000000..c94e53aed09ba4f2c02bbc1a63947783bf1dd641 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001684.fa @@ -0,0 +1,35 @@ +>PROKKA_02150 +MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH +PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT +VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT +VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT +TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA +IELVRMRSEVSAAWTEMRRSTDPR +>PROKKA_01863 +MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH +PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT +VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT +VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT +TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA +IELVRMRSEVSAAWTEMRRSTDPR +>PROKKA_00612 +MKPAGALALEFRADSFDHPGGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH +SVPVDHRAVVQARVVHTDGADVHVQTRLLLPEVKDESGDPVVATSSLVVYSAEEDGARVT +VPAWVPSTPGQIERDEQASRSTVARRAVERGMARLPFPSPGQAPEEMSTLAFLAPASEAT +VGGTMNAGAILRWLDEAAAVCAARWTGHESVVAVFGGGVRFVRNILVGDLVRVDALLVNT +TERSMQVALRVYAGRPTGVQPRLVAHSIAVMVDVSAEDKAQPVRQYVPESEGARSLQEAA +VQLVRLRSEVGAAWTETRRSPESR +>PROKKA_00536 +MMRSGALSLDFRADSFDHPSGLVDAGTAIGWIDKVGYAVAASWSGTYVRARYMGTMQFRH +PVPVDMRVTVQGRVVRTHGAAVHVQLRLLLPEVLDDDGRPVVSTSTLSVYYAEEDGQMLQ +VPEWTPSTPDQIERDERARVSSVERRGIEQVMARLPFPEPGQEHEEMTTLAFIAPMAEAS +VGGTVAAGAVMRWLDEAAGVCAARWTGHENVVAVFAGGVRFVRPVKVGDLVRVDALLVHT +SERSMHVALRVHAGPRHQRDHRLVAHSIAVMVDVTREGRAESVRPYAPGSPAAHRLEESA +VELVRLRSEAGAVWSDPS +>PROKKA_02093 +MRPPGALALEFRADSFDHPTGLVDAGTVVSWIEKAGYAVAASWAGTFVRARYMGHTQFRH +PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEDGVPVT +VPAWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT +VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT +TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEGQAQPVRQYVPESESARRLQETA +IELVRMRSEVSAAWTETRRSTDPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001685.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001685.fa new file mode 100644 index 0000000000000000000000000000000000000000..dcecda151b5e822975c14fc901e4104dd2bc2f2f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001685.fa @@ -0,0 +1,25 @@ +>PROKKA_02151 +MTAFDRFPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPDDVTSGAARA +LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVLASRAGSLRRDA +AVDRTLVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA +ELALEQLAIRLDRPGLRVSLEG +>PROKKA_01864 +MTAFDRLPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPDDVTSGAARA +LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVLASRAGSLRRDA +AVDRTLVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA +ELALEQLAIRLDRPGLRVSLEG +>PROKKA_00611 +MTAFDRLPLPAEPQTPHDRLRRRVAAAVAERGEAAVAGLAVRLLTGSVTPADVTSGAARA +LTGDDGDLTAGATGALALGHAWHRSALPALTSALSAPEPDVRSAAHLVLAARAGSLRADV +AVDRALVDAVRAGCADPDPQVRASAASALGALAGPQDLEAALPVLTGMVMDVDADLATAA +ELALDHLAERLDRPDLRVGAEG +>PROKKA_00535 +MTSRDLPLPVEPQTPHTRLARRVEAAVSARGEAAVAGLAVRLLTGAPTPEDVTSGAARDL +IGDDGELTPGATGALALGVVWHRGAAGALAAALDAPEPEVRAAALLVLAARADRLRADAQ +AGRALVEAVTARASDADPQVREAAASALGALARAEDLSAVEPVLSALVMDVDPELATAAE +LALAHLAARLDRPELDPTPQA +>PROKKA_02094 +MTAFDRLPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPEDVTSGAARA +LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVIASRAGSLRRDA +AVDRALVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA +ELALEQLAIRLDRPGLRVSLEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001692.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001692.fa new file mode 100644 index 0000000000000000000000000000000000000000..7177cef96265090eb3798b2d53263bd34445f2dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001692.fa @@ -0,0 +1,30 @@ +>PROKKA_02163 +MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD +VDFASGAFTAIMGPSGSGKSTLLHCLAGLDARTSGSVRIGGTEITGLDDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRALGLADRLGHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELVDPTVESVTAALTALSAPAEGGVR +>PROKKA_01877 +MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD +VDFASGAFTAIMGPSGSGKSTLMHCLAGLDAPTSGSVRIGGTEITGLDDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRTLGLADRLGHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELVDPTVESVTAALTALSAPAEGGVR +>PROKKA_00594 +MSTTADSHSAHSTPPGAGASGPGMPSSSTTTTTAPAASARALTKTYGRGDAEVHALRGVD +VDFAAGAFTAIMGPSGSGKSTLMHCLAGLDTPTSGSVVLGGTEITGLGDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRKPDRAWLDEITATLGLTDRLKHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDSATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELLDPTVESVTNALAALSAPGAADAAGTFDAPADGGR +>PROKKA_00517 +MDITSPRSAAHDAGAHALATPLAHAAAPPAPAVSARGLTKTYGRGDAAVHALRGVDVDVE +TGRFTAIMGPSGSGKSTLMHCLAGLDTPDAGVVTLGDTVITGLSDAALTRVRRDRVGFVF +QAFNLVPTLTAEQNIVLPMELAGRTPDRAWLAEIVDRLGLSDRLAHRPHELSGGQQQRVA +VARALLTRPDVVFGDEPTGNLDSATGAQVLDLLRRATRETGQTVIMVTHDPVAAAAADRV +VLLADGALAGELHAPTAERVAEALTALQQGRPLPQGRPLPQDGGR +>PROKKA_02108 +MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD +VDFASGAFTAIMGPSGSGKSTLMHCLAGLDAPTSGSVRIGGTEITGLDDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRTLGLADRLGHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELVDPTVESVTAALTALSAPAEGGVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001713.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001713.fa new file mode 100644 index 0000000000000000000000000000000000000000..28831d2c4686e4c1a97c42ff81a012856053a22d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001713.fa @@ -0,0 +1,30 @@ +>PROKKA_02196 +MSSTPTDADHHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV +LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA +LRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLSVAPEAV +VGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA +VASAPVPRDAVVLTLPPVREN +>PROKKA_01909 +MSSTPTDADHHGPGPAPDPAHLDDLPPATLVARGLTLRGSRGPVFGSLDLVLPPQTHLAV +LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA +LRARTAVAHTTDVVELEPALTAAEVVDERCLTDGVRRRAGRARFALLADAVRLTVAPEAV +VRELSAPDRALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA +VASAPVPRDAVVLTLPPVREN +>PROKKA_00548 +MSSTPTDADHHGPGPVSVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV +LGTQGSGRSALLLALTGRLRGVRGELVLTGGPVDVALDGPERPAARAYRPLIDATRHPYA +LRARTAIAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLTVAPEAV +VGELSAPDRALLAAVVACLRPARLVTFDDVDATLTLDELVALHAALDVLKDHGHPFAVSA +VASAPVPRDAVVLTLPPVREN +>PROKKA_00479 +MTEDQTPAPIETDDVVAERAPEPAPGGSHQVGRALTARGLTLRSIRGTVFGPVDVDLPPG +VPGAVLGTQGSGRSALLLALVGRLQGVGGELTLGDMDGIRHPHRLRRATTVARITDYVEL +EPLLTIRECIDEHCLAEGISRRTGRKRFARLEAAVGFHPDHGDQVSSLPVEDRTILTCML +ACLRPADVIVYDDIDSSLTRPQLEHVYRVLETLGRLGHRFVVSALTSAPVPRGAVVVELP +TPGHDDLPAALPTRPSLED +>PROKKA_02140 +MSSTPTDADHHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV +LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA +LRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLSVAPEAV +VGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA +VASAPVPRDAVVLTLPPVREN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001726.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001726.fa new file mode 100644 index 0000000000000000000000000000000000000000..dd2ccf5fbb911752c1f3374a971f8a250c51a8ff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001726.fa @@ -0,0 +1,55 @@ +>PROKKA_02241 +MTSGPPSPALPAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLL +HVLTGRITPDVGRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAA +AALAEAPDDAGAGHRYSTALERAHLYDAWDAGRRVDMDLEGLHACTDREHPLTSLSVGQR +HRVRLAVTLGSRPDLLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDRALLRAVCTD +IVDLDPSQDGRPRRYSGGYAGWAKGRRRARAAWEQEYAEQNAERERLELAVEDAREQMQG +SWRPPKGTGKHQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADMPDGDPRDG +ADAAAGTAGGPGTAGDDVLLTADAVRVAGRLEQPMGAALVPGGRVLVTGPNGAGKSTLLR +VLAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVGADEAGVDDLGR +PLPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALV +DEMTEALQVTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV +>PROKKA_01943 +MTSGPPSPALPAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLL +HVLTGRITPDVGRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAA +AALAEAPDDAGAGHRYSTALERAHLYDAWDAGRRVDMDLEGLHACTDRERPLTSLSVGQR +HRVRLAVTLGSRPDLLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDRALLRAVCTD +IVDLDPSQDGRPRRYSGGYAGWAKGRRRAQAAWEQEYAEQNAERERLELAVEDAREQMQG +SWRPPKGTGKHQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADMPDGDPRDG +ADAAAGTAGGPGTAGDDVLLTADAVRVAGRLEQPMGAALVPGGRVLVTGPNGAGKSTLLR +VLAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVGADEAGVDDLGR +PLPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALV +DEMTEALQVTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV +>PROKKA_00715 +MTLTPPHAPALPAGASAHIRAECITLTLGDRTVLDQADVTVSAGSRLAIVGENGRGKTTL +LHVLAGTLAPDAGTVTRAGTLALVEQDLDADDDRTVGDLIHDAVGESLAVLDRLEAATRA +LAEGRPGADDDYARALETATALEAWDAERRIDVALEGLSACTDRTRPLNSLSVGQRYRVR +LAVVLGSAVDLLLLDEPTNHLDAGALEHLTRALREHPGGVAVVTHDRALLKDVAETFLDL +DPTSDGRPRQYAGGYAGWEKGRSAERAAWEQAHEQQVAEHAALAEAAEAARGRLQDRWRP +DKGTGKHQRATRAAGVVQAFNRRVRDLEAHEVTVPEPPRALAWPASSTRAARPLLNAEGV +DVAGRLRGPVSADLTGGDRLLLTGPNGAGKSTLLHVLAGRLDPTAGRVLRHTGARIALLT +QEAPAWNPRHTARQAFEVHLHRRGLLADDDGGAPPLASLGLLEPRSMDAPVGRLSQGQQR +RLHLALCLAERPDLLMLDEPSNHLSATLVDELTEALRATRSAVVVATHDRQMLRDLSDWP +RLELTAEAVAR +>PROKKA_02173 +MTSGPPSPALPAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLL +HVLTGRITPDVGRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAA +AALAEAPDDAGAGHRYSTALERAHLYDAWDAGRRVDMDLEGLHACTDRERPLTSLSVGQR +HRVRLAVTLGSRPDLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDRALLRAVCTDI +VDLDPSQDGRPRRYSGGYAGWAKGRRRARAAWEQEYAEQNAERERLELAVEDAREQMQGS +WRPPKGTGKHQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADRPDGDPRDGA +DAAAGTAGGPGTAGDDVLLTADAVRVAGRLEQPMGAALVPGGRVLVTGPNGAGKSTLLRV +LAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVGADEAGVDDLGRP +LPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALVD +EMTEALQVTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV +>PROKKA_02213 +MPTSRSLRSCVWNGTPQGHAAHIRAESIHITLGDRHVLNGVDVTVSVGSRLAIVGDNGRG +KTTLLHLLAGILQPDSGVVTQAGSLVLVKQDMATEGDRTVGDLIAEATGPSKSALEALDA +TSAALAEGDDAADAYSAALERATLLDAWDAERRVDIALEGLNACSDRDRVLSTLSVGQRY +RVRLAVALGSTPDLLLLDEPTNHLDAAGLSFLTERLRDHAGGLALVSHDRALLRDVATTF +LDLDPTRDGRPRTYAGGYQGWVEGRQRERVSWEQDHAAQVARHAQLTRAAAEARSRLSQG +GWRPDKGTGKHQRATRAAGVVQAFNRRVEDLERHEIDVPEPPLRLAWPKSSARRGMSIVN +ASMLTVERRLDTPVSIGVNGGDRLVVTGPNGAGKSTLLAVLGQRLVPTTGYVQVNPSARI +ALLSQEVPDWDRTSPAHVAYETYLGKLGCRSQAPSLGSLGLLEASATSTPVGRLSQGQQR +RLHLALCLAQDPDLLLLDEPTNHLSSSLVDDITTELLQTPCAVIVATHDRQMLDDLADWP +HLDLDPKDMP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001749.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001749.fa new file mode 100644 index 0000000000000000000000000000000000000000..88da44b30f31cbdc886c217b965c04407ac16388 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001749.fa @@ -0,0 +1,60 @@ +>PROKKA_02301 +MDPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLSADMADIFEIANSLP +NVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLM +TALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAI +GAIVLYLGMFGAYRAGDDLAGWTSAQTVVLAGGHTLGVVLQAVILFLPLRGLGLGLRPRF +GWKGIGLRDTGRIAGYTLITMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSAEMA +QAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFT +VPLMFCLAGVVVLAGPLGRVFGSTAETAMVAGVAVGSVLLALALSIPFRSGSFYLLRVFY +AAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMALWVAVASSVSYVYQFVLTHVLTVR +RFGDYGLASVLRAHVQTGLAALAAAAAGAVVVWLLGGYTGGFAWNSIGTALLTCAVAAVA +MGPVYLMVLRAMRFPELDDALRPLVARVPALGRLLRVG +>PROKKA_01994 +MDPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLSADMADIFEIANSLP +NVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLM +TALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAI +GAIVLYLGMFGAYRAGDDLAGWTSAQTVVLAGGHTLGVVLQAVILFLPLRGLGLGLRPRF +GWKGIGLRDTGRIAGYTLITMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSAEMA +QAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFT +VPLMFCLAGVVVLAGPLGRVFGSTAETAMVAGVAVGSVLLALALSIPFRSGSFYLLRVFY +AAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMALWVAVASSVSYVYQFVLTHVLTVR +RFGDYGLASVLRAHVQTGLAALAAAAAGVVVVWLLGGYTGGFAWNSIGTALLTCAVAAVA +MGPVYLMVLRAMRFPELDDALRPLVARVPALGRLLRVG +>PROKKA_00436 +MASPDPSAHRGAPLPSALGAWHRRPQPPARPEPAPAPGPRPAASGLPTVEEVSAGGVVVR +EHDGGLEVAIIARYNRGGRLEWCLPKGHPEGVEDHRQAAVREVEEETGIAGDILEPLGAI +DYWFTVSRHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERRI +VDLARQVVDRHFPRAPPGAPAPDPPPRTRGSSDHDWVTLEQQPLPAPRAGTPPAPAVADE +EPTTADPAPATDPEAPAREDRPDETPEGERRAGRSTAIMASGTLISRVLGLVRAMLVTVA +IGLSTDMADIFEIANSLPNVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGT +LVMLGGTLVVMAVAAPLMTALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNAN +GRFGAYMWAPVLNNVVAIAAIGLYLAMFGAYRAGEDVAGWTSTQTLVLAGGHTLGVILQA +VILFLPLRGLGLGMRPRFGWKGIGLRETGRIAGYTLVTMMVTNVVLLLCQRYVTSATEAR +DRGELRIPGTEAWSTEMAQAAIPGVAAYNMAMLIAVLPHSVFVLSLATVLFNRLARAMTR +QDMPAVRRTTAQGLRAFTVPLMFSLAGIVVLAGPLGRVFGSTAETSMVAGIAVGAVLLAL +ALSIPFRSGSFYLLRVFYAAEDAKVPMVVQVSSSLLMLLLSWAGAMLLPLWSMALWVAIA +SSVSYVYQFALTHVLTVRRFGDYGFASVLRAHGQTGLAALAAAAAGAVVVWLLGGYTGGF +AWETIVTALITCAVAAAVMAPVYVVTLKLLRFPELDDALRPVVSRVPALGRLLRVG +>PROKKA_00388 +MSSRTAPRRALPADDAPRPKEVEDVVLPASDPEAPAQAQEEVPEGERRAGRSTAIMAAGT +MISRVLGFVRAALLTIAIGTTVGTVADIFEVANSLPNVIYLLLVGGVFNVVLVPQLIKHA +KDADRGADYTSRLMTLAVLVMLAATVLVTAAAAPLMAALTRGWSPEMLQLGTVFALWCLP +QMFFYGMYALVGQILNANGRFGAYMWAPVLNNVVAIAAIGLYLVMFGRYSGGDLLGRWTP +EQTLVLAGGHTLGVILQALILFLPLRGLGLGLRPRFGWRGMGLRHTGRIAGYTLFTMAAS +NIVLLLSHRYINGASAAREDPSVRVPGTEGWDPAMADALIPGLTAYNQAMLISVLPHSVF +VLSLATVLFNKLARSMAAGDHAAVRETTARGLRTFAAPIMFSLAGVVVLAGPLGRLFGST +AESAQVTGMAVGAVILLMSLSMPFRSGSFYLLRVFYAAESARIPMVVQVTTSLLTLAVTA +AGAYLLPLWAITYWAALASVVSHAFQFFFAHVLAVRRFGDYGFTHVLAAYATTGAAGVVA +GAAGAVVAWLLGAYSGGWAWGSILSALVTCAVVGLVMAPVYVVALRVLRFPELASAAAPL +ARRVPALGRLLGAR +>PROKKA_02242 +MDPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLSADMADIFEIANSLP +NVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLM +TALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAI +GAIVLYLGMFGAYRAGDDLAGWTTAQTVVLAGGHTLGVVLQAVILFLPLRGLGLGLRPRF +GWKGIGLRDTGRIAGYTLVTMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSAEMA +QAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFT +VPLMFCLAGVVVLAGPLGRVFGSTAETAMVAGIAVGSVLLALALSIPFRSGSFYLLRVFY +AAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMALWVAFASSVSYVYQFVLTHVLTVR +RFGDYGLASVLRAHVQTGLAALAAAAAGAVVVWLLGGYTGGFAWNSIGTALLTCAAAAVA +MGPVYLVVLRAMRFPELDDALRPLVARVPALGRLLRVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001762.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001762.fa new file mode 100644 index 0000000000000000000000000000000000000000..81f13d98f8988be40b46616b3acf6704d372cc81 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001762.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001764.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001764.fa new file mode 100644 index 0000000000000000000000000000000000000000..fda1b561a1abd249ef5985963f8dacfa85a88864 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001764.fa @@ -0,0 +1,35 @@ +>PROKKA_02133 +MLRLIGKRLLLLIPTLFGLSVLLFVWVRSLPGGPATALLGDRATPEAVARVNAAYGFDKP +LLEQYVTYMGRLLRGDFGTSIMTNRPVVEEFADRFPATLELSIFAIVFAVVIGIPLGYWA +ARHVGRWQDDVAVVLSLIGVVVPVFFLAFILKWVFAVKLGWLPTDGRQDPRIDATHYTNF +YVWDGIITAEWDAALNALTHLVLPGIALGTIPLAIIARITRASVLDVQDADFVRTARAKG +LAPRLIRDRFIMRNALLPVSTTLGLQLGLLISGAVLTETVFAFNGIGRFLAQAIFQLDFP +VLQGFIIFIALLYSLINLVVDVSYGLIDPRVRVS +>PROKKA_00090 +MTALASRPGAASRASRSAPVSPASRSTRRTHRRRTLVGAGTVLRRLAGAVGVVWATATLT +FLMQFLLPGDRATLVFNLRAGQAQPRTAEELAPLNALFGFQDPVLVQYLHFLGGLLRGDL +GTSYVTFEPVTTVIGDQLAPTLLLTGASIAIAWAVALVLLVATVRRARWVSGLASAVEAL +LAALPHYWLGVILLVVFALGLGLFPVVGGTGPAALVLPALTMGLPLAGYLAQTMRSEYAS +VLDQPFILTARTRGQSDAGIRVRHALRHALLPGLSLTGWAVGAQFSAAVIAEGVFSRPGI +GGVLVDAANGRDLPVVCGVVVLIAIVYVLANLAVDVLYTVVDPRLRSAR +>PROKKA_00267 +MLRLIGKRLLLLIPTLFGLSVLLFLWVRSLPGGPATALLGDRATPEAVARVNAAYGFDKP +LLEQYTTYMGRLLRGDFGTSTMTNRPVLEEFADRFPATLELSLFAIVFAVAIGIPLGYWA +ARHVGRWQDNIAVVLSLIGVVVPVFFLAFILKWVFAVKLGWLPTDGRQDPRLDATHYTNF +YVWDGISTGEWDAALNALTHLVLPGIALGTIPLAIIARITRASVLDVQNADFVRTARAKG +LAPRLIRDRFIMRNALLPVSTTLGLQLGLLISGAVLTETVFAFNGIGRFLAQAIFQLDFP +VLQGFIIFIALIYSLINLVVDVSYGLIDPRVRVS +>PROKKA_00135 +MARRILLRLALALAVLLGAYTAAFLILYVMPGDPVTAMAAGGLEAGAISDADLQALRAEH +GLDRPLPVQYLSQLAAAVTGDLGTSVQTGQPVTEAILDRLPTTLRLAWAALLVAVVAGPA +IALVAAGTRRRWVRATASAIPALGAALPTFWTGLLLVQVFSFGLGWLPALGDDGLAGLVM +PALTLGLPLSALIAQVMLRALDESGTQEYVETALASGQSRRRVLITHMLPNAALPTLAML +GVITGNVVAGAVVVETVFSRPGVGQLTVQAVTAQDLPVVLGVVLLSSLVFVLVTLTVDLL +SPLLDPRVGPAGAV +>PROKKA_00125 +MLRLIGKRLLLLIPTLFGLSVLLFVWVRSLPGGPATALLGDRATPEAVARVNAAYGFDKP +LLEQYVTYMGRLLRGDFGTSIMTNRPVVEEFADRFPATLELSIFAIVFAVVIGIPLGYWA +ARHVGRWQDDVAVVLSLIGVVVPVFFLAFILKWVFAVKLGWLPTDGRQDPRIDATHYTNF +YVWDGIITAEWDAALNALTHLVLPGIALGTIPLAIIARITRASVLDVQDADFVRTARAKG +LAPRLIRDRFIMRNALLPVSTTLGLQLGLLISGAVLTETVFAFNGIGRFLAQAIFQLDFP +VLQGFIIFIALLYSLINLVVDVSYGLIDPRVRVS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001789.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001789.fa new file mode 100644 index 0000000000000000000000000000000000000000..242eb2fc9dc6442ccbc4794556240317aad6a7ba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001789.fa @@ -0,0 +1,18 @@ +>PROKKA_00217 +MTANHSRHTAAADGQGAAAEHAGTGTATTDPRRDTRSRWGCSSRLGGGTGRLMGVSLAVG +VVGALGLGSAAWATTVAAGHADSLAWIAAGAMALNGLLFGLLLTWLALVDRHSIRGADTN +PEESIEGRWYEKATSGAFHDTLVVVGLGAAILSFGGYVISPAAVGAALFVLMGCAAAIRY +QIQKRRG +>PROKKA_02210 +MATTPHTTTDLARDRRPRWGRSARLGGGSGRLILVSLVAGVVIALLIGAASYGLASSQGD +AGPRFPAVTGAVMAASALPVGAALAWLFLVDRTTLRGAVRDTEETIEGRWLEKAQSGAFG +DLLVVLGLGTFVVALAGWQPSLPLVGAGLLLFAGASVAVRYALQKRRG +>PROKKA_00168 +MNTTADPRSRSASGPERAASTSAAATPAGSAAPSAWGRSARLGGGTGRLVVVSLVFGVLL +AAMLGVIAYGLAGTADPADPRRPWVLGLVVASGALPVLAGTVWMLLVDRATIKGAVRDPE +ESIESRWYDAAAGGAFHDLLVVLGLGTFVVSMTGWTAELSLVGAGLVLFMMADVAIRYRV +QKRRG +>PROKKA_00217 +MATTPHTTTDLARDRRPRWGRSARLGGGSGRLILVSLVAGVVIALLIGAASYGLASSQGD +AGPRFPAVTGAVMAASALPVGAALAWLFLVDRTTLRGAVRDTEETIEGRWLEKAQSGAFG +DLLVVLGLGTFVVALAGWQPSLPLVGAGLLLFAGASVAVRYALQKRRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001790.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001790.fa new file mode 100644 index 0000000000000000000000000000000000000000..8bf5a3c271dc1491274af4b305bd359f5fa9bf31 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001790.fa @@ -0,0 +1,48 @@ +>PROKKA_00219 +MTRTVPARRRTTLAAAVAAVSLAVTAAAPALSAPGNGNGNGNGNGSASQGQARSNDLSAT +RGNKVNDAAALAPHLVGQTLDWEACDFGSERLNARFNAIPGTACADVTVPRDWKNPEDGH +TITLRVAKTETSKGNPERQGIALVNPGGPGGSGLPWGPAMAERAPELAEQYDFIGFDPRG +VGQSTALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVLGEEKT +SYIGYSYGTWLGSWYQRVFPQHTHRFLLDSAVDISRDGLQTTWDLQPRSRDRQFQDAMLP +YVARHDEIFGLGDNPMQIRQRWEDVGGTRTQLGMIVAGSFLLPAMYDTSQYLDAGSVIAA +YIRIMESEAAATDPAGQRTQIERILAEARASLPAEERDSFDRFAARGLETVGEREQLVAA +TQAGDAVTFEGAFSAIRCQDGQWNTSQGYWTSWVDDLGRKAPWIGVLMGPSECMYWPAQT +SMPAQPGGKGAPNTVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYRTEC +VDAPIRDYFLTGAQPAEKSLCDAVPLPLETQPVQVAGTPTHKGDIKISMRTDAVREANRI +THDAIERQLIDSRAVTPDVEAFLED +>PROKKA_02213 +MTRTVPARRRTTLAAAVAAVSLAVAAAAPALSAPGNGNGNGSASQGQARSNDLSATRGNK +VNDAAALAPHLVGQTLDWDACDFGSERLNARFNAIPGTACADVTVPRDWKNPEDGHTITL +RVAKTETSKGNPERQGIALVNPGGPGGSGLPWGPAMAERAPELAEQYDFIGFDPRGVGQS +TALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVLGEEKTSYIG +YSYGTWLGSWYQRVFPQHAHRFLLDSAVDISRDGLQTTWDLQPRSRDRQFQDAMLPYVAR +HDEIFGLGDDPMQIRQRWEDVGGTRTQLGMIVAGSFLLPAMYDTSQYLDAGSVIAAYIRI +MESEAAATDPAGQRTQIERILAEARASLPAEERDSFDRFAARGLETVGEREQLVAATQAG +DAVTFEGAFSAIRCQDGQWNTSQGYWTSWVDDLGRKAPWIGVLMGPSECMYWPAQTSMPS +QPGGKGAPNTVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYRTECVDAP +IRDYFLTGAQPAEKSLCDAVPLPLETQPVQVAGTPTHKGDIKISMRTDAVREANRITHDA +IERQLIDSRAVTPDVEAFLED +>PROKKA_00161 +MTRTAPTRRRTTLAAAVAAAAALTISAAAPALSAPGNGNGNGNGQSSASQGQARSNDLST +TRGNQVNDAAALAPHLLDQELAWEACDFGSPALNTRFGAIPGTACADVTVPRDWKDPQDG +HTITVRVAKTETSKGNPDRQGIALVNPGGPGGSGLPWGPAMAERAPELAEQYDFIGFDPR +GVGQSTALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVMGEEK +TSYIGYSYGTWLGSWYQRVFPQHAHRFLLDSAVDVSRDGLQTTWNLQPRSRDRQFQDMML +PYVARQDAVYGLGTDPMEIRQRWEDAGGTRTILGQIVAGSYLLPAMYSTSQYPMAASMIA +AFISIMETETAATDEAGMQAQLERITAEARATVPAADRAAFDRFIEQGSEVVAERDELAA +AVRTGQPVTFSGTFSAIRCQDGQWNTSEGYWTSWVNDLGRKAPWIAAFMGPSECMYWPAQ +TSMPSQPGGKDTPSAVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYRTE +CVDAPIRDYFLTGEMPAEKSLCEAHPLPGETQTHQVAGTPTHKGDIKISMRTDAVREANR +ITLDAIERQLLDSRAVTPDVEAFLER +>PROKKA_00220 +MTRTVPARRRTTLAAAVAAVSLAITAAAPALSAPGNGKGNGSASQGQARSNDLSATRGNK +VNDAAALAPHLVGQTLDWEACDFGSESLNARFNAIPGTACADVTVPRDWKNPEDGHTITL +RVAKTETSKGNPERQGIALVNPGGPGGSGLPWGPAMAERAPELAEQYDFIGFDPRGVGQS +TALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVLGEEKTSYIG +YSYGTWLGSWYQRVFPQHAHRFLLDSAVDISRDGLQTTWDLQPRSRDRQFQDAMLPYVAR +HDEIFGLGDDPMQIRQRWEDGGGTRTQLGMIVAGSFLLPAMYDTSQYMSAGAVIAAYIRI +MESEAAATDPAGQRAQIERILAEARASLPTEERDSFDRFADRGLETVGEREQLIAATQAG +DAVTFEGAFSAIRCQDGQWNTSQGYWTSWVDDLGRKAPWIGVLMGPSECMYWPAQTSMPS +QPGGKGAPSTVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYGTECVDAP +IRDYFLTGAQPAEKSLCDAVPLPLETQPVQVAGTPTHKGDIKISMRTDAVREANRITHDA +IERQLIDSRAVTPDVEAFLED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001794.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001794.fa new file mode 100644 index 0000000000000000000000000000000000000000..3859eb544ed2629534015909d25d46d6679bf2c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001794.fa @@ -0,0 +1,23 @@ +>PROKKA_00252 +MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADAAVLHAPG +LVGTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLVFGLLAEHVRDAH +RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDIGVELGKILYRNGPGAAAPVV +GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLVQDLQDA +>PROKKA_02264 +MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADAAVLHAPG +LVGTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLVFGLLAEHVRDAH +RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDIGVELGKILYRNGPGAAAPVV +GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLIQDLQDAWLT +RRPRRP +>PROKKA_00118 +MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADATVLHAPG +LVSTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLAFGLLAEHVRDAH +RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDLGVELGKILYRNAPGTAAPVV +GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLIQDLRDAWLT +RRPRRR +>PROKKA_00252 +MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADAAVLHAPG +LVGTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLVFGLLAEHVRDAH +RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDIGVELGKILYRNGPGAAAPVV +GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLIQDLQDAWLT +RKPRRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001808.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001808.fa new file mode 100644 index 0000000000000000000000000000000000000000..2afedb9f84f5168829e616e1f862c4b2c15a77e5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001808.fa @@ -0,0 +1,15 @@ +>PROKKA_00390 +MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARPIASYGAPAPGTLGG +VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA +DGHVAAAIENGKVGRMLDRLTALVPEIR +>PROKKA_00114 +MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARPIASYGAPAPGTLGG +VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA +DGHVAAAIENGKVGRMLDRLTALVPEIR +>PROKKA_02566 +MAAVRALRTLLAEGYATPEAPVAVTGAGWPDYDARVLPGLAAAQELAGVDVDYLRHVDRV +SDAGIDAASLADLGTLFTYVLRGERFSEGHIGAALANGKVGRMLDRLAELVPQVR +>PROKKA_00396 +MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARQIASYGAPAPGTLGG +VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA +DGHVAAAIENGKVGRMLDRLTALVPEIR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001816.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001816.fa new file mode 100644 index 0000000000000000000000000000000000000000..9d7bc36b98978bf3ef03a4be0789ba97826305c5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001816.fa @@ -0,0 +1,20 @@ +>PROKKA_00569 +MDSRVNSGGVVGKVDNLTCLAGLVTTEDPARVRALRGTVLAVALLNGAYLVVEIILALGI +GSVALVADSVDFFEDFAVNLLIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKIG +DPDPPAAGVLLGAAVGSLLVNLVCVALLARVRTDGGSLTRAAWLAARNDLVAGAVLIALS +GITVLTASGWADIIVGVLLVLLNGSAAKEIWEAATEEHLAAQALAGEVDDD +>PROKKA_00293 +MNRAAVADRRRTRTLRGTVLAVALLNGAYLVVEIILAVGIGSVALVADSVDFFEDFAVNL +LIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKIGDPEPPAAGVLLGAAVGSLLV +NIVCVVLLARVRVDGGSLTRAAWLAARNDLVAGVVLIALSGITVLTASGWADIIVGVLLV +LLNGSAAKEIWEAATEEHLAAQALAGEVDDD +>PROKKA_02259 +MDAMTETSHPRPDPARVRALRGTVLAVSLLNLAYMLVEIGVALGIGSVSLVADSVDFFED +FAVNMLIVIALGWPLARRARVGKVMAGIIVLPAIAALAMAAVKVGDPEPPATGPLFWTGV +GSLLVNLVCVGLLARFRADGGSLTRAAWLAARNDLIAGIVLIALAGATALTASGWADIIV +GVLLVVLNGGAAKEVWQAATEERLAAQALAGEFDDD +>PROKKA_00571 +MNEVPEADRRRTRALRGTVLAVALLNGAYLVVEIILALGIGSVALVADSVDFFEDFAVNL +LIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKVGDPDPPAAGVLLGVAVGSILV +NLVCVALLARVRTDGGSLTRAAWLAARNDLVAGVLLIALSGITVLTASGWADIIVGVLLV +LLNGSAAKEIWEAATEEHLAAQALAGEVDDD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001830.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001830.fa new file mode 100644 index 0000000000000000000000000000000000000000..65c52bc9de528297672ebe57845c9802e4809d15 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001830.fa @@ -0,0 +1,40 @@ +>PROKKA_00663 +MTASTPAPAAQSAPTVAERNAAGHARLEQELADLVARTSLGGPERSRERHTGRGKLLVRD +RIDALLDEGSPFLEVGALAAHGLYDGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYY +PMTVKKHLRAQEIALENRLPCIYLVDSGGAFLPRQDEVFPDREHFGRIFRNQALLSSQRI +PQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH +AERSGVADHLADDDLHAMQILRDIVATLPPAEAPAWEVAPAAEPAKDPAELTRVVPVDVN +TPYDVREVIDRLVDGGSVHEFKPLYGTTLVTAFARIDGHPVGVLANNGILFGDSARKGAH +FIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMVTAVATARVPKLTVVIGGSFG +AGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMSSEEVEAF +QAPVRRQYEDQGSPLYSTARLWDDGVITPGQTRRVLSLALDVISRSPLPDSRFGLFRM +>PROKKA_00400 +MTASTPAPAAQSAPTVAERNAAGHARLEQELADLVARTSLGGPERSRERHTGRGKLLVRD +RIDALLDEGSPFLEVGALAAHGLYGGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYY +PMTVKKHLRAQEIALENRLPCIYLVDSGGAFLPRQDEVFPDREHFGRIFRNQALLSSQRI +PQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH +AERSGVADHLADDDLHAMQILRDIVATLPPAEAPAWEVAPAAEPAKDPAELTSVVPVDVN +TPYDVREVIDRLVDGGSVHEFKPLYGTTLVTAFARIDGHPVGVLANNGILFGDSARKGAH +FIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMVTAVATARVPKLTVVIGGSFG +AGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMSSEEVEAF +QAPVRRQYEDQGSPLYSTARLWDDGVITPGQTRRVLSLALDVISRSPLPDSRFGLFRM +>PROKKA_02300 +MTASTTAPDSESAPTAAERNAAGHARLEQEVAELVARTALGGPERSRERHTARGKLLVRD +RIDALLDEGSPFLEVGALAAHGLYDGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYY +PLTVKKHLRAQEIALENHLPCLYLVDSGGAFLPRQDEVFPDREHFGRIFRNQALLSSRRI +PQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH +AERSGVADHLADDDLHAMQILRDIVATLPPPPAPAWEVAPAQEPAKDPAELTSVVPVDVN +TPYDVREVIDRIVDGGSVHEFKPLYGTTLVTAFARIDGHPVGILANNGILFGDSARKGAH +FIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMVTAVATARVPKLTVVIGGSFG +AGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMDAAEVEAF +QAPVRQQYEDQGSPLYSTARLWDDGIITPGQTRRVLSLALDVISRPPLPDTRFGLFRM +>PROKKA_00633 +MTASTPAPAAQSAPTVAERNAAGHARLEQELADLVARTSLGGPERSRERHTGRGKLLVRD +RIDALLDEGSPFLEVGALAAHGLYGGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYY +PMTVKKHLRAQEIALENRLPCIYLVDSGGAFLPRQDEVFPDREHFGRIFRNQALLSSQRI +PQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH +AERSGVADHLADDDLHAMQILRDIVATLPPAEAPAWEVAPAAEPAKDPAELTSVVPVDVN +TPYDVREVIDRLVDGGSVHEFKPLYGTTLVTAFARIDGHPVGVLANNGILFGDSARKGAH +FIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMVTAVATARVPKLTVVIGGSFG +AGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMSSEEVEAF +QAPVRRQYEDQGSPLYSTARLWDDGVITPGQTRRVLSLALDVISRSPLPDSRFGLFRM diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001845.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001845.fa new file mode 100644 index 0000000000000000000000000000000000000000..698e8b926df25c018b61c67d18c44399b98c1838 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001845.fa @@ -0,0 +1,36 @@ +>PROKKA_01016 +MSTPTGYRVQDPSTDQVVETFPALADGEVDQVLAAAETAQRAWAARPIEERATIVQKVAD +LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETYGGGRAM +IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV +PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY +IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVSADIHDAFVAELVSLAEAMKPGEAA +DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD +AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAKAERIARQLEVGMANVN +TPAGEGAEIPFGGVKRSGFGRELGPLGMDEFVNKQTYFVQD +>PROKKA_00730 +MSTPTGYRVQDPSTDQVVETFPALADGEVDQVLAAAETAQRAWAARPIEERATIVQKVAD +LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETYGGGRAM +IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV +PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY +IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVTADIHDAFVAELVSLAEAMKPGEAA +DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD +AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAQAERIARQLEVGMANVN +TPAGEGAEIPFGGIKRSGFGRELGPLGMDEFVNKQMYFVQD +>PROKKA_01872 +MSTPTGYRVQDPSTDQVVETFPTLADGEVDQLLAAAETAQRAWAARPIEERATIVQKVAD +LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETFEGGRAM +IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV +PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY +IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVSADIHDAFVAELVSLAEAMKPGEAA +DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD +AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAQAERVARQLEVGMANVN +TPAGEGAEIPFGGVKRSGFGRELGPLGMDEFVNKQMYFVQD +>PROKKA_00960 +MSTPTGYRVQDPSTDQVVETFPALADGEVDQVLAAAETAQRAWAARPIEERATIVQKVAD +LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETYGGGRAM +IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV +PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY +IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVSADIHDAFVAELVSLAEAMKPGEAT +DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD +AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAQAERIARQLEVGMANVN +TPAGEGAEIPFGGVKRSGFGRELGPLGMDEFVNKQMYFVQD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001889.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001889.fa new file mode 100644 index 0000000000000000000000000000000000000000..5811536b9f9912a3fb7b40023807b60027ce3dba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001889.fa @@ -0,0 +1,28 @@ +>PROKKA_01846 +MSGERVGFTGAEALWLPGWRHVYSGKVRDLYEPADAEPGRSATLLVVASDRISAYDHVLE +PPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVAGRAMVVKRLDMFP +VECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSAKAEVGEHDENITF +EQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVDPATGQVVLGDEVL +TPDSSRFWDAEDYEPGRPQASFDKQFVRDWLTGPDSGWDKTSGEAPPELPADVVAKTRDR +YVEAYERLTGRPFDA +>PROKKA_01542 +MSGERVGFTGAEALWLPGWRHVYSGKVRDLYEPADAEPGRSATLLVVASDRISAYDHVLE +PPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVAGRAMVVKRLDMFP +VECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSAKAEVGEHDENITF +EQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVDPATGQVVLGDEVL +TPDSSRFWDAEDYEPGRPQASFDKQFVRDWLTGPDSGWDKTSGEAPPALPADVVAKTRDR +YVEAYERLTGRPFDA +>PROKKA_01022 +MSHETPASDTTPHSGAAPRGFAGAEALELPGWRHVYSGKVRDLYEPADAAPGESETLLVV +ASDRISAYDHVLSPPIPDKGAVLTQLTLWWFERLSEGYNGAAGAPVEHHVVSTDVPEAVA +GRAMVVKRLRMFPVECIARGYLTGSGLAEYRESGTVTGLPLPTGLVDGSRLDPAIFTPSA +KAEVGEHDENITFEQMSERVGAEAAERLRYLTLDLYSRAEAIARDAGIILADTKVEFGVD +PATGQVVLGDEVLTPDSSRFWDAEDYEPGRAQASFDKQFVRDWLTSDASGWDRASGAEPP +ELPADVVEKTRARYVEAYERLTGRPFEA +>PROKKA_01766 +MSGERVGFTGAEALELPGWRHVYSGKVRDLYEPADAEPGRSATLLVVASDRISAYDHVLE +PPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVAGRAMVVKRLDMFP +VECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSAKAEVGEHDENITF +EQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVDPATGQVVLGDEVL +TPDSSRFWDAEDYEPGRAQASFDKQFVRDWLTGPDSGWDKAGGEAPPALPADVVAKTRDR +YVEAYERLTGRPFDG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001945.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001945.fa new file mode 100644 index 0000000000000000000000000000000000000000..8866c1ae8012ea8068705ae1e3b841a73096d801 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001945.fa @@ -0,0 +1,12 @@ +>PROKKA_02259 +MNVSAEQLIGDESGVHRGLYRRVVDHVPWLRGFVCDDLHNFGPEDRWILAR +>PROKKA_00463 +MTRLLPGDSLTLDLAPEDPADLLARLRAAGVAMNESAERLITDARVCAVVPERVTVVERT +LAELGLPDGGTLPELRRAVEAAGLRECPPTVAPLLRLVTLDQANAPDSLLRHGRAPDDSA +HVFSPSLSDEPGVHRGLYLRVVDHVPWLRGFVCDDLHVFGPEDRWILAL +>PROKKA_00700 +MADLIDRAGIELTLAGDPHELLTQLQAAGVRFNDSARTLLFRPALARDLQTSRPVRVVER +SLTDLGLPNGGTLPQLRRAALAAGLAPCPPAVAPLLRLRTLDQVNAPDSVLRHGRAPEGS +VHVLSPSLGEDPRVHRGFYLRVVDEAPWLRGFMCDDLHVMGADDRWVLSAPTSAP +>PROKKA_02190 +MNVSAEQLIGDESGVHRGLYRRVVDHVPWLRGFVCDDLHNFGPEDRWILAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001949.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001949.fa new file mode 100644 index 0000000000000000000000000000000000000000..fbc6370790021e325c36db58e94012df2c519ac7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001949.fa @@ -0,0 +1,32 @@ +>PROKKA_02283 +MPPATTAPSPASLPLDGVLVADFSRVLAGPLATMTLADLGARVIKVEHPVRGDDTRGWAP +PRSATGATYFESVNRNKESVGWDLKDPEDQRRAAALAARADVVVHNLKPGTMERLGLGYD +DVARENPSVVYAAVSGFGDREGRDLPGYDFIVQAAGGLMSITGEPDAPMKAGVALVDVLT +AKDLTAGVLAALLRRERTGEGAHLRLNLLSSLQGALANQGQAWLGAGVVPRRMGNDHPSI +APYQLLACRDAPLAVAIGNDAQFRTFAAALGVPELAEDPRFTTNTDRVEHREELRTALED +ALSAQTAAHWRDVLQAERLPAGLVSTVAEGVELAESLGLEPTVEVQDRSGAPAGRQFRHP +VQWDPPVAHPRHAPPALGADTAAVNTWLDAR +>PROKKA_01974 +MPPATTAPSPASLPLDGVLVADFSRVLAGPLATMTLADLGARVIKVEHPERGDDTRGWAP +PRSATGATYFESVNRNKESVGWDLKDPEDQRRAAALAARADVVVHNLKPGTMERLGLGYD +EVARENPSVVYAAVSGFGDREGRDLPGYDFIVQAAGGLMSITGEPDAPMKAGVALVDVLT +AKDLTAGVLAALLRRERTGEGAHLRLNLLSSLQGALANQGQAWLGAGVVPRRMGNDHPSI +APYQLLACRDAPLAVAIGNDAQFRTFAAALGVPELAEDPRFTTNTDRVEHREELRTALED +ALSAETAAHWRDVLQAERLPVGLVSTVAEGVELAESLGLEPTVEVQDRSGAPAGRQFRHP +VQWDPPVAHPHHAPPALGADTAAVNTWLDTR +>PROKKA_00808 +MEHTDEPRGGGPLEGIVIADFTRVLAGPYATMLLADMGATVIKVESPGGDDTRTWRPPEH +EGVSTYYLSVNRNKRAVALDLSDREDLDTAYALLDRADVFLENFKPGGLAKFGLDPDSVA +ERWPHLVHASITGFGTASGTALPGYDLLAQAVSGMMTVTGEPDGAPQRSGVAIFDVITGL +HAAIGVLGALQERTRSGRGQHLELNLLSSALSGLVNQTSAAIAGGVTPHRMGNEHPSLYP +YGPFRAADRELIIAVGNDRQFARLVEQLGRPELAEDPRFLTMKDRNAHRGELGPLLEEAL +AAQSAGEWFEQLRDAGIPCSPILTLPEGVEFAAGLGLDPVVEVGEQRIPTVRHPIRFSRT +PARHELAPPALDADRDWVRAWIDQTPPSTAADAD +>PROKKA_02222 +MPPATTAPSPASLPLDGVLVADFSRVLAGPLATMTLADLGARVIKVEHPVRGDDTRGWAP +PRSATGATYFESVNRNKESVGWDLKDPEDQRRAAALAARADVVVHNLKPGTMERLGLGYD +DVARENPSVVYAAVSGFGDREGRDLPGYDFIVQAAGGLMSITGEPDAPMKAGVALVDVLT +AKDLTAGVLAALLRRERTGEGAHLRLNLLSSLQGALANQGQAWLGADVVPRRMGNDHPSI +APYQLLACRDAPLAVAIGNDAQFRTFAAALGVPELAEDPRFTTNTDRVEHREELRTALED +ALSAQTAAHWRDVLQAERLPVGLVSTVAEGVELAESLGLEPTVEVQDRSGAPAGRQFRHP +VQWDPPVAHPHHAPPALGADTAAVNTWLDAH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001965.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001965.fa new file mode 100644 index 0000000000000000000000000000000000000000..e2503b6f4481699593b6f28504d78ce962088549 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001965.fa @@ -0,0 +1,20 @@ +>PROKKA_01700 +MSITQTDTPLTQDELARTIAADIAPGSFVNLGIGQPTTVSNYLEAEKNVTLHTENGMLGF +GPQAEGEQIDEDLINAGKIPVTELPGAAYFHHADSFAMMRGGHLDVCVLGAYQVSATGDL +ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDPKLLAECTFPLTGVGCVSRIY +ADRGVFLLDASGVVRVRELHGITWEELEAAHPGVRFEKLED +>PROKKA_00851 +MSFTQTDTPLTQDELAKVIAADIAPGSFVNLGIGQPTTVSNYLEAEKNVTLHTENGMLGF +GPQAEGEQVDEDLINAGKIPVTELPGAAYFHHADSFAMMRGGHIDVSVLGAYQVSATGDL +ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDPKLLAACTFPLTGVGCVSRIY +ADRGVFLLDASGVVRVRELHGITWEELEEAHPGVRFEKLEA +>PROKKA_00788 +MGFTHTENPLSHEELAQVIAADIAPGSYVNLGIGQPTTVSDYLDADQHVTLHTENGMLGF +GPQAHGEQVDEDLINAGKIPVTELPGASYFHHADSFAMMRGGHLDVCVLGAYQVSATGDL +ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDRKLMPECTFPLTGVGCVSRIY +ADKGVFLLDSSGVVKVRELHGITFEELQATHEGVTFEEVDASA +>PROKKA_01928 +MSITQTDTPLTQDELARTIAADIAPGSFVNLGIGQPTTVSNYLEAEKNVTLHTENGMLGF +GPQAEGEQIDEDLINAGKIPVTELPGAAYFHHADSFAMMRGGHLDVCVLGAYQVSATGDL +ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDPKLLAECTFPLTGVGCVSRIY +ADRGVFLLDASGVVRVRELHGITWEELEAAHPGVRFEKLED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001998.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001998.fa new file mode 100644 index 0000000000000000000000000000000000000000..d05feca8bff0a7f632cf4ce1fe0284255f753e21 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001998.fa @@ -0,0 +1,12 @@ +>PROKKA_00271 +MFNGKDDWTAAPVGVRAWASQRAVELIAAHTPWFGFQGVDVDRLRQRPGWEDAKPHIVVS +AQLLNRVHRRTSLRADGLLVIADDHHLRDDSRLTYRRMRAASVQGLSDGALDHLLDTMYF +GPSNQSRLLQAVDVLTYFEQRRRHVTERHRDAVRRMNAIGRSLNKIRQHSYVWTP +>PROKKA_02286 +MFNGKDDWTAAPVGVRAWASQRAVELIAAHTPWFGFQGVDVDRLRQRPGWEDAKPHIVVS +AQLLNRVHRRTSLRADGLLVIADDHHLRDDSRLTYRRMRAASVQGLSDGALDHLLDTMYF +GPSNQSRLLQAVDVLTYFEQRRRHVTERHRDAVRRMNAIGRSLNKIRQHSYVWTP +>PROKKA_00269 +MFNGKDDWTAAPVGVRAWASQRAVELIAAHTPWFGFQGVDVDRLRQRPGWEDAKPHIVVS +AQLLNRVHRRTSLRADGLLVIADDHHLRDDSRLTYRRMRAASVQGLSDGALDHLLDTMYF +GPSNQSRLLQAVDVLTYFEQRRRHVTERHRDAVRRMNAIGRSLNKIRQHSYVWTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002008.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002008.fa new file mode 100644 index 0000000000000000000000000000000000000000..149ccedad1f3aa05f5842ec790dddddb3f9ec1eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002008.fa @@ -0,0 +1,27 @@ +>PROKKA_00525 +MGAVAPPEARPARRHASLGLVPDGQAAWTRSPWNPLVTPASPRLFEAVLAIGLVMEAFTA +PGLPIPFAEFSAILLLLLASFRQPRRDLSQYGVLALVALALVAYLVAVTVHNDLDPTRRA +TRITLLILLIYAIASERIDIKGVLYGMTAGALINVPLFYAGLAPDTYGGYLTGFLGDKNV +SGLFYALLPVLLVATMQRMGPKLLVLGAGFALTFLTGSRTSMAGLLCAVVWILVSPYLGR +VLRIALGVVLGWFVSWAEVNLADLGIFGDRTGTDWFREQIQEASAEKVADTSFFGQGLST +AFVELDNVTMFFHNSYLGLLVEGGWPFLIVVVGAYLWLCLRPFARTHRSPSRVAVEAAAL +IILVTSLQLGEVFITIFGAVVLGCGLLLSAQENEESQGAPAKDRAHRRKLDRIIERSRRA +GV +>PROKKA_00246 +MRPSTPRDRTAARAMGAVAPPEARPARRHASLGLVPDGQAAWTRSPWNPLVTPASPRLFE +AVLAIGLVMDAFTAPGLPIPFAEFSAILLLLLASFRQPRRDLSHYGVLALVALALVAYLV +AVTVHNDLDPTRRATRITLLILLIYAIASERIDIKGVLYGMTAGALINVPLFYAGLAPDT +YGGYLTGFLGDKNVSGLFYALLPVLLVATMQRMGPKLLVLGAGSVLTFLTGSRTSMAGLL +CAVVWILVSPYLGRVLRIALGVVMGWFVSWAEENLADLGIFGDRTGTDWFRAQIQEASAE +KVADTSFFGQGLSTAFVELDGVTMFFHNSYLGLLVEGGWPFLVVVVGAYLWLCLRPFART +HRSPSRVAVEGAALIILVTSLQLGEVFITIFGAVVLGCGLLLSAQESDESHGAPAKDRAH +RRKLDRIVERSRRAGR +>PROKKA_00525 +MRPSTPRDRTAARAMGAVAPPEARPARRHPSLGLFPDGQAAWTRSPWNPLVTPASPRLFE +AVLAIGLVMDAFTAPGLPIPFAEFSAILLLLLASFRQPRRDLSHYGVLALVALALVAYLV +AVTVHNDLDPTRRATRITLLILLIYAIASERIDIKGILYGMTVGALINVPLFYAGLAPDT +YGGYLTGFLGDKNVSGLFYALLPVLLVATMQRMGPKLLVLGAGAALTFLTGSRTSMAALL +CAVVWILVSPYLGRVLRIALGVVMGWFVSWAEENLADLGIFGDRTGTDWFRAQIQEASAE +KVADTSFFGQGLSTAFVELDGVTMFFHNSYLGLLVEGGWPFLVVVVGAYLWLCLRPFART +HRSPSRVAVEGAALIILVTSLQLGEVFITIFGAVVLGCGLLLSAQESDESHGAPAKDRAH +RRKLDRIVERSRRANR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002019.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002019.fa new file mode 100644 index 0000000000000000000000000000000000000000..e9c678e17d377217fcee338abba65980d38a12d2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002019.fa @@ -0,0 +1,14 @@ +>PROKKA_00888 +MSGNVFTAASADVAEDAVLGDGTKVWHLAQVREQARLGERCIVGRAAYIGTGVELGDDCK +VQNLALVYEPARLGRGVFIGPGVVLTNDTYPRAVNPDLSQKSGDDWEAVGVDIGDGAAIG +ARSVCVAPVRIGEWALVAAGSVVTRDVPDFGLVAGVPAKRIGWVGRTGRRLEEKDGVWVC +PDTGETFIERDGALRPAEPAQEEENHG +>PROKKA_00610 +MSGNVFTAASADVAEDAVLGDGTKVWHLAQVREQARLGERCIVGRAAYIGTGVELGDDCK +VQNLALVYEPARLGRGVFIGPGVVLTNDTYPRAVNPDLSQKSGDDWEAVGVDIGDGAAIG +ARSVCVAPVRIGEWALVAAGSVVTRDVPDFGLVAGVPAKRIGWVGRTGRRLEEKDGVWVC +PDTGETFIERDGALRPAEPAQEEENHG +>PROKKA_01215 +MSKLRMLSRMPKKGRFMFIISGGDRARYMSRKGLVRGMGENVWFQPRALPNDPNLIRFHN +NIVVASGVTFVAHDVINLMIGRKNGVRLPVNEDCIEVMDDVFIGSGSVILPGVGIGPRAI +IAAGTVVTKDVPPDSIVRGVPAKRLGDFSVLEAQRLADAGRFDGMTRAQIDDVLWE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002026.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002026.fa new file mode 100644 index 0000000000000000000000000000000000000000..f4873e5e32ea1820a9943bfbc1271e793250ddbc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002026.fa @@ -0,0 +1,12 @@ +>PROKKA_01040 +MAALDDETAGIPEGNRGPSAGLVYAWGEHSRADPVFGDYPERVLALKYAEPGVELPLWSK +RQGDDASVAELSWGPRWGTLWRDTALEFSPGFTTSPTRHTRPTTASFATGRWTG +>PROKKA_00753 +MAALDDETAGIPEGNRGPSAGLVYAWGEHSRADPVFGDYPERVLALKYAEPGVELPLWSK +RQGDDASVAELSWGPRWGTLWRDTALEFSPGFTTSPTRHTRPTTASFATGRWTG +>PROKKA_00982 +MAAALYDEAAGTPEGNRGPSAGLVYAWGEHSLADPVFGDNPEWFFTLEHAESGVLLPFRS +EGLGDDAAVAELSWGPRWGTLWRDTTVDSFTGFHYLADATYPTDDRLVLDWSLDGMTKSE +DVIITQDAARSDVFALVELLADGQKPWALNVPAGEDAPSPGEADPVPPAEQEPVDTPAPV +AGEEPGEGTGGEETHTTPDTVETGREVRRARSERSRPSARDSCSWPGGGCAGSDTPGRRG +GRGAVDGRPSAAPRSVLSRPERIRWGRCSPRLRSRRCSHRRHCG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002030.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002030.fa new file mode 100644 index 0000000000000000000000000000000000000000..3fd3694aa6d6993956adc4a602e40eda4a9bfb95 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002030.fa @@ -0,0 +1,21 @@ +>PROKKA_01385 +MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG +LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL +LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA +VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR +WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR +RDLDQTTTST +>PROKKA_01113 +MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG +LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL +LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA +VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR +WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR +RDLDQTTTST +>PROKKA_01340 +MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG +LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL +LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA +VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR +WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR +RDLDQTTTST diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002033.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002033.fa new file mode 100644 index 0000000000000000000000000000000000000000..046bf4d34180e3b791f4838ffdfe1b48397359af --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002033.fa @@ -0,0 +1,9 @@ +>PROKKA_01395 +MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR +LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG +>PROKKA_01128 +MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR +LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG +>PROKKA_01345 +MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR +LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002089.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002089.fa new file mode 100644 index 0000000000000000000000000000000000000000..c2e9b932620e8c8db784eecd182c6a6887c1f966 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002089.fa @@ -0,0 +1,27 @@ +>PROKKA_01704 +MRERVALIGAGPSGMALLRSLALAEDAGAAVPEVVAFERQDDWGGQWNLDWRTGADRHGE +PVHSAMYRDLWINGPKECMEYPDYPFDAHFGRAVSSYLPREAMRDYIVGRVAEVAGRIRP +QIRFATAVRWVQPLDDGGFGVTSEDLVTREAVTERFDRVVVATGHFHTPHLPSWPGVETF +PGQVQHAHDYRSPEPYTGRRVLVVGSSYSGQDLALQLHRAGAAHVTTAYRARPQDIAWPA +GMDEAPEVQGFDGAEVTFADGSTAEYDAVLLCTGYRHHYPFLPGELALAGPNLLAPFGLW +KGVVWHADPRVLYLGATQQLFTLTLLDAQAFFARDVLLGRVPVPGDEERRADMDAWFERM +TRIDGPPAALAYQGAYIQDLSSHTDCPEVDVEAVARTFLEMRDARIEDVRTFRDRRHRST +VTGTLAAAHPVPWMDRPDDSLEEYLRRFPA +>PROKKA_00783 +MTERVALIGAGPSGMALLRALALAEDEGAVVPEVVAFERQADWGGQWNLDWRTAADRFGE +PVHSAMYRDLWINGPKECMEYPDYSFDAHFGRPVSSYLPQEAMKDYILGRVAHVAERIRP +LIRFGTVVRWVQPLDDGTFEVTSVDLTTGAARTEAFDRIVVATGHFHAAHTPSWPGVEDF +PGLVQHAHDYRTPEPFAGRRVLVIGSSYSGQDLALQLHRGGAAHVTTAYRKAPQELDWPA +GMDERPEVQGFAGSRVAFADGSSAEYDAVLLCTGYRHHYPFLPAELALSGPNLPFVPSLW +KSVVWQADPRVLYLGATQQWFTLTLLDAQAFFARDVLLGRAPVPSAQERQADIDAWTARM +AAIDSTPVALAFQADQIRDLTAGTGYPEMDLDGVIATFLQMGEDKRESLTRYRDRTHRSL +VTGTRAAAHPVPWMHHPDGSLEGYLAHFPG +>PROKKA_01932 +MRERVALIGAGPSGMALLRSLALAEDAGAAVPEVVAFERQDDWGGQWNLDWRTGADRHGE +PVHSAMYRDLWINGPKECMEYPDYPFDAHFGRAVSSYLPREAMRDYIVGRVAEVAGRIRP +QIRFATAVRWVQPLDDGGFGVTSEDLVTREAVTERFDRVVVATGHFHTPHLPSWPGVETF +PGQVQHAHDYRSPEPYTGRRVLVVGSSYSGQDLALQLHRAGAAHVTTAYRARPQDIAWPA +GMDEAPEVQGFDGAEVTFADGSTAEYDAVLLCTGYRHHYPFLPGELALAGPNLLAPFGLW +KGVVWHADPRVLYLGATQQLFTLTLLDAQAFFARDVLLGRVPVPGDEERRADMDAWFERM +TRIDGPPAALAYQGAYIQDLSSHTDCPEVDVEAVARTFLEMRDARIEDVRTFRDRRHRST +VTGTLAAAHPVPWMDRPDDSLEEYLRRFPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002099.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002099.fa new file mode 100644 index 0000000000000000000000000000000000000000..5a06b499bab69800e56fe4e713a1b2c3f9ad2c5a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002099.fa @@ -0,0 +1,7 @@ +>PROKKA_01854 +MGMKQRISKVGAGVAVAGPLAVSGAVPAQALTDSGRQDCSAGLLLSGTYGYCYYPY +>PROKKA_00549 +MGMKQRISKVGADVAVAGLLAVSGAVPGQALTDSGRQDCSAGGGYVGARGEQQRYGDRMS +FDVGGRTTKVVNRYTYGFDSGLRMSQNWRVSSESLLLSGTYGYCYYPY +>PROKKA_02084 +MGMKQRISKVGAGVAVAGPLAVSGAVPAQALTDSGRQDCSAGLLLSGTYGYCYYPY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002127.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002127.fa new file mode 100644 index 0000000000000000000000000000000000000000..cc253c64c921fded73c1a4da0ed21264fdaa30ec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002127.fa @@ -0,0 +1,11 @@ +>PROKKA_00488 +MVNETRAISRRQVTKGVTWSVPAIAATAAAPAFAVSSVGVVAGATLYANPLMTKYVQAQN +GTTALYLNATPGVGIPDATACQSVQNKKISIVYTAPAGIVDFRKVLNARKAGTPYNTYTN +GSVGDSKTFYTLKVGDRFVTGTNPAYWEVTKLASDGSSITLTYSAPITGCYYYAQPSFNP +YFWAKDVASMVNQVHLTAYIGTQRVAFDTGAASNVTWSADRLEIIGPKTTN +>PROKKA_00208 +MSECLMPVEVPQVLRSATKGIGMVNETRVISRRQVTKGVSWSVPAIAATAAAPAFAVSNP +GVVAGATLYANPLMTKYVQPQNGTTALYLNATPGVGIPDATACQSVQNKKISIVYTAPAG +IVDFRKVLNAQKAGTPYNTYTNGSVGDSNFFTLKVGDRFVTGTNPAYWEVTKLASDGSSI +TLTYSAPITGCYYYAQPSFNPYFWAKDVASMVNQVHLTAYIGTQRVAFEKGAGTNVTWSD +DRLEIIGPKTTN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002142.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002142.fa new file mode 100644 index 0000000000000000000000000000000000000000..a3f87f9800c147a6c9acc4c0900734080d392014 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002142.fa @@ -0,0 +1,32 @@ +>PROKKA_00893 +MAVATPAPRRPRMAMLVGNQVVGDSRVEKAAVSAVRAGYEVVVVGVSHRTTFNLGRYGSV +PILRVPVTFRRHLAWQTLHGTARPDVTDWSAVLDPEEAAAMTAWDLAHEVGAGLLQAVVR +GLSPHALPDRARGRLGRAARRLGRLGPARGRRDPAAMRGRRALKNFAAGRTGAWREVWPL +IADYEDGFLRALIDLAPDLVHVHDRHPLPAAAAYDHYRAARGLPPVPWVYDAHEWLPGQM +MPGPVDQRIAWKAAEAELIHEADAVVAVTDELAERMREYHALQERPVTVINGPWGTQLPM +GPAERLPLRTELGLSDDVPLLVYLGKLAAVRGVGTLVDALPLLPGVHIAFVGSPDPDARQ +GLRDRAAQLDVADRMHIVDYVPSASVTWYVSSATAGVSPLLPTPAHESAVPTKLRECLLA +GLPLTVSDLREQARFVREQGVGTVFAPGDAADLARAVRDLLARRTELTAAARSPEIAARH +GWEAAERALHGLWRRLVPTPAAPPPVEIAPDPAREPQPRGLLVVGDPPTVRPLADAWPAG +AGPVTLRPPRDFPEGRGLVVGGPEAVWGVLQDWVTDDRAHGTVLIGGEGPLWGRAEQSPV +HELLSLRARGRQVALVAGERILAGVERRLAAVPGHPWGGLDPDARAALDRRIRRQGRPFQ +AALAAGVPVLSHRRVEALLTPGVLWLPAPIPTPTDRGPGRDGASAPRSVLILPGDRTSAE +SAAVDELVAELAARGIPVEAPSGPRFRRRPDAFHGDVVVAPLHTEDLEVAALQALAAGSA +VVAGPPVTPAPDECAPPVTETDDATLLATVLGLLEETSAAAGERRERAREHHARLHAPEA +VLVRLQALLSPAETTDGPAAV +>PROKKA_00615 +MPVDTPAPRRPRMAMLVGNQVVGDSRVEKAAVSAVRAGYEVVVVGVFHRTTFNLGRYGSV +PILRVPVTFRRHLAWQTLHGTARPDATDWSAVLDPEEAAAMTAWDLAHETGAGLPQAVVR +GLSPHALPDGARGRLGRAARRLDRLGPARGRRGPAATRGRRALKNFAAGRTGAWREVWPL +IADYEDGFLRALIDLAPDIVHVHDLHPLPAAAAYDRYRAARGLPPVPWVYDAHEWLPGQM +MPGPVDQRIAWKAAEAELIHEADAVVAVTDGLADRMREYHALQERPVTVINGPWGAQVPM +DPAERLPLRTELGLSDDVPLLVYVGKLAEVRGVRTLVDALPLLPGVHVAYVGSPDPGARQ +GLRDRAAQLDVADRMHIVDYVPSASVTWYVSSATAGVSPLLPTPAHESAVATKLRECLLA +GLPLIVSDLREQARFVRDQGVGTVFAPGDAADLARAVRALLARQAELTAAARAPEITARH +GWEAAERALHGLWRRLVPTPAAPQPVEIAPDPARDPRPRGLLVVGDPPTVRPLLDAWPAD +AGSATQRPPRDVPEGRGLAVGGPEAVWGVLQDWVTDDRAHGTVLSGGEGPLWGRAEQSPV +HELLSLRARGRHVALVAGERILAGIDRRLAAVPGHPWGGLDPDARAALDRRIRRQGRPFQ +AALAAGVPVLSHRRVEALLTPGVLWLPAPIPTPTDRGPGHDGASAPRSVLILPGDRTSAE +SAAVDELVAELAARGIPVEAPSGPRFRRRPDAFRSDVVVAPLHTGELEIAALQALAAGSA +VVAGPPVTAAPDGCAPPVIETDDATLLATVLSLLEETSAAARERRERAHEHHARLHAPEA +VLVRLQALLSPAETTDGPAAV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002148.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002148.fa new file mode 100644 index 0000000000000000000000000000000000000000..3d16319a721da738cc6dfab3c68b255253454443 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002148.fa @@ -0,0 +1,12 @@ +>PROKKA_00968 +MTPPTGVLPRAALVMRLLHEAGPAGLRLSQLVQRTGLPQPTAHRLLADLAEQGAVTRRGA +AYALGDRWGPVGFEPVTPRCLIEREASRAVVQAAADELGDTVYLAARAAGGVAYLLRCDG +DSPVRVFTVEVGEVKRLAAGYAGIALLASLPPERRRAEVDAVVARPPRRWNLTDDGALHD +LLDTLLRQMDEQGWCGGVPVVPGVAGVACGVPARTGGIPQVSLTASAAEQRMPPARVPEV +AEVLRAAATRLAEIGG +>PROKKA_00681 +MTPPTGVLPRAALVMRLLHEAGPAGLRLSQLVQRTGLPQPTAHRLLADLAEEGAVTRRGA +AYALGDRWGPVGFEPVTPRCLIEREASRAVVQAAADELGDTVYLAARAAGGVAYLLRCDG +DSPVRVFTVEVGEVKRLAAGYAGIALLAALPPERQRAEVDAVVARPPRRWNLTDDGALHD +LLDTLLRQMDEQGWCGGVPVVPGVAGVACGVPARTGGIPQVSLTASAAEQRMPPARVPEV +AEVLRAAATRLAEIGG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002158.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002158.fa new file mode 100644 index 0000000000000000000000000000000000000000..dadb2b2d87ab356357eee64f9435759c86b930b6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002158.fa @@ -0,0 +1,6 @@ +>PROKKA_01497 +MSAPATAVTFPGVTLFLPDGVMTGDLTYDARTSQLAITYADGETEVLSIDLTLEGYVAAP +GEALIKDWSEHSGFTAALVDAGIVMRVETLQIGPFDSRAYRVLVLTEAVTGR +>PROKKA_02209 +MSASTATATFPGVTLFLPDGVMVGDLIYDARTSQLAIVYSDGETEVLSIDLTLEGYLPTP +GEALIKDWSEHSGVTSALVDAGLVMRTETLVVGPFSSRAYRVLVLTPEVTGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002189.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002189.fa new file mode 100644 index 0000000000000000000000000000000000000000..7b91049d764cb1d8117551dc317d27a856933844 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002189.fa @@ -0,0 +1,6 @@ +>PROKKA_00016 +MSAPLPSHLTIVQSADLLQVSRDTIRRLIASGDLKAYRIGPSTNRRRPIRVDRDSLLALR +EPVTSLAALKAGEAA +>PROKKA_00035 +MAAAASKPRPSFDPRPRLTIAEVADYTGTSPSSVRRWIARGELRAYKYGPRAIRIDPADV +DAMRQPVTSLADLRGGDAQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002195.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002195.fa new file mode 100644 index 0000000000000000000000000000000000000000..f25b6726549425404a07645213fa31a39f6ec560 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002195.fa @@ -0,0 +1,10 @@ +>PROKKA_00300 +MSTERDALFQGVEGAGGPSQAAGEDMSASETSDTATACHSGVQVEQQTDSQVNTGRADAE +AVRQSHGGAKRRRGGGGRLDTRFDDATLAALRTRAKRLGLAPSTWVRTVVRDALHASRSE +ELDAAVAAQLLGVEERVQASADARELAAQVRPLAINVNDLDRRARAGEPVALSAEVPELI +ELLHEVRALLGDRAAS +>PROKKA_02368 +MSADQHPLFQGIEGGGAPSQAGLEDTSVSDVSDRPTACHSGVQVEQQADSQVKTGRADAE +AVRQSHGGAKRRRGGGGRLDTRFDEATLGALRTRAERLGLAPSTWVRSVVRDALHASRSE +ELDAAVAAHLLGVEARVQASADARELAAQVRPLAINVNDLDRRARAGEAVALSAEVPELI +ELLREVRTLLGDRTAS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002220.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002220.fa new file mode 100644 index 0000000000000000000000000000000000000000..339e168066008816d65c6503dbb38317a22bee0b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002220.fa @@ -0,0 +1,10 @@ +>PROKKA_01969 +MTAPQLHLPRTVVSDQTDRAVDLLGHYFTPGKFIGGRWDGFDPSGTRAASANVFTSDDVA +SAALLNTPVPGHAVVHLLITQRVHFAGLLEAVGPDRDFIDVDPDPSGKDMAPVYELYEAL +KTLPKIGPTIASKLVARKRPRLFPIIDAELRQTVFHETRKDGYVGRALLHAEFSAQERTI +WQRLASYHSAASLPTEVSVLRVFDVLAWMEAKAYWGPVP +>PROKKA_00458 +MTAPQLHLPRTVASDQTERAVDLLQLYFKSRKFIGSQWDGFDPSGRRAASANVFTADDVA +SAALLNTPVPGHAVVHLLITQRERFSELLRIVGPDRDFIDADPDPSGKDMAPVYELYEAL +KDLPKIGPTIASKLVARKRPRLFPIIDSDLRRTVFHETRKDGHVGRALLHADFSAQERTM +WQRLESYRCAAALPAEVTTLRVFDVLAWMEAKAY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002250.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002250.fa new file mode 100644 index 0000000000000000000000000000000000000000..55afe065c93db4c6fc646c9666aa5ca491e97213 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002250.fa @@ -0,0 +1,18 @@ +>PROKKA_00340 +MSAEEKNLPHGEESTTVGEMNDTVATGLPEEPRTEEGADAPQGARAENPQSDAAAGQCPV +AHGGAALPHPTSGDANQQWWPNRLNLKILAKDQPVQSPHEADFDYPAAFEALDLAEVKET +IAEVLTTSKDWWPADFGNYGPFMIRMAWHSAGTYRVTDGRGGAGEGQQRFAPLNSWPDNA +SLDKARRLLWPVKKKYGQSLSWADLIVLAGNVAHEIMGMPTFGFSGGRIDAYEPADDVYW +GPETEWTNGGAERYKGERDLDNPLAAVEMGLIYVNPEGPEGEPDPLKSAKDIHETFSRMG +MDAEETVALIGGGHTFGKTHGAGPVEPHIGPEPEAADLEQMGLGWKNTYGQGKGRDTITS +GLEVTWTYHPTRWDNEFFHILYAYEWELMESPAGAKQWRPVNGGGSDMVPESDFQGRREP +RMLTSDLALRFDPVFGEISRRFKDDFAAFQDAYSRAWFKLTHRDMGPRPRHRGVEVPQEE +LLWMDPVPAPESVPGDAEVKAVKDAVAQAGLSVTDVVKTAWAAASSFRSSDFRGGANGGR +IRLEPQRSWEVNEPAVTGPVIDALEKIAQEAGVSFADTVVIAGNWAVEKAAADGGVQVTV +PFTPGRGDATAEQTDVTSFGHLEPKVDGFRNWDPRGSKTFPAEFALVDRANLLGVSAPEM +TVLVAGLRVLGAVHGDSQDGVWTDRVGVLSQDFLTAVTDIDTQWEKVAEGRYRGVTADGR +ELTGTRNDLVFGSNPELRTLAEVYAADDAREKFVQDFVRAWAKVMDADRFDAK +>PROKKA_00280 +MHGKGASLPHPTSGDANQQWWPNRLNLKILAKEQQVINAHDADFDYPTAFAALDLDEVKK +TIAEVLTTSKDWWPADVGNYGPFMIRMAWHSAGTYRSGDGRGGAGTGQPLTARPAADDGR +PPHRVGARSAFPPGAGPCLQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002287.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002287.fa new file mode 100644 index 0000000000000000000000000000000000000000..760962c2a4d385d1454244acceafe394eceda182 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002287.fa @@ -0,0 +1,6 @@ +>PROKKA_00852 +MALFRKTAAWGATAAGAVALAAAAMAATWTGPGYTVVNDHSNIFDYKGSIKTTSCVRQSD +GTHLIGGYIRYVQGGRDTGRLWTPTATSCGQTVSRSTTFKDSLALNAPKTQFYYGLNKAP +YGALSEPLGGN +>PROKKA_00789 +MGDSRCGQTVSCSTTFGDSLGLNAPRTYFNFDLNDVPYGALSEPVDGN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002291.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002291.fa new file mode 100644 index 0000000000000000000000000000000000000000..4a0d7885d0c212c3b755b912d7eec29d554aef7e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002291.fa @@ -0,0 +1,8 @@ +>PROKKA_00908 +MSTRSSIPDAVDTDRTAGTIELLEPPREAVEWMASPAPATDLWWTATVCGEADPDWHRLE +TTVAETIEVLVSWAQGHGLPLPYGAALRTYGNPPDLGLVA +>PROKKA_01870 +MSAPGSITADGARGLATHRAPGAVELVEPPREAVEWMASSAPATDLWWTATVCGEEDPGW +HRLESAAQIADLVHALTDPRDKLILEDEPPTRYAQIMLLGDGLFMVEIAKRFEGLGAYNW +RIGRGRAADEAANDPQDLVQPLQELTAAETVEVLVSWAQGHGLPLPYGAALRTYGTPPDP +GLGFDS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002297.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002297.fa new file mode 100644 index 0000000000000000000000000000000000000000..b1c71791080ae22733d0dd7c074d21c75912c52f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002297.fa @@ -0,0 +1,22 @@ +>PROKKA_00960 +MAQNTAGEGLLESIRQGYSFEDATVTLGAAVVDGQVHADAPVRLPLRMMNRHGLVAGATG +TGKTKTLQMMAEQLSSAGVPVFLADVKGDLSGLAVAGEASEKLAERTTATGMPWQSQAYP +VEFLALGGDGVGVPVRATVDAFGPVLLSRIMELNETQESSLQLMFHWADQRGLAMDDLAD +LKAVVTHLTSDEGKADLKGLGGVATSTANVILREVTGLEAAGMAAFFGVPEFETAELLRV +APDGRGVISCLELPTLAAKPQLFSTFMVWLLADLFAELPEAGDLDQPKLVFFLDEAHLLF +DGASKAFLDAITTTVRLIRSKGVGLFFVTQTPQDLPAEVLGQLANRVQHALRAFTPQDAK +ALKQTVQTFPTTEYDLAETLTSAKVGEAVVTVMDPEGAPTPVALTRMWSPQSAMEPAPEE +AMRQIVGASALLPVYGTAQDRESASEVLSAQAAAAAPSTGGSARGSAAGAGDTRVADGHG +GGTVVSGVDLGDIEALRREEEKATARARKEADKPSDFERAMGNFMKSAGTQLGREVVRSV +LGTRGRRGGGLLGGLFRR +>PROKKA_00900 +MAENTALLDTLRAGYTFDDPTITLGAAVVDGEVHADVPVRLPLRMMNRHGLVAGATGTGK +TKTLQMMAEQLSAAGVPVFLADVKGDLSGLATAGTASDTLTERTRATGMPWQAQAYPVEF +YALGGDGVGVPVRATVDSFGPVLLSRIMELNETQESCLQLMFHWADQRDLPLDDLKDLKA +VVVHLTSDEGKADLKGLGGVSTATANVILRKVTGLEASGMDQFFGVPEFETAELLRVAPD +GRGVVSCLELPTLQSKPELFSTFMIWLLADLFAELPEAGDLDKPKLVFFLDEAHLLFDGA +SRAFLEAITTTVRLIRSKGVGLFFITQTPKDVPGDVLAQLANRVQHALRAFTPEDAKALK +ATVQTFPKTDYDLEEVLTGAKVGEAVVTVMDPDGAPTPVALTRMWSPQSTMGPTPEDAMK +AAVAASPLMGQYGTAQERESAAEKLAAQAAAPQGETAVPATGESARDGGNVTVSGVDLGN +IEEIRREEDARARRAQEKADKPSDFEKAMGNFMKSAGTQIGREVVRSVFGTRRRSGGGLL +GGLFG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002300.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002300.fa new file mode 100644 index 0000000000000000000000000000000000000000..817315e9ade6a5ffd2d052cc0334a7b0bda13e4e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002300.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002326.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002326.fa new file mode 100644 index 0000000000000000000000000000000000000000..efe73202ab2558866ab16756c7bb773506fcc1f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002326.fa @@ -0,0 +1,14 @@ +>PROKKA_02652 +MATLAEQVQGERMARVALSMIAEPNDPITGYVLARHGGVETLRLIESDDEVPGLARADTL +MWRERLTARVTPGLLDQMAQAERHGFGTLIPADKEWPAGLNDLSDRAPYLLWTRGAVSFL +MTALSDRATITGARAATAYGEQVAGELAAGLADEERVVVSGGAYGIEGAAHKSVLAASGQ +TIAVLAGGLDRPYPAGHSELLNRIGDVGLLVSELPPGAAPTRHRFLARNRLLAALSGATV +IPEAGPRSGSMTTVIAARELSRGVGAVPGPVTSVASAGPNELIKQGFASLVTQPSDVIDL +LDADRTPDRTVTRPEVGREFGHRHPSPGTPGRSL +>PROKKA_01771 +MSGVAGLGVDERRARVVLALLAEPDDPVTGGLLRRLGAVETLGLLDTDTTVPGLGRVDGQ +VWRDRLTSQGRLDGLDQRLRVLEESGIVILIPGDAQWPRALDDLGERAPYVLFVRGAASF +LARPMQDLVTVTGSRAASAYGEYVAAELAGDLANRERVLVAGGAYGVESAVHRAALAAGG +DTIAVLAGGVDRPYPSGNRDLLDRVGDVGALVSELPPGSVPTRHRFLARSRLLGAMSAAT +VVVEAGARSGAIGVAAEAHQLGRQVGAVPGPVTSVTSHGPHELLRAGHARLVTSAADVEE +LTANRATHRPGLSADFTRHTAPAAGPPERSL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002392.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002392.fa new file mode 100644 index 0000000000000000000000000000000000000000..a33c72621d3b214cd64c0a02f66bee0695a94ec7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002392.fa @@ -0,0 +1,3 @@ +>PROKKA_00621 +MVSAEHGPSGSPYGEVLPGVGGNDSAQDPLVTWWLVLYGLSNLVRYHPAAWRATLDVDKS +TLAVPLEQLVSFASEKVPDLLFEAFVDLGGGRQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002395.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002395.fa new file mode 100644 index 0000000000000000000000000000000000000000..17b4f758b55418d44f8cf30dad0ca1b6f76f1879 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002395.fa @@ -0,0 +1,13 @@ +>PROKKA_00703 +MTARIAVVGSALTRSALVADPRLSVPAGHFLARVSMAGLGTPPVEDADLTGVASDFRREL +VRRDVDRMLVADLVRLDPDAIVVDVADERFALDVLPSGAVVTVSPEYLESAPPQDGRRRV +PSGDDEHFALWVAGWRTFLSTLDAVGLRERLILHHGGMAVRTADGTAARHEAAILAAARY +ADRLADRAAQDLDPARVVRVDDAIRHAALADDGTADPLALAPAAAAALAAGVVAVLDGRD +PWEVDGLVDVSPDAEPVEPAAPQAPAEPAAPEPSAEPAAPEPSAPYRDVVESDYANYGVD +PVRWGSVEEFAASGFGPGLHILPLPDGNHLDLIIRGDLGGVGERESVVVFLTGAMSQRNS +VAPPFFAGRRLSYELGIPWVAVSDPSMQLADDLLLGWYTGSPGSQAHATLLATLRALADG +LGRDLLLVGGSGGGFAALRLNEELEGRSSVFAWNPQTDLLDYHPPTVRDYLRTLFPGKEL +DPVAEREAVEARLAEEGIGHRVGTLDAGRRVVVFQNAGDHHVEGHLLPLVHRTPGMTGGP +RRFATDAEHQVRIATWGAGHAALPAHVTARAVDAMRRGHSASTVATDIDALLAHERGDDS +DGPDVLVTAEPGGLSRVDWAAFPGEADDGHACTLSRMHGEDVVDQVEHIGPPVVLPRLDD +GEHWRLEAFDARGRRVHEIHVDGRGDPVLFGGTGGSARPRRARQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002421.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002421.fa new file mode 100644 index 0000000000000000000000000000000000000000..a269b4d8052ad3ae230fb6982bca1223c40247ab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002421.fa @@ -0,0 +1,3 @@ +>PROKKA_01959 +MNKHDETLAQLREFVAERDWARFHTPASLAKSISIEAAELLEHFQWTEDGADMAEVQDEL +ADVLTYAFMFADHMGWDVDEIIQAKLVKTRVKHPVPTGGDEEATSS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002431.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002431.fa new file mode 100644 index 0000000000000000000000000000000000000000..f7896ec3e82e774b6c0d5a801e852b1bd6f44cf2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002431.fa @@ -0,0 +1,8 @@ +>PROKKA_00014 +MIPSEEEVDWSEVTGSAHSSGPSGSTRETGPIGPTLDAVDGWLSRFIRTTTPEDIHLLTL +WAAHTYVVEQTYTSPRLQIDSVMPGSGKTTCLEHLAHLARRPLSASTISSEALLPRVLES +GIRTILIDEADRSLDMKNPIMAGVLATINTGYKRGGSRPVLVKDAEGNWTDREMSTFAPV +ALAGNNPNLPDDTRSRCIRVLLMPDLDGTAEPSDWEDLEDDADRLQVQLSEAMDAARDAV +AEARPELPPGCVARHREKWRPLARVAAVAGGRWPSIVERLILRDLQEHETEKEEGLMNRP +LRVHLLFDLAEVWREGEAFVPTPELIARLAHVAPHRWGAESLKGLTPQGLGRMLMTGYKI +ASDREPTGARRRGYTRQALEPAWRLFHIDLSDSDRTSPV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002459.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002459.fa new file mode 100644 index 0000000000000000000000000000000000000000..c13797aa1b8287fad4818b315ce5584624ffa838 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002459.fa @@ -0,0 +1,2 @@ +>PROKKA_01699 +MVRGIFWVSHSKEAIMALLRKTAAWGAAAVGAVARVQYGALSEPIGGN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002477.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002477.fa new file mode 100644 index 0000000000000000000000000000000000000000..8f906cc1806ee321c509458c9c5a39791439eda5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002477.fa @@ -0,0 +1,8 @@ +>PROKKA_02221 +MSTTKTAPAYTTAEDIRAQVHAHAEEERRDASAHGAMLNLMQKIGDGREDPEPDLDAAYE +QARISGDWEEYERIFRAHDDWADRSAKRARMANNLRSRAIPNPERRRTLKGDAGRLTLAY +LAGALPSILDAAQRLTLHGVPSTAEAAMTADPRTRGRYLEAAAVVDAYRALRRAQAAAVT +DINATASDSFGGPSKVSSQSVLTIGQFRDALHLDATWLSNRRNAIGQLRSSATRAHLRRY +VPGIVEFLDDAPAELFGPITADGFPAECTTVPARAQWLATWSTRLDFWVPEFEDLQQLQH +LYGAAINPGHWQDRKGLVLANTYEGESAADNAERLALVNLDYRRPDWDTPQSEPTAEDLD +ATTANRAALPREQHPGLRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002498.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002498.fa new file mode 100644 index 0000000000000000000000000000000000000000..cf80771e94156ccabfa35054c146104990252180 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002498.fa @@ -0,0 +1,6 @@ +>PROKKA_00103 +MTTTAAAPVTAPAPDAMVGFVRTTSRVGTATMLVGLLLSLAGPAYLYFFTDLGVTPQEIL +KAYVAVALVFGVLWIVEPLSYFPVLGSSAMYQAFMIGNISSKLLPAAVVAQDTVKARPGT +PRGDVAAVMAICGAATVHLLSLFVFVGLLGTWLVSVLPADLMLVVGTYILPAVLGAVFVQ +AIMSYKAPRTTLIALAVGALITFLVVPAVPTLKFVGVPLTVVLTVVLAWFARPRTAPTRA +DDDVELHY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002510.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002510.fa new file mode 100644 index 0000000000000000000000000000000000000000..f69c6891bc16dcd10867eccfa5e71ed824e267e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002510.fa @@ -0,0 +1,3 @@ +>PROKKA_00179 +MDRIVVHDALDRLGPPQDEILRLAFHKDLPQKEIAERLQMPLGTVKSHIHRGLAALRATM +TRTEEVHDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002551.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002551.fa new file mode 100644 index 0000000000000000000000000000000000000000..820494d0e896fe3b9a158c4874fe7ce365da378b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002551.fa @@ -0,0 +1,2 @@ +>PROKKA_00498 +MKFVILIHSHPQPWAHPTSEHTAEYQALPPATQERAEEIAAAFSCPGDTVELRPVWEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002561.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002561.fa new file mode 100644 index 0000000000000000000000000000000000000000..22c0e48b0b2515048d9189a9bc8345bab8b6c2d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002561.fa @@ -0,0 +1,3 @@ +>PROKKA_00555 +MGHRIFTTAVADVYPHYVAKVERKGRTVEELHQVISWLTGYDDAALARHLETGTTFEDFF +AEADMTADADLITGSVCGVKVQEVEDPLMKRIRQLDKVVDELAKGKSVEKVIRTPAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002604.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002604.fa new file mode 100644 index 0000000000000000000000000000000000000000..b9311aad418b53ccc1ec9d0142a114a7cf752cd3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002604.fa @@ -0,0 +1,7 @@ +>PROKKA_00821 +MFRRTVGDHAEWKELISRSFVPLESEPLRPSRSFSGRLDVSEFGGIGLTTLAAGPHAVHR +TERLAAAGGGGMFKVSLQLSGRGLLLQDGREVLLEPGRLAIYDTSQPYTLSFDRDFTSHV +LMFPHTALGIAPGQAAQVTATALDEGHRLGPAVSAFLTQAADAMPVLDPATGGRLAHNVV +DLVGTLVADLLGLPPRPAEGARPAPAEGTDDARGRQRAAVLRHIDEHLADPALSPASIAA +AHFMSVRSLHLLFEGTGETVAATIRRRRLERCRDELGDPGNAGRPVAVVGARWGFADPAH +FSRAFRARFGVTPGGYRRQAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002624.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002624.fa new file mode 100644 index 0000000000000000000000000000000000000000..2a67276568d6f8b4e18157bff0c46a54c28da029 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002624.fa @@ -0,0 +1,7 @@ +>PROKKA_01222 +MRILLSSVGRRPYLVRWFRDALAANGVEGTVLAADVDPDAPSRPFADGFVSAPKVVDPGY +ESWLRQTLVDHDVDLAVSINDFELSTWATLPEDPAWAPLVRLDAGTQRLVEDKFATSQAL +LEAGVTSPVTWLGSTPPSTEDAAGPFVTKGRYGSASRGLRFVDRAGLPGALEEASGEVTT +RQGVPALQQDAVPPAELIVIQERIDGVEYGLDVVCDLEGRYAGVLARRKITMRSGETDRA +VSVDAAPFESIARGIAEAIPHPGTIDVDVFVDASGDIYVIDINPRFGGGYPFSHMAGARV +PECYVAWALGRKAGAEWLRCRPDVVAGKFVEITATSEGGTGADA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002630.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002630.fa new file mode 100644 index 0000000000000000000000000000000000000000..a22093a32d023dbbb564bcbc853bacab2307c1ec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002630.fa @@ -0,0 +1,5 @@ +>PROKKA_01289 +MPLATPTLDTERLRLRPFTEADGDALFALMTDAEVLRYWDSPPWKDRGSVERFMAGNVRA +AEEGTGARVAVECRSDGAFLGWCTFNSWDPDFRSASLGFCFTRDSWGQGYATEAARALLQ +WAYSTLDLNRVQAECDTRNPASARVLEKLGFRLEGTLREDCIVDGVVSDSWVYGLLRRDW +QMHGASAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002635.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002635.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a07e8bdd009c6a92d3f9f7e4ab7c1ef8144bead --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002635.fa @@ -0,0 +1,8 @@ +>PROKKA_01307 +MNIAWTRRPRARVVCVGVVLAVLLTGCGASRGDGSTPSSSSAPPGTPTLGEGSSSGDQDT +LAYVDRALDVLDTGLYASGERWERARAQVQEAARTARSPRDLDSVLRYATGVAGGKHSSF +APGADPDVRGGRSTSSASESPRMNVALPTVTTTDGVSTLSLPALPVASDDPQASEYAMVL +ADGIDAAAPATCGWVVDVQGNLGGNMWPMLSGVSALLPEGPVMFFRDRAGEDTAVTVQED +GAGTEGMTFVSVGPRTQRDGAPIAVLQDRSTSSSGEAVLAAFRGLPNARSFGQSSSGYGS +GNATHVLPDGSRITLTAAEFVDRGGEVLGDRPVDPDVPIRRDGGGGTDAAQAAARIWLQE +RGCP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002643.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002643.fa new file mode 100644 index 0000000000000000000000000000000000000000..7eb9054e924dedfc17c333a691d18badb3ac2296 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002643.fa @@ -0,0 +1,8 @@ +>PROKKA_01341 +MTFHVAVDARSPRMSHCSCSSPRIGVSWVSSPGGVLALVGAHVQGEHVERRAAGDPAVDA +GGLEAGAAAQGRGVGDGHVLLPRAAGAGGQRVHVTDLGVARVFEDLARPPVVGRLVVVPL +GDDGDVRVQGAEVVVHHVVAVAAAELVQRLGDLGRLLRDEVAPGGLAGHLEGLRDGVVRV +DRVAGVQEEVGLRGVHRRVAAHAADLRVDAVALPRGVRGPHEGLGGGGLPAEPRAGRRGE +AGHGRLAQAAGLVLERVRHLEAGAGGQRVREDLRGVVGGPVDPAGVQGQPASEAAAQHLP +VLVDRAQRGVQARTAGRARPQHGRVRGDVAGGDAGRQRQTGRGQATGGVAGRTGGGGVGE +GGGGEHGGGRRGEHRTAGGGVGQGCGGLLHGARVGHAGEGHVASG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002663.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002663.fa new file mode 100644 index 0000000000000000000000000000000000000000..d7518915efc89c438a57176f3d649616b760131a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002663.fa @@ -0,0 +1,3 @@ +>PROKKA_01725 +MPGAGGDGGRQDVPPGGGLGVLESLGQAGDAVRSDADAERGEDLHEGLVRDGLGRAVLAD +VVRLHAVRAGESAQQRAGFQGHRVLHAVVSGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002758.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002758.fa new file mode 100644 index 0000000000000000000000000000000000000000..009a19dba3aa73461a59baa12a657e83c6a89fb5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002758.fa @@ -0,0 +1,4 @@ +>PROKKA_02267 +MSRTSDPVQPSRPRPVLLLALAVGAVLVYALQGLVPLLMDGEVPRPDELLAPPSPVVLGG +PIAWAAALAALVLPRGRAHPLATTAVGTLAYVAGLALGAFVEIGPGTGGWNWGWESVVAI +LLVTGVWVPALVAAAALAWLARPRRTPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002767.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002767.fa new file mode 100644 index 0000000000000000000000000000000000000000..038e67afbb7a211c70c9a1a23747e23adc2354a3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002767.fa @@ -0,0 +1,5 @@ +>PROKKA_02405 +MRSTRPGMFSVIIPTLQKSPELREVVRRCAAHPAVAEVLVVNNAPEPLGWTEPKMRVLQQ +SENIYVNPAWNLGAREARGDLLAIVNDDVLFEPEVLDECRKVLRRGLFAVIGPGEACFEA +APRGRIGHQVAPFFSFKGRFGTFMAMRREDYVEIPEQLRIWGGDDWLLMQQRRPNAVLTN +TRFVTDMGTTSSSPEFRALRERELTVARRVLNPLYRSRWWHRPIEYLDRLRRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002791.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002791.fa new file mode 100644 index 0000000000000000000000000000000000000000..266c7b4f275671b6d57756adda10022e99e13ac2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002791.fa @@ -0,0 +1,2 @@ +>PROKKA_02654 +MHDPHDRTRPLRVGSLFSGYGGLDLAVEHALDGETIWFSENNEHVSRIFAHH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002792.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002792.fa new file mode 100644 index 0000000000000000000000000000000000000000..7bfaf1772e04c883eec37db9b2f4a6e4fa4f8a46 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002792.fa @@ -0,0 +1,7 @@ +>PROKKA_02655 +MGKRAGLAPGTRSGLWSYMAAAIDALQPQLVVIENVRGLLSSPAVRAPLEEDDDAQSNPD +HATPGDAALREVEPDPWGLGDLAARPLRAVGAVLGDLADLRYDTQWIGLPASLVGAPHPR +LRVFILARSRGTVQDAARHGLDSWRRVTGTGEGEAGDDRALASDHRPRAKRAGWLAEQEQ +RTRDAVVPDRGHLRRWGRYARAIARWEHVTGRIAPALLDRTSGPRPSPEFVEWLMGLPSG +WITDPIHQLTANQQIAALGNGVLPLQALSAMRVGALVQADAASLAGVQHPMVSRGCTVSQ +EEEGEDEKAGESA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002803.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002803.fa new file mode 100644 index 0000000000000000000000000000000000000000..efa8b1bb1311c5ab23651ceddcebb1f746b00cad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002803.fa @@ -0,0 +1,2 @@ +>PROKKA_02672 +MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWGSSPS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002822.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002822.fa new file mode 100644 index 0000000000000000000000000000000000000000..aad6449e9c4eb7213a68df340f28ea3b8b40ba98 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002822.fa @@ -0,0 +1,3 @@ +>PROKKA_00210 +MVTTATRHHRRTPAGTLRTAAPFFAVLAARHGIPAPDAPTPARTPTTAPRATQDTRPAQD +HLPNLEGHQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002824.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002824.fa new file mode 100644 index 0000000000000000000000000000000000000000..a3a9745dc7b08636c3cb6809b6ad61a0297696de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002824.fa @@ -0,0 +1,3 @@ +>PROKKA_00212 +MSAPDRYRLDPAVLDVEARTPAAGARLPSGWVRAATAAARAMGEPFTPARLRAALPEPVH +PAHFGAVVRHLHAARVIRPAGLALERSPDGSARPVRVWEAVPEDAQDPAEDTATPAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002837.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002837.fa new file mode 100644 index 0000000000000000000000000000000000000000..e5b61edb3919fc7497282f762ecf72c37a05647f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002837.fa @@ -0,0 +1,3 @@ +>PROKKA_00311 +MPVISTLRRVGAAVTAAAALTTLGAGAASAADYKLPYPSGESYRVTQGNFGNYSHTGAYN +QYA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002860.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002860.fa new file mode 100644 index 0000000000000000000000000000000000000000..bd3e982223b8e3eaf4e60768b5d76c5e39339165 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002860.fa @@ -0,0 +1,6 @@ +>PROKKA_00438 +MSKNPQTVTDVAATGAISRVELTWTPLPWEPLIDHYRVYALPTSGRGGTPDETHLVGKTV +YPRFVHHGLDPAGEAFRYVVVAVSDAGRRGRPSSAVVGESQRSVTATGRELARIGEFDGK +SLELRFAPAQYGQIPKAYPKAVIDYVQGVDTPAEAWPYLLPGPGDAWAGRKAYRARWTVT +LDAAPQREVDLALWFVDTTRLGGRLDVAVNGQSVRSVELAKGATRGSREGDATLPGSTLL +RSYHEFTLPTGALAAGENVVEFTLAEGGWVAWDALGLYERAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002881.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002881.fa new file mode 100644 index 0000000000000000000000000000000000000000..f0ca9ec268ad8cb19f2fb44e025285ffcb126eb0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002881.fa @@ -0,0 +1,4 @@ +>PROKKA_00623 +MGDGVEDPESQREAIRAEASRIHESAVFSAQGQFEAAKRWRLVHWGLAVLAAGLSSGTAV +FTFADGAQAWSAVLAVLAAISTTVLASARPDRLAERAQVAGTGYTTLRNDVRRFHGITVP +QGDPQDLAGELDALADRAAALDQSADPVPRWAYERARKNIEHDGGQAFEADV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002893.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002893.fa new file mode 100644 index 0000000000000000000000000000000000000000..ae566c11e1da10b943988982db32e0bfa72aa6a6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002893.fa @@ -0,0 +1,8 @@ +>PROKKA_00681 +MRDRRLFRELERPGLIVSNLTPNWFASIMGTGIVAVAAASLPLQFPGLRTAATVVWAIAA +VLLVALTIATVLHWVRYRSTAAKHHLNPVISHFYGAPPMAFLTVGAGTILLGKDWIGLPA +AVTVDWVLWTIGTIGGLLTAVLVPYLAFTRHENTPESAFGGWLMPIVPPMVSASTGALLL +PYAPAGQARETLLWSCYGFFGLSLITSLVVITLIWNRLAQHKVGAAGMVPTLWIVLGPVG +QSITAVNLLASNAPAVVDASTAHALLVVALVYGFAMLGFALLWTVIALAITIRTAREHLL +FSLTWWSFTFPVGTCVTGLNGLALHSGLTVVAVLAVVYYVGLVAAWITVAVRTFHGSVIR +GTLLAPPQPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002918.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002918.fa new file mode 100644 index 0000000000000000000000000000000000000000..4b8b608934973cd627a5d1f43cc5a126f4314a0c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002918.fa @@ -0,0 +1,3 @@ +>PROKKA_00871 +MHRTTITAPTSSRRHRSAGVAVGLAVVGLVMTACSAGKAQEPRPTTSAHVQAQGEGASRR +SRKWREPGRWSTT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002972.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002972.fa new file mode 100644 index 0000000000000000000000000000000000000000..b07e9166858af155b1628b73a59622ee74d77474 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002972.fa @@ -0,0 +1,6 @@ +>PROKKA_01782 +MTHTTTPTTGTAAETGRGSSATPSTPHPDRADFRTSEGLRALLEHLAEHGWRNNPQAKEL +LEFAAERFAPLARKHGLDVWEAASAAFDVMRTPAARKAADPWAVVTHAVRITCIYEERAQ +GLMCSVHQARRAHISAHHDPERFSDRETPLYEYHPAFHLTDLHHREDAEPSEDVGASVQA +AVADATGLFALLGWPEASARAGVDHVTNALARIGSRRGTYEALRRDKHARALLDLPAPAW +TCLLRVLLGHPEPAYATTTAGRGILLRLLLGETLADLLGDDALVASIVRATPGRGRVRS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002988.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002988.fa new file mode 100644 index 0000000000000000000000000000000000000000..177a005f81d4a1e33a37670d3b76c43443521c88 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002988.fa @@ -0,0 +1,6 @@ +>PROKKA_01833 +MTSNATDQPHVILVPGYWLGAWAWDDVVPALKEHGLDVEAVTPPGLDEQDLNRKNATLQE +QVNALQALVEQAGGDVVLVGHSGANAAVSTVTDRIPQLLRRVIWVDSGPMTDGAAFAPEL +PQDIEELPLPDFDTLGQQASLEGLSDGQLKTFRARAVPEPAGVARASVSLNNDRRYGVPT +TLICCSLPSSQVLELAQARHPMFAAVNDLIDVQFIDLPTGHWPMWSRPEDLGKAIATAAL +AS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002989.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002989.fa new file mode 100644 index 0000000000000000000000000000000000000000..eadb1a553a25f1515c7f0311e56575684415106a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002989.fa @@ -0,0 +1,3 @@ +>PROKKA_01834 +MTDQRVLRIDFVSAAGEHTRRDVEPILFAGTRGSWYLIGWCRLRGAVRWFSLDRIRKATL +TRHPCSGHTVDEIGTPPDTAASVALD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002997.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002997.fa new file mode 100644 index 0000000000000000000000000000000000000000..1fb20fdcca9553f6f5b59522046793c775fcd6a8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002997.fa @@ -0,0 +1,7 @@ +>PROKKA_01978 +MTDSTLLFDAAVTGDRGAVRSSAEALAAVLAADPGDPDAWAALPAAQWAAEQTALTGYAE +LFNTALPAALALRVAAGSGGRLPEGVAGAWAARLDPTLDAERRAGIDAALADAVAGERER +RGVPTPEPFEDEPRTVFPRGFMAALTRLRSAALPVPPLYTAALRVVEAPVDEPAEPRPAR +PLGELLDALVALEDLEWRRPATEKQIATLEQRTGVTLPADYRAFLERANGSKDREFEGAH +EVARDAKEPPVYSHGTGEFVILDCAPGPEGTAGKVLSYGEGETRVTHPDFRAWLQDHVED +LED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003000.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003000.fa new file mode 100644 index 0000000000000000000000000000000000000000..ccb791b255fbee5cfbe071d00004bd0100bf2430 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003000.fa @@ -0,0 +1,10 @@ +>PROKKA_01981 +MASSLESRADESDPPRRRPDGMNGLISRHQTAEMTCANAINALYGGTRYVQVSADGSAPP +AGSEAYGMSREMLNSASGAGETPWGMPAVWDKPWYLDVADAVVDFGSGVWESLKGTVTGL +LAMVNPFDWETFSATWKGIGTLAVDLAVTATPVGLLVSDERRAQSGQRLVQVGEAVLNVE +MWKENPAKAAGMLTGDLATALVPGGAAVKGASVAAKSGKAASVLGKAARAADTVKELGTA +AKFKVAFKAEDLVRGLSDKKFAVTDALHSKASAFAYRHPQVGAMASTMRTVWEFDVNKAA +KVFSDGMLAKVPAVGVLADGGVMWVKSGESFSSVLRRAVDEGVSPVRSGGGGLPAGVVEG +KGTMVMRPSPKWDLSTAEGRASYEAFVGKVDQYKQFVSSPERLGFTKPDARTIKRSDFMK +DPDYALGRVTDLRGNQAPALLKGVEDDILRRLEDEMTRHNAAKGSRGEIADWHELPQYTQ +ERAVRAAMKGFDLDHARDLQLGGRDAHENLQWLEKSANRSAGFAGAASSG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003017.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003017.fa new file mode 100644 index 0000000000000000000000000000000000000000..85ce072c9df400c18559e71f90096b517ce641f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003017.fa @@ -0,0 +1,6 @@ +>PROKKA_02238 +MDVSGIPTHDGLDDAFASVGMTIPRDTPSGESITKPRRMRTAFETADSNGLKATRRLISA +LVDELRHRDVFQHPAPEIVAAVQAVRQLITEGGATLTTDGFITTAVAFPTVDAGQRETVD +RLIARLRRNDQDPASILGTAKDLLEATSKHVLHERAPQQRQKDMPNIVYEAMEALDLSTK +PSSINGPSAGAIAQLHQLIARTAQAVTASRNDGGDGHGHLNPTGVSPELAEYVRVVTLAA +TKFLLDNAT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003047.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003047.fa new file mode 100644 index 0000000000000000000000000000000000000000..480b5c2f2506b49404fb94d8df222cc5b46d7462 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003047.fa @@ -0,0 +1,5 @@ +>PROKKA_00892 +MKSVLHTRTAIAAALLLGLTACGDTASPAEEDAPAAAGSSTASAPAGAEEETEADEPEQQ +AGGTAGTREDPLPLGTPIEGEDWVVTVNEVTPDATDAVMAANQFNDAPAEGTQYLLADVT +VEYTGDESEMIMLGTGFAFVTATGETIDAGDAFAVGPEELDTAQELYNGGTAQGNVVLQV +PEGADGLLRVTTGMFGGEKTFVALD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003048.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003048.fa new file mode 100644 index 0000000000000000000000000000000000000000..d8f665564402bacfdd4f70adcd1e5e46e07f79ff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003048.fa @@ -0,0 +1,3 @@ +>PROKKA_01015 +MALDIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPIGLDAAAYKGRNVIERQYAHLK +QWRGLATRYDKYAIIYRAAVVLNAVIAWSKRLSDMP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000174.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000174.fa new file mode 100644 index 0000000000000000000000000000000000000000..309769e3f7471c8aa7fe20a0e22b05c6ff63fa0e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000174.fa @@ -0,0 +1,50 @@ +>PROKKA_00001 +MVADQAVLSSWRSVVGSLEDDARVSARLMGFVYLAQPQGLIGNTLLLAVPNETTRETLQG +TQVADALTDALTQEFREEILLAISIDANLQPPRTPSSEARRSSLAGGPSGAAAPDVELPP +AATAATSRRAVAEELPGFRIEPPADVVPAANAAPNGNGKPTPAPPSTSAETSRLNDRYHF +ETFVIGSSNRFAHAAANAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGLRV +RYVNSEEFTNDFINSIRHDEGASFKQVYRNVDILLIDDIQFLADKEATVEEFFHTFNTLY +NNNKQVVITSDLPPKQLSGFEDRLRSRFEWGLITDIQPPDLETRIAILRKKAEAEGLVAP +PEALEYIASRISTNIRELEGALIRVTAFASLNRQTVDIELAEHVLKDLITDETAHEITPE +LILHATGEYFNLTLEELTSKSRTRTLVTARQIAMYLLRELTEMSLPKIGQVLGGRDHTTV +IHADRKIRELMAERRTIYNQVTELTNEIKRKQRGA +>PROKKA_02006 +MVADQAVLSSWRSVVGSLEDDARVSARLMGFVYLAQPQGLIGNTLLLAVPNETTRETLQG +TQVADALTDALTKEFREEILLAISIDANLQPPRTPSSEARRSSLAGGPSGAAAPDVELPP +AATAATSRRAVAEELPGFRIEPPADVAPAATAAPNGNGNGKPTPAPPSTSAETSRLNDRY +HFETFVIGSSNRFAHAAANAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGL +RVRYVNSEEFTNDFINSIRHDEGASFKQVYRNVDILLIDDIQFLADKEATVEEFFHTFNT +LYNNNKQVVITSDLPPKQLSGFEDRLRSRFEWGLITDIQPPDLETRIAILRKKAEAEGLV +APPEALEYIASRISTNIRELEGALIRVTAFASLNRQTVDIELAEHVLKDLITDETAHEIT +PELILHATGEYFNLTLEELTSKSRTRTLVTARQIAMYLLRELTEMSLPKIGQVLGGRDHT +TVIHADRKIRELMAERRTIYNQVTELTNEIKRKQRGA +>PROKKA_00423 +MVADQAVLSSWRSVVGALEDDARVSARLMGFVYLAQPQGLIGNTLLLAVPNETTRETLQG +AQVAEALTDALTAEFREEILLAISIDANLQPPRAPEPEARRSALAGEPVTPAAPAAPGPE +QSAGTGEPSRRAVAEELPGFRTEPPADVVPPEAAGAQAGKPTPAPPSTSAETSRLNDRYH +FETFVIGSSNRFAHAAANAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGLR +VRYVNSEEFTNDFINSIRHDEGASFKQLYRNVDILLIDDIQFLADKEATVEEFFHTFNTL +YNNNKQVVITSDLPPKQLSGFEDRLRSRFEWGLITDIQPPDLETRIAILRKKAEAEGLVA +PPEALEYIASRISTNIRELEGALIRVTAFASLNRQSVDIELAEHVLKDLITDETAHEITP +ELILHATGEYFNLTLEELTSKSRTRTLVTARQIAMYLLRELTEMSLPKIGQVLGGRDHTT +VIHADRKIRELMAERRTIYNQVTELTNEIKRKQRGA +>PROKKA_00376 +MAADQELLDRWREVVTALDDDPRVSARLMGFVYLAQPQGLIGNTLLLAVPNETTRETLQG +AQVADALTDALTAVFREEILLAISIDSSLQPPRTPSADDRRAEELPDLAAARAETSPAPA +PAAGMHRGVAEELPGMPAPREEPAPSRAAAPAAGAPTPAPPSTSSETSRLNDRYHFDTFV +IGSSNRFAHAAANAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGLRVRYVN +SEEFTNDFINSIRHDEGASFKAVYRNVDILLIDDIQFLADKEATVEEFFHTFNTLYNNNK +QVVITSDLPPKQLSGFEDRLRSRFEWGLITDIQPPDLETRIAILRKKAEAEGLVAPPEAL +EYIASRISTNIRELEGALIRVTAFASLNRQPVDIELAEQVLKDLITDDATQEITPELIVH +TTAEYFNLTIDELTSKSRTRTLVTARQIAMYLLRELTEMSLPKIGQELGGRDHTTVMHAD +RKIRELMAERRTIFNQVTELTNEIKRKQRGA +>PROKKA_00001 +MVADQAVLSSWRSVVGSLEDDARVSARLMGFVYLAQPQGLIGNTLLLAVPNETTRETLQG +TQVADALTDALTKEFREEILLAISIDANLQPPRTPSSEARRSSLAGGPAAAAVPDVELPP +AATAATSRRAVAEELPGFRIEPPADVAPAATAAPSGNGKPTPAPPSTSAETSRLNDRYHF +ETFVIGSSNRFAHAAANAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGLRV +RYVNSEEFTNDFINSIRHDEGASFKQVYRNVDILLIDDIQFLADKEATVEEFFHTFNTLY +NNNKQVVITSDLPPKQLSGFEDRLRSRFEWGLITDIQPPDLETRIAILRKKAEAEGLVAP +PEALEYIASRISTNIRELEGALIRVTAFASLNRQTVDIELAEHVLKDLITDETAHEITPE +LILHATGEYFNLTLEELTSKSRTRTLVTARQIAMYLLRELTEMSLPKIGQVLGGRDHTTV +IHADRKIRELMAERRTIYNQVTELTNEIKRKQRGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000178.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000178.fa new file mode 100644 index 0000000000000000000000000000000000000000..cb63f5422c43a2c42cac1cfa54122c164c771626 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000178.fa @@ -0,0 +1,65 @@ +>PROKKA_00005 +MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG +MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT +EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF +ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL +TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEDAEQEPQRRSVTYLYENGLLDYVQHLN +SAKKVEYVHDNVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG +FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE +ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP +GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN +AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG +HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ +ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV +>PROKKA_02010 +MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG +MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT +EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF +ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL +TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEEAEQEPQRRSVTYLYENGLLDYVQHLN +SAKKVEYVHDDVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG +FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE +ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP +GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN +AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG +HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ +ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV +>PROKKA_00419 +MLAAPSPDAAPETPEAPALAKDRRVPGEYGASAITVLEGLEAVRKRPGMYIGSTGPRGLH +HLVYEVVDNSVDEALAGYASGIDVTLQADGGVRVADDGRGIPVDLHPTEGKPTVEVVMTI +LHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSFADGGVPQGELVQ +GEATDATGTVQTFYPDPEIFDSIEFDWETLRARFQQMAFLNKGLRITLTDERVQEDNEVV +DDEIAGEAAAEENAEQGLDEAAAQAPQRRQVTYLYENGLLDYVQHLNSAKKVDFVHEDVI +AFEAEDAEAGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEGFRAALTSLVNRYA +REKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSEARAFVSKAVTDHL +GDWLERNPGPAKEVIRKAIMASHARMAARKARDNARRKSPLESFGMPGKLADCSSKDPSR +CEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGNAEIQSMITAFGTN +IGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAGHVFLAQPPLYRIK +WSNAPHDYVFSDAERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQELWDTTMDPEHRT +LLQVSMEDAAAADAVFSMLMGEDVESRRNFIQQNAKDIRFLDV +>PROKKA_00371 +MVDAAPEQPEQPSAPAPDTNPAHQVQEYGASAITVLEGLEAVRKRPGMYIGSTGPRGLHH +LVYEVVDNSVDEALAGFADGIDVTLQADGGVRVQDNGRGIPVDIHPTEGKPTVEVVMTIL +HAGGKFGGGGYAVSGGLHGVGISVVNALSTRVETEIRRQGHAWRMSFANGGIPQGELVKG +EATEETGTVQTFWPDPEIFESVEFDYETLRARFQQMAFLNKGLRITLTDERVQEDNEVQE +DEIVGEGTAGEDAAAENGLDDEQTPQRRCVTYLYEDGLLDYVKHLNSSKRAELVHEDVIA +FDAEDAERGMALEVAMQWTTAYSESVHTYANTINTHEGGTHEEGFRSALTALVNRYAREK +EILKAKDDNLSGEDIREGLTAVVSVKLSEPQFEGQTKTKLGNSEARGFVSKVVTDHLGDW +LERNPGPAKDIIRKAVQASHARMAARKARDNARRKSPLESFGMPGKLADCSSKDPARCEV +YIVEGDSAGGSAKQGRNPDTQAILPLRGKILNVERARLDKALGNAEIQSMITAFGTNIGE +EFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAGHVFLAQPPLYRIKWSN +APHDYVFSDEERDAAIEAGLARGWRYPKDNGVQRYKGLGEMNYQELWDTTMDPEHRTLLQ +VTMEDAAAADQVFSMLMGEDVESRRNFIQQNAKDIRFLDI +>PROKKA_00005 +MPENPAEEPTAASAAPNPEAVPDAVGQPETPVKDRKVPGEYGASAITVLEGLEAVRKRPG +MYIGSTGPRGLHHLVYEVVDNSVDEALAGYATGIDVTLQADGGVRVADDGRGIPVDLHPT +EGRPTVEVVMTILHAGGKFGGGGYAVSGGLHGVGISVVNALSRRVDTEVRRQGHVWRMSF +ADGGVPQGELVKGEATDATGTVQTFYPDPEIFDSIEFDYETLRARFQQMAFLNRGLRITL +TDERVQESNEVVDDEIAGEGAAGEDVAENGLAEEAEQEPQRRSVTYLYENGLLDYVQHLN +SAKKVEYVHDDVIAFEAEDVSDGRSMAVEVAMQWTSAYSESVHTYANTINTHEGGTHEEG +FRAALTSLVNRYAREKEILKPKEDNLTGEDIREGLTAVISVKLSEPQFEGQTKTKLGNSE +ARGFVSKAVTDHLGDWFERNPGPAKEIIRKAIMASHARLAARKARDNARRKSPLESFGMP +GKLADCSSKDPERCEVYIVEGDSAGGSAKQGRNPETQAILPLRGKILNVERARLDKALGN +AEIQSMITAFGTNIGEEFDISKLRYHKIVLMADADVDGQHITTLLLTVLFRYMRPLIEAG +HVFLAQPPLYRIKWSNAPHDYVFSDEERDAAVEAGLAKGWRYPKDNGVQRYKGLGEMNYQ +ELWDTTMDPEHRTLLQVTMEDAAAADAVFSMLMGEDVESRRTFIQQNAKDIRFLDV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000180.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000180.fa new file mode 100644 index 0000000000000000000000000000000000000000..86e335898ae77fc7184344cb33662f776dd803f0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000180.fa @@ -0,0 +1,20 @@ +>PROKKA_00007 +MSTSASSRPGQGRSTGKAAEPRSGRPVRKASGSSQEDLVRAVPKAKVRRARLVLTRVDPW +SVLKLAFLLSVALGILTVVAAVALYSLSDVLGIFDRVNDVIGTVLGSEAGRYTVASLAPL +STVTSLATVLAVVNVILLTALATVAALLYNLCASLVGGIGVTLTDD +>PROKKA_02012 +MSTSASSRPGQGRSTGKAAEPRSGRPVRKASGSSQEDLVRAVPKAKVRRARLVLTRVDPW +SVLKLAFLLSVALGILTVVAAVALYSLSDVLGIFDRVNDVIGTVLGSEAGRYTVASLAPL +STVTSLATVLAVVNVILLTALATVAALLYNLCASLVGGLGVTLTDD +>PROKKA_00417 +MSTSASSRPGKAAGAGRTAERSGRPVRKASGSSQENLVRAVPKAKVRRARLMLNRVDPWS +VLKLAFLLSVALGILTVVAAVALYSLSDALGLFQRINDALGTVLGAESGRYTVQSLAPLS +TVVSLATVLAVLNVILLTALATVAALLYNVCAALVGGVGVTLTDD +>PROKKA_00369 +MSTSASSRPAGAKGASASRPARRSSSRDSQEDLVRAVPKAKVRRARLQLTKVDPWSVLKL +AFLLSVALGIILVVATVGFYTLAELTGVFGKINDVLGTVLGTESGTYTVENLAPLSTVVS +LATVVAVLNVILLTALGVVGALLYNVCASLVGGVGVTLADD +>PROKKA_00007 +MSTSASSRPGQGRSTGKAAEPRSGRPVRKASGSSQEDLVRAVPKAKVRRARLVLTRVDPW +SVLKLAFLLSVALGILTVVAAVALYSLSDVLGIFDRVNDVIGTVLGSEAGRYTVASLAPL +STVTSLATVLAVVNVILLTALATVAALLYNLCASLVGGLGVTLTDD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000183.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000183.fa new file mode 100644 index 0000000000000000000000000000000000000000..f2c43167db2af75470e6d4178fb0b35436be955b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000183.fa @@ -0,0 +1,40 @@ +>PROKKA_00014 +MARKTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG +RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH +EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS +AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE +EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVQRLRQGAEQYAGAAEK +DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV +EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR +>PROKKA_02032 +MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG +RRKAQDAKQEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH +EVQQQFAAARKDAEKAAKKGRHRGGRKAKQLRRDGRQAAKGARKDAQRSAALFSDRAGQA +KDAAAAGGLTLAGLLATGLSALQEQGGKVGPQVQARLADAGDYAQRRKEEVLPVAAARLA +DGAAHARKTAHDVEVPDALEQALIRLTGDKAIVQRLRKGAEQYAGAAEKDLNRAAGRRTS +RSGGRAWIVAGMAAAAAGAGYALWRLTKPVQDPWTAPVPGPIAANIPVVEANNPYAQQQK +VVAEAGSAAAGEGVRVDTAAPDPVAAANAKVLGVQPGQQR +>PROKKA_00383 +MARTTLNDEIQHDGGADTFVTRQTENLRHWAAPKLEAARTWGEYGAAFTGVGASVAAEEG +RRAAHDAKQEYGPRVEKQAKRAGDAVADRYAKLAPAVATGAGVLQDVLHRLQEQAQEAGH +EAQKQFADARKDAEKAAEKGRKRGAKKAKQVRRAGRGARKDVTKAARGARKDARQAGSFL +ADRAGQAGSAAAAGGLTLAGALAAAVNALQEQGEKLAPQVQARLSDAGDYAQRRKEEVVP +LAAARLADGAAHARKTAHDVQVPDAVEQALIALTGDKAIVRKLRKGAEQYAGSAEKDLNR +AAGRKARSGGRGWILGGMALAAAGAGYALWRLTKPVQDPWTAPVPGPITANIPVVEANNP +YAQQQKVVAESGSAAAGEGVRVDTAAPVTTAVPAQDPVAEANAKVLGTDR +>PROKKA_00364 +MARTTLSNEIEHNGSADTFFARQAENLRHWAAPQLENARAWAEVTTGFGQVGGKVAAAEG +RRLAEEEVAPRVKDSAERVNAAAKGRYEKAAPVVATGLGAAGTVLQQLLEAAQDKAQQAG +QQVQDLAEQAQKDAKKSAKRTRKDAKKAGKRVSKKADKAQSLFASKAGDAKGAAAAGGLN +VAGLLAAAVAAAQDRGQELAPQVKGRVEQAAQYAQDRRAEYAPKAAASLAGVAGRAEKAA +GDVTVPASVEQLLVKLTGDKNAVKHLRQDVQSRARETQKGLKKQARQESRRGGATGWIIA +GMAAAAAGAGLAVWKLTKPVQDPWAAPVPGPITANIPVVQADGTVNPYAKQEQAVAEARA +AQGGMVNVRPQVG +>PROKKA_00014 +MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG +RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH +EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS +AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE +EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVKRLRQGAEQYAGAAEK +DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV +EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000184.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000184.fa new file mode 100644 index 0000000000000000000000000000000000000000..15b071a53204c75e3d262a4762663e6732e4e91d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000184.fa @@ -0,0 +1,20 @@ +>PROKKA_00015 +MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL +YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS +QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA +>PROKKA_02033 +MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL +YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS +QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA +>PROKKA_00382 +MARMANATHIATIKTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL +YSGTVFHRIIKDFMIQGGDPLGMGVGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS +QFFITSVPTGWLNGKHTIFGEVKDEESQQVVDRLNAVATDPRDRPLEDVVIESVEIAEA +>PROKKA_00363 +MTRMTNATQIATIHTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL +YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS +QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDQLNSVATDPRDRPLEDVVIESVEISEA +>PROKKA_00015 +MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL +YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS +QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000185.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000185.fa new file mode 100644 index 0000000000000000000000000000000000000000..ff917f4c0d62e1f5a900609a1ac765c56b6a6e51 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000185.fa @@ -0,0 +1,34 @@ +>PROKKA_00016 +MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS +GVVAGPAPTVAPAGAAASVPARRRTGFTASPVTWILLAVTTVVYAAQWMTRDQASGVTEA +LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY +VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS +FLLPGVAWQVHMGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQVAGLVVVAAALAALTV +LGAARVTVAGLLG +>PROKKA_02034 +MSTTPSDPYGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS +GVVAGPAPTSPPAAGAAATVPARRRTGFAASPVTWILLAVTTVVYAAQWMTRDQASGVTE +ALWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLAL +YVLSAVGGAVFALWASDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVF +SFLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARLPSVGAQVAGLVVVAAALAALT +VLGAARVTVAGLLG +>PROKKA_00381 +MDCAAQGGAPAGTTTSPAAVGSPGPGGVGMAGAAGRGAPARRRTGLAAAPVTWTLIAVTV +AAYVAQWATRDTVPGVTEALWYAGLYTSPFGLEPWRMATYALVHDLSGPTHLILNMLALW +VIGRVLEPALGWWRFAALYVLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLVTRV +RGGQVRSIAVLIGLNLVISFLLPGISWQVHVGGLITGAVVALVYSLAGGLRPGRASAPSA +GAQAAGLVLVAAVLAVLTVLGADRIGLDAVLR +>PROKKA_00362 +MSTTPSDPHGPDVAEGTPPVCPRHPGRAAYVRCASCADPVCLDCQRPAAGGLTLCPDCAA +RLAAGVPGPASGTTTSPAPASAGAGRGGVGAALRAAPVTWTLLAVTLLVYAGQWLTRGSR +TGVTESLWYAGAYTSAIGMEPWRMLTYALVHDVSGPTHVALNMVALWVIGRVLELALGWW +RFLALYLVSALGGAVFALWTADPLQPVVGASGAVYGLFAALFAVTRFRGGQVTSIAVLIG +LNLVFSFLMPGISWQVHVGGLLTGAVAGALLVSAGGPPGRSAAADGTARRSSAGVHVAGL +VLLAAVLAVLTLVGAARLSPAALLG +>PROKKA_00016 +MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS +GVVAGPAPTVAPAGAAASVPVRRRTGFAASPVTWILLAVTAVVYAAQWMTRDQASGVTEA +LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY +VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS +FLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQAAGLVVVAAALAALTV +LGAARVTVAGLLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000187.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000187.fa new file mode 100644 index 0000000000000000000000000000000000000000..d7c28f13959cd5e640f8d556c341c3408a003fa3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000187.fa @@ -0,0 +1,25 @@ +>PROKKA_00018 +MQSPEVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG +PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE +HPMFEGVPSPFTATRYHSLATVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE +SVLTEGGYRMLGNWLESVGLSGAAERGGRLSPLVRQD +>PROKKA_02036 +MQSPQVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG +PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE +HPMFEGVPSPFTATRYHSLAAVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE +SVLTEGGYRMLGNWLESVGLSGAAERGGRLSPLVRQD +>PROKKA_00379 +MSGTVPSPEVSVLVVDNYDSFVYTLVGYLEELGARTTVIRNDEVDAARALELAAEHTAVL +ISPGPGAPADAGVSLDLIRAAADGGRPLYGVCLGHQAIAEAFGATVTHAESLMHGKTSLV +RHGDHPMFAGLPERFTATRYHSLAAVRSTVDEAVLQITAETEDGVVMGLAHRSAPLWGVQ +FHPESVLTEGGYRMLGNWLESVGLTGAADRGGRLSPLVRGD +>PROKKA_00360 +MSTPPESAPTAVSVLVVDNYDSFVYTLVGYLQELGARTTVIRNDEVSPARALELAAQHDA +VLISPGPGTPSEAGVSLDLIRSAADGGRPLYGVCLGQQAIAEAFGATVTHAESLMHGKTS +VLTHTDHPMFAGVPARFTATRYHSLAAVRHTVDESVLEITAQTDDGVVMGLAHRTAPLWG +VQFHPESVLTEGGYRMLGNWLESVGLVGAAERGGRLSPLVRAAD +>PROKKA_00018 +MQSPEVSVLVVDNYDSFVYTLVGYLEQLGARTTVIRNDEVTPARALELAAEHTAVLISPG +PGAPADAGVSLDLIRSAADGGRPLFGVCLGHQAIAEAFGATVTHAESLMHGKTSLVRHGE +HPMFEGVPSPFTATRYHSLAAVRPTVDEAVLEITAETEDGVVMGLAHRTAPLWGVQFHPE +SVLTEGGYRMLGNWLGSVGLSGAAERGGRLSPLVRQD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000191.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000191.fa new file mode 100644 index 0000000000000000000000000000000000000000..f68df16915f6741fb23f50c03b769eb666f12ee9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000191.fa @@ -0,0 +1,46 @@ +>PROKKA_00022 +MTEVISPARPRRNIELVLLLAALTIALGADLLGMIGTDAPLDSTAWVPLGIFGAATLVLH +VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLVWSVLAVLVASALVF +LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA +IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG +MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRDFGGS +YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYLLLV +TRMMRAALGVRDAFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA +NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPPGGGEER +>PROKKA_02040 +MTEVISPARPRRNIELVLLLAALAIALGADLLGMIGTDAPLDSTAWVPLGVFGAATLVLH +VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLVWSVLAVLVASALVF +LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA +IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG +MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRDFGGS +YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYLLLV +TRMMRAALGVRDAFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA +NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPPGGGEER +>PROKKA_00374 +MTEVISPARPRRNIELVLLLAALAIALGADLLGTIGTDAALDSTAWVPLGIFGAATLVLH +VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLVWSVLAIVVASALLF +LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA +IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG +MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRNFGGS +YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYFLLV +TRMMRAALGVRDGFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA +NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPMRGGEAR +>PROKKA_00356 +MTEVISPPRPRRATELMLLLGAVALTLGADLLGTYTTTGALESTAWVPLTVFGCASLVLH +AVLRLRARYADPFILPIATLLNGLGIAMIHRLSADTAAARPTSQLAWSVLAVLVAAALVF +LVRDHRMLRRWPYVFLAVSGVLLLLPLVPGLGLSANGARIWINVGVGTFQPGEIAKITLA +IFFAGYLSTNRDLILLAGRRVGPMTFPRMRDLGPLLVAWAVAMGVLVFQRDLGSALLFFG +MFMAMLYIATSRASWVLLGLSLVAVGAAVAFLFLPHVTARFEIWLNAFDPEIYRRDFGGS +YQVVQGLFAMASGGLLGTGLGGGNPTQVPLSFSDMILAAIGEELGLVGLSAVLVLYLLLV +TRMARAALGVRDAFGKVLAAGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA +NWIILGLVLRISHAARRPAVVDGMVNASGPGAGHLDPGAALPEPAQRPGPWRAAAPAGGE +AR +>PROKKA_00022 +MTEVISPARPRRNIELVLLLAALAIALGADLLGMIGTDAPLDSTAWVPLGIFGAATLVLH +VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLAWSVLAIVVASALVF +LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA +IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG +MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRDFGGS +YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYLLLV +TRMMRAALGVRDAFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA +NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPPGGGEER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000192.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000192.fa new file mode 100644 index 0000000000000000000000000000000000000000..c78046eff7363b9a71ff5eef8ff0feedb2e9a3ad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000192.fa @@ -0,0 +1,54 @@ +>PROKKA_00023 +MTLVLRYAARSDVGRVRAKNDDSAYVGRHLVVLADGMGGHVGGDVASASTVLDLAPLDAV +GYEDPATVLPDEIQNANLILNELVHANPKLAGMGTTCTAALLAGTTLHIAHIGDSRAYRL +ANGEFSQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMRVLGDVDASPELDVFEVPVAP +GERWLFCSDGLTDVVSPEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG +TAEELAPVPDVHLSEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVRTDRIPV +VTRSSTRRRAAALLGETPVPENRPRRTAAVLTDGPDPDVAARPDPSAPPAAPRGTAAAVG +SSSAATPAATAADQPSDEAAEASATAPTPAPATSGPAGGPEDGAARRRRGKDDRPVQYRR +GWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLELSHVDRQ +TDLPVDALPAYARDRVNAGMPARDVDHAEQIVAELRDSLHPNAPAPAGEPSERARPSTTP +SSSSARPSDASGSTAPTSPASSPSATGGEAP +>PROKKA_02041 +MTLVLRYAARSDVGRVRAKNDDSAYVGRHLVVLADGMGGHVGGDVASASTVLDLAPLDAV +GYEDPATVLPDEIQNANLILNELVHANPKLAGMGTTCTAGLLAGTTLHIAHIGDSRAYRL +ADGEFSQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMRVLGDVDASPELDVFEVPVAP +GERWLFCSDGLTDVVPPEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG +TAEELAPVPDVHLSEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVKTDRIPV +VTRSSTRRRAAALLGETPVPENRPRRTAAVLTDGPDPAAAPRPDASVPPAAPSGTAAAAG +SSSAATPAATAADHPSDEAAEPMTTAPTPAPATAGPAGGPEDGAARRRRGKDDRPVQYRR +GWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLELSHVDRQ +TDLPVDALPAYARDRVNAGMPARDVDHAEQIVAELRDSLHPNAPAPAGEPSERARPSTTP +SSSSARPSDASGSTAPTSPASSPSATGGEAP +>PROKKA_00373 +MTLVLRYAARSDVGRVRAKNDDSAYVGRHLVVLADGMGGHVGGDVASASTVLDLAPLDAV +GYEDPATVLPDEIQNANLILNELVHANPKLAGMGTTCTAGLLAGTTLHMAHIGDSRAYRL +ADGEFSQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMRVLGDVDASPELDVFEVPVAP +GERWLFCSDGLTDVVSSEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG +TAEEMAPVPDVHLTEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVKTDRIPV +VTRSSTRRRAAALLGETPVPENRPRRTAAVLTDGPDRDAAPRPDASAPPAAPSGTAAAAG +SSSAAAPTATVADHPSDEAAEVSTRAATPAPATAGPAGGSQDGAARRRRGKDDRPVQYRR +GWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLELSHVDRQ +TDLPVDALPVYARDRVNAGMAARDVDHAEQIVAELRDSLHPDAPAPAGEPSERAQPSTTP +SSSSARPSDASGSAAPTSPTASPSATGGEAP +>PROKKA_00355 +MTLVLHHAARTDVGRVRSKNDDSAYAGRHLAVLADGMGGHVGGDVASASTVLDLAHLDDV +GYEDPATVLPDEIQNANLVLTSLVHANPKLAGMGTTCTAGLLAGEVLHMAHIGDSRAYRL +KDGEFTQVTRDHTFVQKLVDEGRLEAAEAQFHPNKNVLMRVLGDVDASPELDVFEVPVAP +GERWLLCSDGLTDVLSVERIRELIEPPATLAEAADALVAHTLRGGAPDNVTVVVFDVAEG +SPEELEPAGEVHLSDEALAAAHPADRGPVSGRLLAEELDARPHELVGAADAAVHSDRIPV +VTRSATRRRAGVLLGESPVPENRPRRTAAHLTAPNASDVDDAPAAPLTAAASPIETPAPA +DAATETPAVDAPAPAPGPEVDPADADAAPAPAADPAPAHAVETGRTSRRRRRDRPVEYRR +GWFIPVFTALLALILVVVAVWSYLWTQTQYYVGEDAGSVAVFQGVPQQLGPLELSHLDHT +TDIPLDRLPAYAQERVGRGMAATDRAHADQIVEELRTVSDTAAKGGGTP +>PROKKA_00023 +MTLVLRYAARSDVGRVRAKNDDSAYVGRHLAVLADGMGGHVGGDVASASTVLDLAPLDAV +GYEDPATVLPDEIQNANLILNELVHANPKLAGMGTTCTAGLLAGTTLYMAHIGDSRAYRL +VDGEFCQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMRVLGDVDASPELDVFEVPVAP +GERWLFCSDGLTDVVSPEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG +SAEELAPVPDVHLSEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVKTDRIPV +VTRSSTRRRAAALLGETPVPENRPRRTAAVLTDGPGPAADAAPRPDASAPPAAPSGTAAA +AGSSAAATPAATAADRPSDEAAEASTTAATPSPVTSGPAGGSEDGAARRRRGKDDRPVQY +RRGWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLELSHVD +RQTDLPVDALPAYARDRVNAGMAARDVDHAEQIVGELRDSLHPDAPAPAGEPSERARPST +TPSSSSARPSDASGSAAPTSPASSPSATGGEAP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000193.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000193.fa new file mode 100644 index 0000000000000000000000000000000000000000..0a810c84a5f1db7856dc3baa63304c4c27a51942 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000193.fa @@ -0,0 +1,25 @@ +>PROKKA_00024 +MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGA +AGAGSSAVDRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ +DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRAVPVGPGTAIRIGKT +VMELEA +>PROKKA_02042 +MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGA +AGAGSSAVDRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ +DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT +VMELEA +>PROKKA_00372 +MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGV +AGAGSSAVDRPAPASTPAPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ +DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT +VMELEA +>PROKKA_00354 +MNELAVAVLRLGLLLALWILIISIVLSQGRDLVVGRRNKLRLEQARRDAGLVTAVPAAGA +HAASADRPAPAATPAAERPAPVPPAPAPRLARTLRITEGPLAGQTVDLGGRPLLIGRAQD +ADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTFVDGDPVTRTLPVGTSSTIRIGKTV +MGLED +>PROKKA_00024 +MSELAVAVLRMGLLLALWVLIISIVMAQGRDLVVGRRNKTRLQQAQRDAGLVTAVPAAGV +AGAGSSAADRPAPASTPSPAASAPTTPAPRLSRTLRVVEGPKAGQTIALEGRPLLMGRAQ +DADLVLVDDYASGRHARLFPQGTRWFLEDLGSTNGTYVNGAPVTRALPVGPGTAIRIGKT +VMELEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000194.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000194.fa new file mode 100644 index 0000000000000000000000000000000000000000..6bfda34763f5ca7e4319d742534dfc66ecf4dca9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000194.fa @@ -0,0 +1,35 @@ +>PROKKA_00032 +MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA +VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVSEGGLA +GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD +TGLGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL +APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLAAAFGV +HSTRYPDQDNAITAPSDTYHY +>PROKKA_02049 +MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA +VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVSEGGLA +GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD +TGLGESPQALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL +APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLATAFGV +HSTRYPDQDNAITAPSDTYHY +>PROKKA_00366 +MTMTLPAAITPSPAFQAVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA +VAPKDKDRARADALAWLTSGHTGWVRLNGYGSKWWEDDVAALAEALPAHLGGPVAEGGLA +GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD +TGLGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL +APEQCAAVNEGLSPSQEELAWAHEFLADFEADGSEIRNGSDLPRKARAEKILGLAAAFGV +HSTRYPDQDNAITAPSDTYHY +>PROKKA_00304 +MTVTLSPSPTQPFQPTPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDVEDSVA +PADKAKALADTVEWLTSGHTAWVRLNGYGSKWWEDDVDALASALPAHLGGPVAEGGLAGV +MLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRDTG +LGESPMALAYTRSQFTIAAKATGLPGAIDGPTVGSTGAKLAEATAVTTEFGMTGKLCLAP +EQCAAVNEGLSPSPEELAWAQEFLEEFAAAGGQIRNGSDLPRKARAEKIQALAAAFGVQL +AHIPDQENRAAAPSDTYHY +>PROKKA_00031 +MTVTLPAAITPSPAFQPVPGQRIDPELARSWLLVNAAQPERFQPAEDSAADIVILDIEDA +VAPKDKDQARADAVAWLTSGHTGWVRLNGYGSRWWEQDVEALAAALPAHLGGPVAEGGLA +GVVLAMVESTDHVNETARRLPGVPVVALVETARGLQRIDSIAAAKGTFRLAFGIGDFRRD +TGLGESPMALAYTRSQFTIAARATGLPGAIDGPTVGSTGVKLAEATAVTAEFGMTGKLCL +APEQCAAVNEGLSPSQEELAWAHEFLADFEADGGEIRNGSDLPRKARAEKILGLATAFGV +HSTRYPDQDNAITAPSDTYHY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000195.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000195.fa new file mode 100644 index 0000000000000000000000000000000000000000..dd3bba68bb5b116b2b475c02c8d97e223b30526f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000195.fa @@ -0,0 +1,44 @@ +>PROKKA_00033 +MTRIPAEDEAVTAPSSPLDNALAQLSAAVKTLGYDEGLHQMLAAPRREMAVSIPLRRDDG +STEVLRGYRVQHNFSRGPAKGGVRFSQDVDLDEVRALAMWMTWKCALLDVPYGGAKGGVA +IDPRQYSKAELERVTRRYTSEIQPIIGPEVDIPAPDVGTDEQTMAWMMDTYSVNVGHTTL +GVVTGKPVSLGGSLGRASATSAGVVHVALAALEHLGIEPSQATAAVQGFGKVGAGTVELL +EAAGVKVVAVSDQYGAVRDDEGLHYDALQRQLWDTGSVKDTPGTASMDADELLEMDVDLV +VPAAVQSVLTEDNAPRVRARLVVEGANGPTTGEADRILSEKGVLVVPDILANAGGVIVSY +FEWVQANQAYWWSREEVDERLKRRMVAAWQAVLATSESRRVSLREAATLTAVQRVAEAHR +TRGLYP +>PROKKA_02050 +MTRIPAEDEAVTAPSSPLDNALAQLSAAVKTLGYDEGLHQMLAAPRREMAVSIPLRRDDG +STEVLRGYRVQHNFSRGPAKGGVRFSQDVDLDEVRALAMWMTWKCALLDVPYGGAKGGVT +IDPRQYSKAELERVTRRYTSEIQPIIGPEVDIPAPDVGTDEQTMAWMMDTYSVNVGHTTL +GVVTGKPVSLGGSLGRASATSAGVVHVALAALEHLGIEPSQATAAVQGFGKVGAGTVELL +EAAGVKVVAVSDQYGAVRDDEGLHYDALQRQLWDTGSVKDTPGTASMDADELLEMDVDLV +VPAAVQSVLTEENAPRVRARLVVEGANGPTTGEADRILSEKGVLVVPDILANAGGVIVSY +FEWVQANQAYWWSREEVDERLKRRMVAAWQAVLATSESRRVSLREAATLTAVQRVAEAHR +TRGLYP +>PROKKA_00365 +MTRIPAPDEAAAAPSSPLDNALAQLAAAVRTLGYDEGLHQTLAAPRRELSVSIPLRRDDG +AVEVLRGYRVQHNISRGPAKGGVRFSPDVDLDEVRALAMWMSWKCALVGVPYGGAKGGVS +IDPRRYSKAELERVTRRYTSEIQPIIGPEVDIPAPDMGTDEQTMAWMMDTYSVNVGHTTL +GAVTGKPVSLGGSLGRASATSEGVVHVALAALRDRGIDPQGATAAVQGFGKVGAGTVELL +AAAGVRVVAVSDQYGAVRCEDGVDFATLSAHVAETGKVVDCPGTEAMDADELLLSDVDLV +VPAAVQGVLTAQNADRVRARVVVEGANGPTTGEADRILNENGVLVAPDILANAGGVIVSY +FEWVQANQAYWWTREEVAERLERRMVLAWEAVQAAAREHDLTLREAATVLAVKRVAEAHR +TRGLYP +>PROKKA_00463 +MTSASSPLANALAQLERAVETLGYDEGTHQLLANPRRELSVSIPLRRDSGEVEVFHGYRV +QHNFSRGPAKGGVRFSPSVDLDEVRALAMWMTWKCALVDVPYGGAKGGVAIDPRTYSQAE +LERVTRRYTTEILPIIGPEKDIPAPDVGTDEKTMAWMMDTFSVAMGYTVQGVVTGKPVSL +GGSLGRAEATSRGVVHIALAALKHKGIEPAQATASVQGFGKVGAGTVEFLADAGVTVLAV +SDQYGAVRREEGIDYAALAAHVAETGSVVDCPGTEPMDPAELLTMEVDVLVPAAVEGVLT +KDNAGDVKAKIVVEGANGPTTGEADAILNENGVLVAPDILANAGGVIVSYFEWAQANQAY +RWTLQEVNDRLAARMRTAWDGVLAASQKHGVSLREAATVTAVKRVKEAHEIRGLYP +>PROKKA_00032 +MTRIPAEDEAVTAPSSPLDNALAQLSAAVKTLGYDEGLHQMLAAPRREMAVSIPLRRDDG +STEVLRGYRVQHNFSRGPAKGGVRFSQDVDLDEVRALAMWMTWKCALLDVPYGGAKGGVT +IDPRQYSKAELERVTRRYTSEIQPIIGPEVDIPAPDVGTDEQTMAWMMDTYSVNVGHTTL +GVVTGKPVSLGGSLGRASATSAGVVHVALAALEHLGIEPSQATAAVQGFGKVGAGTVELL +EAAGVKVVAVSDQYGAVRDDEGLHYDALQKQLWDTGSVKDTPGTAPMDADELLEMDVDLV +VPAAVQSVLTEENAPRVRARLVVEGANGPTTGEADRILSEKGVLVVPDILANAGGVIVSY +FEWVQANQAYWWSREEVDERLKRRMVAAWQAVLATSESRRVSLREAATLTAVQRVAEAHR +TRGLYP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000196.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000196.fa new file mode 100644 index 0000000000000000000000000000000000000000..6ef46fa6b567c073d40526c7c0c13c297ceb2a68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000196.fa @@ -0,0 +1,24 @@ +>PROKKA_00034 +MHAITPGTWNLDPAHSDVDFVVRHAGISKVRGTFHAVEGQLVIAEEFTQSSVEVTVDVAS +ISTKNEGRDAHLRSADFFDVEQFPTMTFRSTEVRGEPEEFTLVGELTLHGVTRTVELEAE +FGGQDKDPFGATRVGFEATGEISRKDFGLTWNAATEAGGVLVSDKVKLEIGAAFVLSEAD +AQA +>PROKKA_02051 +MHAITPGTWNLDAAHSDVDFVVRHAGISKVRGTFHAVEGQLVIAEEFTQSSVEVTVDVAS +ISTKNEGRDAHLRSADFFDVEQFPTMTFRSTEVRGEPEEFTLVGELTLHGVTRTVELEAE +FGGQDKDPFGATRVGFEATGEISRKDFGLTWNAATEAGGVLVSDKVKLEIGAAFVLSEAD +AQA +>PROKKA_00362 +MAQVTTGTWNLDPAHSDVDFVVRHAGISKVRGTFAAVEGVLVVAEDFNASSVEVTVDVAS +INTKNEGRDQHLRSGDFFDVEQFPTMTFRSTEVRGAAEEFTLVGELTLHGVTRTVELEAE +LGGQDVDPFGTTRVGFEATGEISRKDFGLTWNAATEAGGVLVSDKVKLEIGAAFVLPEAD +AQA +>PROKKA_00303 +MAQITPGTWNLDAAHSDVDFVIRHAGISKVRGTFHTVDGQLVVAEDFNQSSVQVTVDMAS +INTKNEGRDQHLRSADFFDVEQFPQMTFRSTEVRGEAEDFTVVGELTIHGVTKTVELEAE +FGGQDKDAFGATRVGFEAKGEISRKDFGLTWNAATEAGGVMVSDKVKIEIGAAFVLPEA +>PROKKA_00033 +MHAITPGTWNLDAAHSDVDFVVRHAGISKVRGTFHAVEGQLVIAEEFTQSSVEVTVDVAS +ISTKNEGRDAHLRSADFFDVEQFPTMTFRSTEVRGEPEEFTLVGELTLHGVTRTVELEAE +FGGQDKDPFGATRVGFEATGEISRKDFGLTWNAATEAGGLLVSDKVKLEIGAAFVLPEAD +AQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000198.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000198.fa new file mode 100644 index 0000000000000000000000000000000000000000..465586850abcbab26ecfd802f48d34bac5029593 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000198.fa @@ -0,0 +1,29 @@ +>PROKKA_00039 +MMASKTPHQNVTFDLPTKDAGQDGDRTGHGYLALPASGKGPGVIVIQEWWGLVDHIKDVC +DRLADLGFVALAPDLYGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSQT +VGAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVPGDFSGVTAAVQGHYAEQDDSFP +VEDARRQEQQIREESGADVEYFYYDAPHAFHNDENPQGNYRPEAAALAWDRAVSFLKEKV +R +>PROKKA_02052 +MMASKTPHQNVTFDLPTKDAGQDGDRTGHGYLALPASGKGPGVIVIQEWWGLVDHIKDVC +DRLADLGFVALAPDLYGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSQT +VGAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVTGDFSGVTAAVQGHYAEQDDSFP +VEDARRQEQQIREESGADVEYFYYDAPHAFHNDENPQGNYRPEAAALAWDRAVSFLKEKV +R +>PROKKA_00361 +MMASKTPHQNTTFDLPSKDASHDGDQVGHGYLALPESGSGPAVIVIQEWWGLVDHIKDVC +DRLAAEGFVALAPDLYGGWIAHDGDEAGEMMQKLPAEEGARQLAGAVDWLLAREEVTSTT +VGAIGFCMGGGFVLALAAQQGEKVSAAVPFYGVGQGVPGDFAGVKAAIQGHYGEQDSMFS +VEDAKKQEQQIRDESGAEVEYFYYDAPHAFHNDDDPQGNYRPEAAALAWGRAVAFLKEKV +R +>PROKKA_00302 +MMASKTPHQNVSFPLPTKDAAHGDQTGHGYLALPAAGKGPAVIVIQEWWGLVDHIKDVCD +RLAEEGFVALAPDLFGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSSRV +EAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVPGSFEGVTAAIQGHYAEQDDFFPV +EDAKKQERQIREESGAEVEYFYYDAPHAFHNDENPQGNYRPEAAQLAWDRAVSFLKEKVR +>PROKKA_00034 +MMASKTPHQNVTFDLPTKDAGQDGDRTGHGYLALPASGKGPGVIVIQEWWGLVDHIKDVC +DRLADLGFVALAPDLYGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSQT +VGAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVPGDFSGVTAAVQGHYAEQDDSFP +VEDAREQAQQIREESGADVEYFYYDAPHAFHNDENPQGNYRPEAAALAWDRAVSFLKEKV +R diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000201.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000201.fa new file mode 100644 index 0000000000000000000000000000000000000000..0c91e90a39bc98af8e5be617ce54effda4d69d94 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000201.fa @@ -0,0 +1,34 @@ +>PROKKA_00043 +MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG +DMVASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA +GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES +VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI +VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA +SRPGADPPTRAELAD +>PROKKA_02056 +MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG +DMIASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA +GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES +VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI +VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA +SRPGADPPTRAELAD +>PROKKA_00357 +MDVVVSDTATPRAHVGGSPLNVAVGLSRLGRPVLFAGRFGRDEHGDMIASHLRDNGVHCL +LEQDAAPTSQATARLDPTGAASYEFELDWTLPPAEELAEEFAAAAGGRLRHMHAGSIATM +LAPGDAEVMSLLERISADTTISYDPNVRPSIVPDRAFARARAEESVRLADVVHASDEDVA +WLYPARPLVETLQAWQRMGPALVVMTRGAEDIVAVTRDGVVERPIVPVDVADTVGAGDSF +TAALLAALDDRSLLGAENRERLNAMDPADVESVLIYASRASAITASRPGADPPTRDELAD +>PROKKA_00299 +MGLVAEYFGVVGEALVDVVLSDTATPRAHPGGSPLNVAVGLSRLGRPVRFAGRYGTDEYG +DMVAAHLADNGVHCVLGADDAPTSVATARLDPTGAASYEFELDWTLPEAAELERLLTGAA +GGRLLHVHAGSIATMLAPGDASVMGLLEAVQPTATISYDPNVRPSIVPDREFARARAEES +VRLSDVVHASDEDVAWLYPDRPLMDSLRAWQQAGPALVVMTRGAEDIVAVTAEHVLEQPI +VPVDVADTVGAGDSFTAALLGALDDRSLLGAENRGRLHAMDLADIRSVLIYAARASAITS +SRPGADPPMRDELAD +>PROKKA_00038 +MGRVAQYCGVIGEALVDVVVSDTATPRVHVGGSPLNVAVGLSRLERPVLFAGRLGRDAHG +DMIASHLRENGVRCLLEPDAAATSVATARLDPTGAASYEFELDWTLPPAAALARDFDDAA +GGPLHHMHAGSIATMLAPGDAEVMALLERISAVTTISYDPNVRPTIVPDRAFARARAEES +VRLADVVHASDEDIAWLYPDRPLRESLQAWQQMGPAFVVMTRGAEDIVAVTAHGVVERPI +VPVDVADTVGAGDSFTAALLAALDDRSLLGAANRGRLHAMDPADVESVLIYASRASAITA +SRPGADPPTRAELAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000202.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000202.fa new file mode 100644 index 0000000000000000000000000000000000000000..055abf54e34741af62c2474c0eb9e6e6f0ce366d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000202.fa @@ -0,0 +1,39 @@ +>PROKKA_00044 +MGGVDTAQQTTAQDTAQDPASTTPRTVTVTGAAGNIGYALLFRIAAGGMLGPDTSVRLRL +LEIPAALGAAEGTAMELADAAFPLLADVEVTDEPARAFDGVQHALLVGARPRTKGMERSD +LLEANGGIFGPQGRAINDHAAQDVRVVVVGNPANTNALIAAAHAPDVPAERFTALTRLDH +NRAVAQLAARAGVAVTDVAGVTIWGNHSATQFPDLTHARVRVDGTWRPALEVVDPVWAGE +EFVPRVARRGAEIIEVRGASSAASAASAAIDHMCDWTLGTGVDADGASRRTSAAVVSDGS +YGVPEGLISSFPVTSDGGTAWRIVPGLEPDESVLPGEGGRLAATVAELEAERDAVRGLGL +L +>PROKKA_02057 +MRRAGVSSAGERGHDGGVDTALQTTAQDTAPDPVSTTPRTVTVTGAAGNIGYALLFRIAA +GGMLGPDTPVRLRLLEIPAALGAAEGTAMELADAAFPLLADVEVTDDPARAFDGVQHALL +VGARPRTKGMERGDLLEANGGIFGPQGRAINDHAAQDVRVVVVGNPANTNALIAAAHAPD +VPAARFTALTRLDHNRAVAQLAARAGVAVTDVSGVTIWGNHSATQFPDLTHARVRVDGTW +RPALEVVDPVWASEEFVPRVARRGAEIIEVRGASSAASAASAAIDHMRDWTLGTGVDADG +APRRTSAAVVSDGSYGVPEGLISSFPVTSDGGTAWRIVPGLEPDESVLPGEGGRLAATVA +ELEAERDAVRGLGLL +>PROKKA_00356 +MRARRRAGLFSAGVRGYDGRVSTVSAPSRAPRTVTVTGAAGNIGYALLFRIAAGGMLGPD +TPVRLRLLEIPAALRAAEGTAMELADAAFPLLADVEVTDDPAVAFDGVQHAMLVGARPRT +KGMERGDLLEANGGIFGPQGRAINDHAADDVRVVVVGNPANTNALIAAAHAPDVPAERFT +ALTRLDHNRAVAQLAARAGVAVTDVDGVTIWGNHSATQFPDLTHARVRVAGAWRPALEVV +DPAWAAEEFVPRVAKRGAEIIEVRGASSAASAASAAVDHMRDWTLGTGAGAGGAGTDAGP +RWTSAAVVSDGSYGVPEGLVSSFPVTSDGGAAWRIVPGLAPDESLLPGTGGRLAATVAEL +EAERDAVHGLGLL +>PROKKA_00298 +MTQDTLRTPATVTVTGAAGNIGYALLFRIASGQLLGPDTPVRLRLLEIPAAVRAAEGVAM +ELADSAFPLLASVDVTDSADAAFDGTTHALLVGARPRTAGMERADLLRANGGIFGPQGAA +INASADASVRVVVVGNPANTNALIASAHAPDVPAERFTALTRLDHNRAVSQLAARAGVGV +ADVDGITIWGNHSATQFPDLTHARVRMSGDDGAPVWRPALEVVDPAWAAEEYIPRVAKRG +AEIIEVRGASSQGSAASAAIDHMRDWSLGTGVDADGAPRRTSAAVVSDGSYGVPEGLISS +FPVTSDGSGAWTIVPGLEPDESLLPGDGGRLAATVAELEAERDAVRALGLI +>PROKKA_00039 +MRRAGVSSAGERGHDGGVDTAQQTTAQDTAPDPASTTPRTVTVTGAAGNIGYALLFRIAA +GGMLGPDTPVRLRLLEIPAALGAAEGTAMELADAAFPLLADVEVTDDPARAFDGVQHALL +VGARPRTKGMERGDLLEANGGIFGPQGRAINDHAAQDVRVVVVGNPANTNALIAAAHAPD +VQAARFTALTRLDHNRAVAQLAARAGVAVTDVSGVTIWGNHSATQFPDLTHARVRVDGTW +RPALEVVDPVWASEEFVPRVARRGAEIIEVRGASSAASAASAAIDHMRDWTLGTGVDADG +APRRTSAAVVSDGSYGVPEGLISSFPVTSDGGTAWRIVPGLEPDESVLPGEGGRLAATVA +ELEAERDAVRGLGLL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000203.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000203.fa new file mode 100644 index 0000000000000000000000000000000000000000..313a1834b4d9a24e62a5efff710a4a825d394f60 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000203.fa @@ -0,0 +1,30 @@ +>PROKKA_00045 +MPALSLPSRRPRMIATDLDGTIIGYRHTRSGRLSPRTIVALRDARDAGVEVVFVTGRPLR +WLGPLSAQLGPVGPVICSNGAVVVDTATDDVLIAHPMRVEAVWTATDRLRALDRTVSFGA +ETLEGFFWEHAFSERAEFRAEVHAAATLEAALPGRLGVVKLMARSDTLAPDAFLAAARAE +LDELVSATHSAPGIALVEMSAPGVHKAATLAEFAASRGVAPADVVAFGDMPNDLEMLQWA +GLGLAVASGHPSLLAAADGVVGACDDDGVAATVERLLELPTD +>PROKKA_02058 +MPALPLPSRRPRMIATDLDGTIIGYRHTRSGRLSPRTIAALRDAHDAGVEVVFVTGRPLR +WLGPLSAQLGPVGPVICSNGAVLVDTATDDVLIAHPMPVEAVWTATDRLRALDRTVSFGA +ETLEGFFWEHAFSERAEFRAEVHAAATLEAALPGRLGVVKLLARSDTLAPDAFLAAARAE +LDELVSATHSAPGIALVEMSAPGVHKAATLAEFAASRGVAPVDVVAFGDMPNDLEMLQWA +GLGLAVASGHPSLLAAADGVVGACDDDGVAATVERLLELPTD +>PROKKA_00355 +MPALPLPPRRPRLIATDLDGTIIGYRHTRSGYLSPRTVAALQEAHETGVEVVFVTGRPLR +WLGALSEQLGQVGPVICSNGAVVVDTATDEVLLHHSMDRDAVWDAVGRLRALDRSATFGA +ETLDGFFWESAFSEWGELEEGFRTAQRLEGVLPAHVDVVKLMARSSTMDPDVFLAAAREE +LGALLNATHSAPGVSLVEMAAPGVHKAATLAEFAARRGVDARDVVAFGDMPNDTEMLAWA +GLGLAVASGHESLLAVADAVVGECDDDGVAQAIELLLELPAE +>PROKKA_00297 +MSALPASARRPRLIATDLDGTVIGYAHTRTGRISPRTVAALRRAHAEGIVVVFVTGRPLR +WLGPLRAQLGEVGPVICSNGAVVADTATDEVLLHHALDRAAIDHVVRRIRALDPAATFGA +EALEGFFWEDAFASDELGQTRAASLEAALPGDATVVKLMAKSGGIEPDVFLAAVRELGDG +LVTATHSAPGMSLVEMSAPGVHKAATLAAFARGTGVEAADVVAFGDMPNDAEMLAWAGLG +LAVASAHASLRAVADGVVGACDDDGVAAAIEALLALPEA +>PROKKA_00040 +MPALPLPSRRPRMIATDLDGTIIGYRHTRSGRLSPRTIAALRDAHDAGVEVVFVTGRPLR +WLGPLSAQLGPVGPVICSNGAVLVDTATDDVLIAHPMPVEAVWTATDRLRALDRTVSFGA +ETLEGFFWEHAFSERAEFRAEVHAAATLEAALPGRLGVVKLLARSDTLAPDAFLAAARAE +LDELVSATHSAPGIALVEMSAPGVHKAATLAEFAASRGVAPVDVVAFGDMPNDLEMLQWA +GLGLAVASGHPSLLAAADGVVGACDDDGVAATVERLLELPTD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000207.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000207.fa new file mode 100644 index 0000000000000000000000000000000000000000..ae413d1d95b381767bef7fc6598ef9f7d582d503 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000207.fa @@ -0,0 +1,50 @@ +>PROKKA_00054 +MSTQPPGLTTDAPDTPDDDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP +RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPATEALITEIVSVRSEVDHALLHLTDWM +EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK +APATAAALRELVPQYLDSALVSVVAGGKECNTALLAEPWDHILYTGGERVGRIVYEAAAK +TLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGEAALRQVT +AELPAALREFYGDDPRASKDYGRLISAEHAERLREMLQADLDAGAELLVGGDVDVAGRYM +APTVVTGVKPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA +FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGAYHGIHGFETFSHLRPSITKSDQVD +TLKTAYPPYGRMKRALLPKML +>PROKKA_02067 +MSTQPPGLTTDSSDTPDDDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP +RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPATEALITEIVSVRSEVDHALLHLTDWM +EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK +APATAAALRELVPQYLDSALVSVVAGGKECNTELLAEPWDHILYTGGERVGRIVYEAAAK +TLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGEAALRQVT +AELPAALREFYGDDPRASRDYGRLISAEHAERLREMLQADLDAGAELLVGGDVDVAGRYM +APTVVTGVTPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA +FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGAYHGIHGFETFSHLRPSITKSDQVD +TLKTAYPPYGRMKRALLPKML +>PROKKA_00344 +MSTQHPGIATDSPVSSDDDLRPGLDAAPVGPAGEDGDDPVREPLPTEALPLAPAGPRPED +PRAAVVRLRAAARSRAAHPRAVRVRQLKGLKRLLTEGQDRLVAALGQDLGKPATEALMTE +VVSVRSEVDHALLHLTDWMEPRPAKLPLALRPASAEVRPRPKGLVLIIGAWNYPVQLTLA +PLVGALAAGNAVVVSPSEKAPATAAALRELVAEHLDSALVSVVEGGKDCNTALLAEPWDH +ILYTGGERVGRIVYEAAAKTLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQT +CVAPDYVLAVGDVAHRQVVEELPGALREFYGADPRASKDYGRLVSAEHAERLRDLLREDL +DAGAVVLVGGDVDVAGRYMAPTVVTGVRPDGALMREEIFGPILPVLRVDTFQEALDFIAE +RPHPLAAYLFTDRPSYHRAFDDQVQAGGLGYDVGLLHAGIATLPFGGVGASGIGAYHGVH +GFETFSHLRASITKSDQVDTLKTAYPPYGWVKRTMIPKML +>PROKKA_00282 +MSTQPPGLTTDSPDSPADDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP +RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPSTEALITEIVSVRSEVDHALLHLTDWM +EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK +APATAAALRELVPQYLDSALVSVVAGGKDCNTELLAEPWDHILYTGGERVGRIVYEAAAK +TLSPVTLELGGKSPAVVTPSRNTGAMARRITWAKFTNAGQTCVAPDYVLAVGEAALRQMT +AELPAALREFYGDDPRASRDYGRLISAEHAERLREMLQADLDAGAELFVGGDVDVAGRYM +APTVVTGVKPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA +FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGAYHGIHGFETFSHLRPSIAKSDQVD +TLKTAYPPYGRMKRALLPKML +>PROKKA_00049 +MSTQPPGLTTDSPDSPADDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP +RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPATEALITEIVSVRSEVDHALLHLTDWM +EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK +APATAAALRELVPQYLDSALVSVVAGGKECNTALLAEPWDHILYTGGERVGRIVYEAAAK +TLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGEAALRQVT +AEIPAALREFYGDDPRASKDYGRLISAEHAERLREMLQTDLDAGAELLVGGDVDVAGRYM +APTVVTGVRPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA +FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGVYHGIHGFETFSHLRPSITKSDQVD +TLKTAYPPYGRMKRALLPKML diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000209.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000209.fa new file mode 100644 index 0000000000000000000000000000000000000000..456a4e024c812feba8837d90ec86251118044448 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000209.fa @@ -0,0 +1,20 @@ +>PROKKA_00056 +METTTRDEDERTLLRGVGLRVTRPRLAVLTALADHPHADASTVLAAVRRALPGTSHQAVY +DCLHALTEAGLVRSLQPAGSPARYEICTGDNHHHLVCRGCGTVVDVPCRTGSAPCLDAPE +GHGFAVDEAEVYYWGLCAGCRE +>PROKKA_02069 +METTTRDEDERTLLRGVGLRVTRPRLAVLTALADHPHADASTVLTAVRRALPGTSHQAVY +DCLHALTEAGLVRSLQPAGSPARYEICTGDNHHHLVCRGCGTVVDVPCRTGSAPCLDAPE +GHGFAVDEAEVYYWGLCAGCRE +>PROKKA_00339 +MVSTDMDTTTQTPDERTLLRAAGLRVTRPRVAVLTALGECPHADAATVLAAVRRELPAVS +HQAVYDSLHTLTDVGLVRSIQPAGSTARYEIRRNDNHHHLVCRDCGTVVDVPCHTGQAPC +LEARTDHGFLIDEAEVYYWGLCPSCRADPGAAAS +>PROKKA_00279 +MSTVTVEQPEESALLRSVGLRVTRPRVAVLQGLRRHPHADAGSLLSAVREDLPQVSHQAV +YDCLHVLTDAGLVRSLQPAGSPARYELAAHDNHHHLVCRGCGDLVDVPCQTGVAPCLHAP +EDHGFLIEEAEVYYWGLCPDCRSGGYTTTSDGTPAPAPPAP +>PROKKA_00051 +METTTRDEDERTLLRGVGLRVTRPRLAVLTALADHPHADASTVLAAVRRALPGTSHQAVY +DCLHALTEAGLVRSLQPAGSPARYEICTGDNHHHLVCRGCGTVVDVPCRTGSAPCLDAPE +GHGFAVDEAEVYYWGLCAGCRE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000210.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000210.fa new file mode 100644 index 0000000000000000000000000000000000000000..baedf1c016efa3dd85cb829a9053de087cfbe3b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000210.fa @@ -0,0 +1,40 @@ +>PROKKA_00057 +MAQPEPVRLVPGGAVDRPAEQALLAAAAACDGDVDAMVELLRAASGAPSGEDAAPLDLPL +TGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLLGVYASESGGRT +PALRPAPDGPDTAWLLDGEKPWCSLADRCAAAVVTGREADGTRRAVLVDLSHPGVAETDS +AWPALGLAPIRTVGLAFDAVPGSAVGGAEWYLRRPGFAWGGIGVAAVWFGGAVGIARTLR +NATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHAMAALLARAADDVDAGRLDHGRGMVE +ADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHARAVADLQVYLRQHHGHRDDARLGAA +LLTGETDGGWTW +>PROKKA_02070 +MAQPEPVRLVPGGAVDRPAEQALLAAAAACDGDVDAMVELLRAASGAASGEDAAPLDLPL +TGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLLGVYASESGGRT +PALRPAPDGPDTAWLLDGEKPWCSLAGRCAAAVVTGREADGTRRAVLVDLSHPGVAETDS +AWPALGLAPIRTVGLAFDAVPGIAVGGAEWYLRRPGFAWGGIGVAAVWFGGAVGIARTLR +NATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHAMAALLARAADDVDAGRLDHGRGMVE +ADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHARAVADLQVYLRQHHGHRDDARLGAA +LLTGETDGGWTW +>PROKKA_00338 +MAQPEPVRLAPPGRTAEPDAARPAERALLAAASACDGDVAPMLALLGAGRAPDTEASAPD +AAAPLELPLTGEGRTRQQWELLASVAAQDLSAARVLEPHLDALSILSQASVPAPAGLLGV +YASESGGRTPRLTPAPHDDDAGSASDGRPDAGPDAWLLDGEKPWCSLADECAAAVITGRE +ADGTRRAVLVDLDHPGVAETSSAWPALGLAPIRTVGLGFDAVPGTAVGGPEWYLRRPGFA +WGGIGVAAVWFGGAVGIARTLRDATRSRAAAEAEGRGPGPDQVAQAALGRVDRLLHAMAA +LLARAAEDVDAGRLDHGRGMVEADRIRGTVAQLCTEVVDVVGQATGPGPLTGSAAHARAV +ADLQVYLRQHHAHRDDARLGRALLDGDADGGWTW +>PROKKA_00278 +MSETPWVHLPGAEGDGRPAAPTEAEAALLAAARDGEDGEAGIEPILALLSGDDAAASLDL +PLTGAGRTRRQWELLASVGAVSLPAARVLEPHLDALSILDQAGVPAPRGVLGVYASESGG +VSPSARPAPGAAVGDEDAVWRLDGDKPWCSLADRCTAAVVTARQEDGLRRAFLVDLGEPG +MEVADPRWPSLGLAPITTVGLRFADVPAVPVGGPEWYLRRPGFAWGGIGVAAVWFGGAVH +VARTLRTSLERRTAAASDGSGPGPDQVGLAALGRVDRHLHAMASLLGRAADDVDAGRLDH +AHGLVEADRIRGTVAQLCTEVLDVVGQATGPGPLTGDAAHARAVADLQVYLRQHHGPRDD +ARLAESLLAADPAERAELQPW +>PROKKA_00052 +MAQPEPVRLVPGGAVDRPAEQALLAAAAACDGDVDAMVELLRAASGAASGEDAAPLDLPL +TGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLLGVYASESGGRT +PALRPVPDGPDTAWLLDGEKPWCSLADRCAAAVVTGREADGTRRAVLVDLSHPGVAETDS +AWPALGLAPIRTVGLAFDAVPGSAVGGAEWYLRRPGFAWGGIGVAAVWFGGAVGIARTLR +NATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHAMAALLARAADDVDAGRLDHGRGMVE +ADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHARAVADLQVYLRQHHGHRDDARLGAA +LLTGETDGGWTW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000212.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000212.fa new file mode 100644 index 0000000000000000000000000000000000000000..b22a44f5a73e557ba57e4fd8a7474a1e91b06d0c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000212.fa @@ -0,0 +1,49 @@ +>PROKKA_00060 +MTLPTPVRLGRMQTSDAAPAADDDRTPSAPGPARLLDRSAVRLREDLAAGELSAREVTEA +ALAAAQTHADLGAFALLDAEGARARAAELDAAHPRVAPRAVPGPRTSPAPDDDGAPASLH +GLPLAYKDLIDVRGMPTRFGSALLADAPPAAQDDPLALRLRAAGTVTLGKTTVPEFGLDS +YSENLVTAPARNPLDPTRTAGGSSGGAAAAVAAGILPFAPGSDGGGSIRIPAAACGLVGL +KPGRGELPMDEHADTVRNLTVSGPLAHTVEDAALLYDVLLSPEGLPGRVLPDLRRTVETA +RAGGAVDARRIGVTTASPFASDLEISLARPAVTALTKAAAALDAGGHAVEDLSPYYGEDY +HRDFRTVWTAGLLRAPLPEDAEAHVGAVAAHFLRTARAAGRAELDDAAHRLEEWARGVRA +QFAAVDVVMTPVLATAPPPVGHFLAMEPEANYEAQCAFTPYTSMVNVLGLPAVAVPVLRD +ERGLNWSVQLIGRPGTSAPLLALAAHLELLLAG +>PROKKA_02073 +MTRATPVRLGRMQTSDAAPAADDDDRTPSAPGPARLLDRSAVRLREDLAAGELSAREVTE +AALAAAQAHADLGAFALLDAEGARTRAAELDAAHPRVAPRAVPGPHTSPAPDDDGAPASL +HGLPLAYKDLIDVRGMPTRFGSALLADAPPAAQDDPLALRLRGAGTVTLGKTTVPEFGLD +SYSENLVTAPARNPLDPTRTAGGSSGGAAAAVAAGILPFAPGSDGGGSIRIPAAACGLVG +LKPGRGELPMDEHADTVRNLTVSGPLAHTVEDAALLYDVMLTPEGLPGRVLSDLRRTVET +ARAGDAVDVRRIGVTTASPFASDLEISLARPAVTALTKAAAALDAGGHAVEDLSPYYGED +YHRDFRTVWTAGLLRAPLPEDAEAHVGAVAAHFLRTARAAGRAELDDAAHRLEEWAHGVR +AQFAAVDVVMTPVLATAPPPVGHFLAMEPEANYEAQCAFTPYTSMVNVLGLPAVAVPVLR +DERGLNWSVQLIGRPGTSAPLLALAAHLELLLAG +>PROKKA_00335 +MQLRDALAAGELSAREVTQAALDAAERHAGLGAFTLLDPEGALARADELDDDGARASLHG +LPLAYKDLTDVRGLPTRHGSALLAGAPAAEEDAPLVRRLVGAGTVTLGKTTVPEFGLDSY +SENLVSAPARNPLDPARTPGGSSGGSAAAVAAGILPFAPGSDGGGSIRIPAAACGLVGFK +PGRGELPVDEPADTVRNLTVSGPLAHTVEDAALLYDELLTPEGLPGRVLADLRRTVETAR +AGGAVEGRRIGVTTASPFAPDVPITLARPAVTALTKAAAALSAGGHAVQDLHPAYGEEYH +RDFRTVWTSGLLRAPLPEDAEERVGAIAAHFLRTARSAGRQEIDDAVRRLEAWARGVRGQ +FAAVDVVMTPVLAAAPPPVGHFLAMEPEDNYAAQCAFTPYTSMVNVLGLPAASVPVLRDE +RGLSWSVQLIGRPGTSGALLALAAHLELLLAG +>PROKKA_00276 +MAVSEPLSPSDQPTSPTPAPDAPARLLGRTALALRDALAAGELSAAEVTEASLAAAHAHA +GLGAFVLLDEDGARVRAAALDARPDDAAGASLRGLPLAFKDLTDVAGLPTRMGSAVLAQA +PAAAEDDPLTTRLRAAGTVLLGKTTVPEFGLDAYSENPVDPPARNPLDPSRTPGGSSGGS +AAAVAAGILPFAPGSDGGGSVRIPAAACGLVGLKPGRGTVPTDPGEDAVTNLTVSGPLAH +TVEDAALLFDVMTSPEGLEGRTGPDLRRFLDARAAGEPVAPVRIGVSTASPFSPDLEITL +ARPALSALARSGAALAAGGHAVDEFVPHYGERYHRDFRTAWTSGLLKAPLPDGAEALVGP +VAASFLASARAAGPEQIATAIGRLEAWAADVRGQFAAVDVVMTPVLAFAPPAIGHFLALD +PEENYAEQCRFTPYTSMVNVLGLPAVAVPVLRDEAGLSWSVQLVGRPGAEGRLLELAGHL +RLLLAG +>PROKKA_00055 +MTLPTPVRLGRMQTSDAAPAADDDRTPSAPGPARLLDRSAVRLREDLAAGELSAREVTEA +ALAAAQTHADLGAFALLDAEGARTRAAELDAAHPRVAPRAAPGPHTSPAPDDDGAPASLH +GLPLAYKDLIDVRGMPTRFGSALLADAPPAAQDDPLALRLRAAGTVTLGKTTVPEFGLDS +YSENLVTAPARNPLDPARTAGGSSGGAAAAVAAGILPFAPGSDGGGSIRIPAAACGLVGL +KPGRGELPMDEHADTVRNLTVSGPLAHTVEDAALLYDVLLSPEGLPGRVLPDLRRTVETA +RAGGAVDARRIGVTTASPFASDLEISLARPAVTALTKAAAALDAGGHAVEDLSPYYGEDY +HRDFRTVWTAGLLRAPLPEDAEAHVGAVAAHFLRTARAAGRAELDDAAHRLEEWARGVRA +QFAAVDVVMTPVLATAPPPVGHFLAMEPEANYEAQCAFTPYTSMVNVLGLPAVAVPVLRD +ERGLNWSVQLIGRPGTSAPLLALAAHLELLLAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000215.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000215.fa new file mode 100644 index 0000000000000000000000000000000000000000..8a7026cca6b43c2188f2948d151ca2e28561ce16 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000215.fa @@ -0,0 +1,45 @@ +>PROKKA_00065 +MIDVKDLIEQPEKYRASQEARGEDASLVDRLVEADASRRSSIAGFEQLRAEQKAFGKRVA +QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV +LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLKGVGARLELALMQL +GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGFHA +GEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEEAEAEHERL +LAWEERMLAAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR +RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNADGSVTVPAALRPYLGG +MERFELV +>PROKKA_02078 +MIDVKDLIEQPEKYRASQEARGEDASLVDRVVEADASRRSSIAGFEQLRAEQKAFGKRVA +QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV +LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLTGVGARLELALMQL +GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGYHA +DEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEDAEAEHARL +LAWEERMLGAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR +RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNVDGSVTVPAALRPYLGG +MERFELV +>PROKKA_00330 +MVPISGAQLTYRLRPAARLKPVIDVKDLIEQPEKYRASQEARGEDASLVDRMVEADASRR +ASITAFEELRAEQKAFGKKVAKAQGEEKQALLAEVKDLAARVKEAEAAAGAAEGRVAELQ +RAFPNLVLDGVPTGGEDDFVVLREVGAPRDFAAEGFEPRDHLELGELLGAIDMERGAKVS +GARFSFLKGVGARLELAIMQMGMDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYR +LERDDLYLVGTSEVALAGYHADEIIDVDAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQF +NKLEMFVYATQEDAEAEHARLLEWEERMLAAIEVPYRVIDIAAGDLGLSAARKFDCEAWV +PTQGTYRELTSTSNCTTFQARRLNIRERVRQEDGDGGARRGGTRMVATLNGTLATTRWIV +AILENHQNADGSVTVPVALRPYLGGMERFELV +>PROKKA_00272 +MIDVKDLIDQPEKYRVSQEARGADVSLVDQVVAADAARRAAISRFEELRAEQKAFGKRVA +QAKGEEKQALLAEVKDLAASVKEAEAASNEAEAELLRLQRLFPNLVIEGVPQGGEDDFVV +VKEVGTPRDFAAEGFEPRDHLELGELIGGIDMERGAKVSGARFSFLKGAAARLELALMQM +GLDLAVENGFVPVIPPTLVRPETMQGTGFDVAHDDEIYRLERDDLYLVGTSEVALAGYHA +DEIIDVADAPIRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFVYTTVERAEEEHAR +LLAWEEQMLARIEVPYRVIDTAAGDLGMSAARKFDCEAWVPTQGTYRELTSTSNCTTFQA +RRLNIRERQVKEDGTGSNAKKGGTRTVATLNGTLATTRWIVAILENHQNADGSVTVPEAL +RPYLGGLERFELV +>PROKKA_00059 +MIDVKDLIEQPEKYRVSQEARGEDASLVDRVVEADAARRSSIAGFEQLRAEQKAFGKRVA +QAKGEEKQALLAEVKDLAARVKEAESAAGAAEARLAELQRAFPNLIVDGVPAGGEDDFVV +LKEVGTPRDFAAEGFEPRDHLELGELLGAIDMERGAKVSGARFSFLKGVGARLELALMQL +GLDLALENGFVPVIPPTLVRPETMQGTGFDVEHDDEIYRLERDDLYLVGTSEVALAGYHA +DEIMDVSAPVRYAGWSTCYRREAGSAGKDTRGIIRVHQFNKLEMFIYAAQEDAEAEHERL +LAWEERMLGAIEVPYRVIDIAAGDLGLSAARKFDCEAWVPTQGTYRELTSTSNCTTFQAR +RLNIRERVRTEDGSKGGTRMVATLNGTLATTRWIVAILENHQNADGSVTVPAALRPYLGG +MERFELV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000216.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000216.fa new file mode 100644 index 0000000000000000000000000000000000000000..049ae04432b8323946ce8f478891fd044074dc16 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000216.fa @@ -0,0 +1,30 @@ +>PROKKA_00066 +MTKKLVCLDVDGTIVDHDGHLHEPVRAAVRAVLDAGHHVVIATGRSRGATLPVARSLGIG +AGFMVCSNGGVTLRLDPELEEGYEVTDLRTFDPRSVLTQLRHRLPSAKYALELPDGTFRS +TERFQDMSFGVAAEGVTFEELMDTTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT +AWLDVAAAGVTKASGLEALRTVLKVAPEDTVAVGDGRNDIEMLRWAGRGVAMGQAVEEVV +AAADEVTGHVDEHGLATVLRSLLEEPAAA +>PROKKA_02079 +MTKKLVCLDVDGTIVDHDGHLHEPVRAAVRAVLDAGHHVVIATGRSRGATLPVARSLGID +AGFMVCSNGGVTLRLDPELEEGYEVTDLRTFDPRSVLTQLRHRLPSAKYALELPDGTFRS +TERFQDMSFGVAAEGVTFEELMDTTAVRLVVFSTDSSAEEFGRAVEGLGLSGVTYSVGWT +AWLDVAAAGVTKASGLEALRTVLKVAPEDTVAVGDGRNDIEMLRWAGRGVAMGQAVEEVV +AAADEVTGHVDEHGLATVLRSLLEEPTAA +>PROKKA_00329 +MEKKLVCLDVDGTIVDHDGHLHEPVREAVKAVVAAGHHVVIATGRSRGATLPVAQSLGIE +AGYMVCSNGGVTLRLDPALEDGYEVTDCRTFDPRSVLSQLRSRLPGAKYAVEVPDGSFLS +TERFQDMSFGVAAEGTTFEELKNTTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT +AWLDVAAAGVTKASGLEALRTVLHVAPEHTVAVGDGRNDLEMLAWAGRGVAMGQAVREVK +EAADEVTASVDDHGLADVLWSLVPEADRPEGVRVQEPAAA +>PROKKA_00268 +MTKKLVCLDVDGTIVDHDGRLHEPVREAVRAVIEAGHHVVIATGRSRGATLPVAESLGID +SGYVICSNGGATLRLDRALEDGYEVTDLRTFDPQSVLAQLRDRLPSAKYALELPDGSFLS +TERFQDMSFGVAAEGVGFEELMATTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT +AWLDVAAAGVTKASALEALRTVLHVDVADTVAVGDGRNDVEMLRWAGRGVAMGQAPDEVK +EAADEVTGGVDEHGLATVLRTLL +>PROKKA_00060 +MTKKLVCLDVDGTIVDHDGHLHEPVRAAVRAVLDAGHHVVIATGRSRAATLPVARSLGIG +AGFMVCSNGGVTLRLDPELEEGYEITDLRTFDPRSVLTQLRHRLPSAKYALELPDGTFRS +TERFQDMSFGVAAEGVTFEELMDTTAVRLVVFSTDSSAEEFGRAVEGIGLSGVTYSVGWT +AWLDVAAAGVTKASGLEALRTVLKMAPEDTVAVGDGRNDIEMLRWAGRGVAMGQAVEEVV +AAADEVTGHVDEHGLATVLRSLLEEPAAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000217.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000217.fa new file mode 100644 index 0000000000000000000000000000000000000000..dc905080b91774aa0a0ba53ffdbbd3b210bea43b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000217.fa @@ -0,0 +1,25 @@ +>PROKKA_00067 +MFVLTINQRDTLDAGDRVDTFLRALQDVPGLDDAVVLPFQRAVGDELIGAVEDPRVAVDV +ALRALRQRRWNVGVGVGTVTHADGAAGAPASGDLHDAGGPGLAAARRAVEAAAVSTARIP +LAVRGRDEEAAAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAAAALGITAQA +VSQAVQRSYWNEEHACRPAAARLLTLAGG +>PROKKA_02080 +MFVLTINQRDTLDAGDRVDTFLRALQDVPGLDDAVVLPFQRAVGDELIGAVEDPRVAVDV +ALRALRQRRWNVGVGVGTVTHADGAAGAPASGDLHDAGGPGLAAARRAVEAAAVSTARIP +LAVRGRDEEAAAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAAAALGITAQA +VSQAVQRSYWNEEHACRPAAARLLTLAGG +>PROKKA_00327 +MLVLTINQRDTLDAGDRVDAFLRSLGDAPGLAGAVALPFQRAVGDELIGAVTDPAAAVEV +ALRALRERRWNVGIGVGALRGADGTEGAPSSGSLDDAAGPALAHARRAVEAAAVSTARIP +LAVRGADAQASAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAADALGITAQA +VSQAVQRAYWNEEHACRPAASRLLALAEEG +>PROKKA_00267 +MFVLTLNQRDTPDAGDRVDALLRELTDAAAAVPGLRSPALPFQRSVGDELVGVLEDPHAA +VDVALRALRQRRWNVGIGVGTVCHADGSAGIPASGDLHHAGGPGLAAARRAVEAAALSTA +RIPLAVRGRDAEAAAEAEAVLKLIGQLVWTRTAAEWSVLDLLVPGVRGQQKPAAQALGIT +TQAVSQAVQRSFWNEEHACRPAAARLLALAAG +>PROKKA_00061 +MFVLTINQRDTLDAGDRVDTFLRALQDVPGLGDAVVLPFQRAVGDELIGAVEDPRVAVDV +ALRALRQRRWNVGVGVGTVTHADGAAGAPASGDLHDAGGPGLAAARRAVEAAAVSTARIP +LAVRGRDEEAAAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAAAALGITAQA +VSQAVQRSYWNEEHACRPAAARLLTLAGG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000219.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000219.fa new file mode 100644 index 0000000000000000000000000000000000000000..f44f7f90d592be58517871da5827f9a8be673ea6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000219.fa @@ -0,0 +1,40 @@ +>PROKKA_00070 +MSDDHATDRPRTAADAEPGAPAEPGPAVAHPVDWAFAARTARSLAAAGPRFTPREATREA +EGLRAAAEAAVPHVHRLTGLEAARDLRDSQVLVVDRPTWSRAATQSFATLLDPTFAHLRD +TRPREHAATTRVTRHATALEMGGILAWMSGKILGQYDPFIALPGPGGTAAGPAGGRLLLV +APNVAQVRAEINVDPADFRLWVCLHEQTHRVQFAAAPWLREHLRGEITALTVGLFDKAES +LPERLRTALAAANPLGREADAGRTGTRDGHDAQDAVAARPAPGLLGAIQDEEDRERLSRL +TAVMSLLEGHANVVMDGVDSSVVSSVKTIRRRFDERGDRRSPLDRMLRRLLGMDAKMAQY +RDGQRFVAAAVAELGMAGFNVVWDAPELLPSEAELHAPETWVARIRAQA +>PROKKA_02083 +MSDDHATDRPRAAADAEPGAPAEPGPAVAHPVDWAFAARTARSLAAAGPRFTPREATREA +EGLRAAAEAAVPHVHRLTGLEAARDLRDSQVLVVDRPTWSRAATQSFATLLDPTFAHLRD +TRPREHAAATTRVTRHATALEMGGILAWMSGRILGQYDPFIALPGPGGTAGGPAGGRLLL +VAPNVAQVRAEINVDPADFRLWVCLHEQTHRVQFAAAPWLREHLRAEITALTVGLFDKAE +SLPERLRTALAAANPLGREADAGRTGARDGHDAQDAAPARPTPGLLGAIQDEEDRERLSR +LTAVMSLLEGHANVVMDGVDSSVVSSVKTIRRRFDERGDRRSPLDRMLRRVLGMDAKMAQ +YRDGQRFVAAAVAQLGMAGFNVVWDAPELLPSEAELHAPETWVARIRAQA +>PROKKA_00322 +MDTAPADRVPQPVDWAFAARTAAALAPAGPRFTAREAAREAAGLRAAAEASVPHVHRLTG +LAAAEDLRDSQVLVVDRPTWSASATQSFATMLEPTFAHLQATRPQEYQAALTPVARHATA +LEMGGILAWLSGKVLGQYDPFAGPSGGRLLLNAPSVAQVRTEINVDPEDFRLWVCLHEQT +HRVQFAAAPWLRGHLQEQITALASGLFDKAESLPERLRSALAAANPLGRGSGAGAASTGP +ASGPDDGRPGPAQAGGDVVPARGAGLLGALQDEEDRARLSHVTAVMSLLEGHANVVMDGV +DADVVSSVKTIRRRFEDRADRRSPLDRMLRRLLGMDAKMAQYRDGQRFVSAAVAELGMDG +FNVVWDAPELLPTEDELHRPERWTARVRAQA +>PROKKA_00264 +MTADQPVPSPAHPVDWDAAARAAGSLAAAGPRIGTREARREAEGLRAAAAASVAHVHRLT +GLAAAEDLRDSQVLVVDRPTWSLANTQSFAGLLEPSFAHLRATRPQEYALTTAPLTRRAA +ALEMGGILAWLSSKVLGQYDPFSALPGPDGVPAGPAGGRLLLVAPNVAQVRREIHVDPAD +FRLWVCLHEQTHRVQFAAAPWLRGHLQGEITALTGGLFDKAESLPERLRSALAAANPLGA +STSPGAGRAGQDDGAAGPGGRPALGLLGAIQDEEDRARLSRLTAVMSLLEGHANVVMDAV +DSSVVSSVKTIRRRFDARGDRRSGLDRLLRRLLGMDAKMAQYRDGQRFVDAAVAELGRDG +FNVVWDAPELLPSEEEIHAPDRWVARIRAQA +>PROKKA_00064 +MSDDHATDRPRTAADAEPGAPAEPGPAVAHPVDWAFAARTARSLAAAGPRFTPREATREA +EGLRAAAEAAVPHVHRLTGLEAARDLRDSQVLVVDRPTWSRAATQSFATLLDPTFAHLRD +TRPREHAAATTRVTRHATALEMGGILAWMSGRILGQYDPFIALPGPGGTAAGPAGGRLLL +VAPNVAQVRAEINVEPADFRLWVCLHEQTHRVQFAAAPWLREHLRAEITALTVGLFDKAE +SLPERLRTALAAANPLGREADAGRIGTRDGHDAQDAAAARPAPGLLGAIQDEEDRERLSR +LTAVMSLLEGHANVVMDGVDSSVVSSVKTIRRRFDERGDRRSPLDRMLRRLLGMDAKMAQ +YRDGQRFVAAAVAELGMAGFNVVWDAPELLPSEAELHAPETWGARIRAQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000220.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000220.fa new file mode 100644 index 0000000000000000000000000000000000000000..abb69296d9cc2a3cee04bb706ffe10317b85aa71 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000220.fa @@ -0,0 +1,40 @@ +>PROKKA_00071 +MPRPEARDPGPTPAGGVGGLPAVGAWPPRTRWPEPLHRAVAAVREALAGDGPRRADVVPG +RAGSRPRGLVALSGGADSLALAVACAVLVGTREGARLGPIGAAVVDHGLQSGSDAVAAAA +ADVARILGLTPVTVTRVEVARTGDGPEADARRARRVALAAAAREAGQGGAAPGAGTAVVL +TAHTADDQAEQVLLGLARGSGTRSLAGIPARGTLPGGAAVARPLLGLTRADTETICRWAG +LTWFEDPHNRDPALLRSRVRTRVLPALEDPDAGLGPGVRAGLVRTAAIAAEDAAALEAWA +GDEFTRLRVDPPGRDPRVVSLDLDTLAALPAAVRHRVIARAARAAGGQAPPRERILAVDT +LVTGARAGGTSAGPVELPGGVAAHRACARLDLIPCLPGP +>PROKKA_02084 +MPRPEARDPGPTPAGGAGGLPAVGAWPPRTRWPEPLHRAVAAVREALAGDGSCRADAGPG +RAGNRPRGLVALSGGADSLALAVACAVLVGTRDGARLGPIGAAVVDHGLQSGSDAVAAAA +ADVARILGLTPVTVTRVEVARTGDGPEADARRARREALAAAARDAGQGRAAVVLTAHTAD +DQAEQVLLGLARGSGTRSLAGIPARGTLPGGAAVARPLLGLTRADTETICRWAGLTWFED +PHNRDPALLRSRVRTRVLPALEDPDAGLGPGVRAGLVRTAAIAAEDAAALEAWAGAEVTR +LRVDPPARDPRVVSLDLDALAALPAAVRHRVIARAARAAGGQAPPRERILAVDALVTGAR +AGCTSAGPVELPGGVAAHRACARLDLIPCLPGP +>PROKKA_00321 +MPSGSAAPPALESWPPRGRWPEPLHRAVAALRPVLAAHDGGALIGLSGGADSCALAVAAA +ALRGTRAGAALGPVGAVVVDHGLQAGSADVAEAAARVARTLGLEPVLVRRVAVREAGDGP +EAAARRARRGAFADAAREAGAGLVLTAHTADDQAEQVLLGLARGSGTRSLAGIPAGGALP +GGTALARPLLGLTRADAEAICRWAGVRWWEDPHNADPALLRSRVRTRVLPALEDLADGLG +PGVREGLVRTAAIAAEDAAALEQWAACALAECRVRGEAGPGPGAEPGDDPGAGTGRSEAP +GRGDVVVRLDLAAFAALPPAVRHRVLGLAVVEAGGPRPTRERTLAVDALAVPADPGAGGP +RGPWSCPAGWK +>PROKKA_00263 +MSSPFVRDVVAVPGAPTLPALAGPWPPRSRWPEPLHRAVESVRAVRAEHPGPVLVALSGG +ADSLALAVACAVLAGTRAGERLGPAGAVVVDHGLQDGSAAVAAAAARTARALGLAPVTVE +AVTVTPAGDGPEASARSARRTALARAAEGVGEGTPALVLTAHTADDQAEQVLLGLARGSG +TRSLAGIPAHGALPGGVALARPLLGLSRADTEAICRWAGLTWFTDPHNADPALLRSRVRT +RILPALEDPDTGLGPGLRAALVRTAAIAAEDAAALDAWADDALARLRLPAPETDRPAPVL +LDLDALAALPAAVRHRVHARAARAAGAGTPSRERILAADALVAAAHAGGGSAGPVELGHG +VTVRRVAAGEGGVGGRKEGGPSGCARLAYIPRPADR +>PROKKA_00065 +MPRPEARDPGPTPAGGVGGLPAVGAWPPRTRWPEPLHRAVAAVREALAGDGPRRADVVPG +RAGSRPRGLVALSGGADSLALAVACAVLVGTREGRRFGPIGAAVVDHGLQSGSDAVAAAA +ADVARILGLAPVTVTRVEVARTGDGPEADARRARRKALAAAAREAGQGDAVPGAGAAVVL +TAHTADDQAEQVLLGLARGSGTRSLAGIPARGTLPGGAAVVRPLLGLTRADTETICRWAG +LTWFEDPHNRDPALLRSRVRTRVLPALEDPDVGLGPGVRAGLVRTAAIAAEDAAALDAWA +GDEVARLRVDPPARDPRVVSLDLDALAALPAAVRHRVIARAARAAGGQAPPRERILAADA +LVTGARAGGTSAGPVELPGGVAAHRACARLDLIPCLPGP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000226.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000226.fa new file mode 100644 index 0000000000000000000000000000000000000000..33b6df1d5df9d5386ecee5191b19e588e7fabc88 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000226.fa @@ -0,0 +1,20 @@ +>PROKKA_00079 +MIALRSGWTLLVVLAAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCIGLGWRVR +RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVGAPTVREAAL +QAAGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRGRPVRPETEGGYARARH +>PROKKA_02092 +MIALRSGWTLLVVLVAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCLALGWRVR +RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVEAPTVREAAL +QAVGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRPARPETEGGYARARH +>PROKKA_00314 +MIALRSWWTVVAVAVAVLLGWLAGLAAPSLGWGAPVVGRSGLITVTAVSVLCLVLGWRVR +RDREKPPAARMDPIAAARTLVLGQAAGFAGAALAGWHAGVALQVAARAGAGAPTVREAAL +QAAGGLVLLAVGLVVERWCRIPPEGDAAEGGRGEDGTAGRGRAPRPETEGGYARARD +>PROKKA_00255 +MISLVSGRTALLAFAAAVLGWLAALTAPSLGLAAPVMHLAALVTVVAVGVLCLVLGWRVR +RDRDRPLAQRMDPLAAARTLVLGQASGLTGAGLAGWHAGVGLEVASRAGIEAPAVLTAGL +LALGGAALLTVGVVVERWCRIPPEGDGAEPGAGQDGGGSGGHGARRPEAEGGFARARD +>PROKKA_00073 +MIALRSGWTLLVVLVAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCLALGWRVR +RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVEAPTVREAAL +QAVGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRPARPETEGGYARARH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000230.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000230.fa new file mode 100644 index 0000000000000000000000000000000000000000..be74e1169ee65c2a75249d0368db2305247f877b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000230.fa @@ -0,0 +1,20 @@ +>PROKKA_00084 +MTDQPEMSPLTEPEREWVRVRRDFAAQEGVDHLDLDAVAAYYDAVLARSQAEADELDPEE +LAVLLDVVAVLLGEHLGARHGMQWVTVADEEGPALALRDTLSDAVVFPQPVVGQSWNDQA +TGEWMGGYVDWLGEQLQQIRADAGTLPGA +>PROKKA_02097 +MTDQPEMSPLTEPEREWVRVRRDFAAQEGVDHLDLDAVAAYYDAVLARSQAEAEELDPEE +LAVLLDVVAVLLGEHLGARHGMQWVTVADEEGPALALRDTLSDAVVFPQPVVGQSWNHQA +TGEWMGEYVDWLGEQLQQIRADAGTRPGA +>PROKKA_00307 +MTEQPEMHPLSEPEQEWVRVRREFAAQEGVDHLDLDAVAAYYDGVLARSVSEAEALDPDE +LAVLLDVVAVLLGEHLGARHGMQWVTVSDDEGPALALRDTLSDAVVFPQPAVGQAWNEQV +TGAWLGEYVDWLGEQLQGIRAGDRPDGVAQQG +>PROKKA_00251 +MSEQQIRPLTAAEQEWVAVRRDFAAQEGTGHLDLDAVDAYHGRLLARSRSEDVDPDELGV +LLDVVAVLLGEHLGARHGLAWVAVTEGDATDLGLRDPLSDAVVFPQSVVAQHWNDGDAHW +IPGYVDWLGAQLAPLREERRAAEG +>PROKKA_00079 +MTDQPEMSPLTEPEREWVRVRRDFAAQEGVDHLDLDAVAAYYDAVLARSQAEAEELDPEE +LAVLLDVVAVLLGEHLGARHGMQWVTVADEEGPALALRDTLSDAVVFPQPVVGQSWNHQA +TGEWMGEYVDWLGEQLQQIRADAGTRPGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000233.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000233.fa new file mode 100644 index 0000000000000000000000000000000000000000..77201d08fccf465ee7adc9e346405a2a99c03646 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000233.fa @@ -0,0 +1,20 @@ +>PROKKA_00088 +MSTAHEPFRDATPHSGAHTPPPTQAEFRAEHESLGEMFQSLSAKLSTLVSQEIALAKAEA +TESAKKAGKGAGLLAGAAVGGFFLLMFLSLALMHLLDVFLPIGWAALIVAVLWGVVAAVL +AVQGKKDIEKIKGLPQTQETLQEIPETLNPAKETR +>PROKKA_02101 +MSTAHEPFRDATPHSGAHTPPSTQAEFRAEHESLGEMFQSLSAKLSTLVSQEIALAKAEA +TESAKKAGKGAGLLAGAAVGGFFLLMFLSLALMHLLDVFLPIGWAALIVAVLWGVVAAVL +AVQGKKDIEKIKGLPQTQETLQEIPETLNPAKETR +>PROKKA_00303 +MSTPYEPIRDATPHAGAHTPPPTQAEFRAEHESLGEMFKSLSSRLSTLVSQEIALAKAEA +TESAKKAGTGAGLLAGAAVGGFFLLMFLSLALMWALGSAMHLGWAALIVAVLWGVCAAVL +ALMGKKHLEKIKGLPQTQETLQEIPETLNPAKETR +>PROKKA_00248 +MSHATPNGGAPRHADPAAHQSTPAAGAHTPPPTQAEFRAEHESLGEMFSSATEKVSLLMR +QEIALAKAEATDSAKKAGKGAGMFAGAAVGGFFLLMFLSLALMYALGSLMPLGWAALIVA +VLWGVVAAVLALQGKKNIEKIKGLPQTQETLQEIPETLNPAKETR +>PROKKA_00083 +MSTAHEPFRDATPHSGAHTPPSTQAEFRAEHESLGEMFQSLSAKLSTLVSQEIALAKAEA +TESAKKAGKGAGLLAGAAVGGFFLLMFLSLALMHLLDVFLPIGWAALIVAVLWGVVAAVL +AVQGKKDIEKIKGLPQTQETLQEIPETLNPAKETR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000234.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000234.fa new file mode 100644 index 0000000000000000000000000000000000000000..724bf3092f06cdd82d28861969e881daef0a63f4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000234.fa @@ -0,0 +1,25 @@ +>PROKKA_00089 +MTTSNNPDEIRADIERTRRELGQDVDALAEKVSPTKAVSRQTNRIKDGFIHAKENIMGSP +EQHRHEPSLGDRAHAVVDDARASAYDAAGQAQDRLGDAGDRVSEWADDAQHALHQAPAQL +RGRTAGNPLAAGLIAFGAGLLLSSLIPASRAEQRAAEGLKDQAAPLVDEAKQAAQQLRED +LEPAAREAAGSVKESAAEAASHLKEQGTDTAQGLKAESQDAARQVKDTAKDA +>PROKKA_02102 +MTTSNNPDEIRADIERTRRELGQDVDALAEKVSPTKAVSRQTNRIKDGFIHAKENIMGSP +EQHRHEPSLGDRAHGVIDDARASAYDAAGQAQDRLGDAGDRVSEWADDAQHALHQAPAQL +RGRTAGNPLAAGLIAFGAGLLLSSLIPASRAEQRAAEGLKDQAAPLVDEAKQAAQQLRED +LEPAAREAAGSVKESAAEAASHLKEQGTDTAQGLKAESQDAARQVKDTAKDA +>PROKKA_00302 +MTTSNNPDEIRAEIERTRHQLGQDVDALAEKVSPTKAVSRQTNRMKDGLLSVKENIMGSP +EDHGRQPSMGDRAHAAADDARASMHGAADQARDAMGHASDRVSGWADDAQHAVQQAPAQL +RGRTAGNPLAAGLIAFGAGLLVSSLIPASRVEQRAAEGLKEQAAPLVDEAKQVAQQLRED +LEPVARDAAQSVKESATEAVDHVKADGADKAQDLKAESQDAARQVKGAAQDG +>PROKKA_00247 +MTTSSNPDEIRAEIERTRHALGQDVDALAEKVSPTKAVSRQTNRVKDGFITVKENIMGTP +EHHEGPGAVDRARFAAQDAAGQVQGTAHDVADQARGYAQQAGEAASQWVDDAQHAVQQAP +AQVRGRTAGNPLAAGLIALGAGWLIGSLIPASPVEKRAAERVKDQAAPLLESAKQEAAQV +AQDVREQVEPEVRDAAASLKDSAAESVQSLKSEGAEKAQDLKGSSQDAAQQVKHAAKHA +>PROKKA_00084 +MTTSNNPDEIRADIERTRRELGQDVDALAEKVSPTKAVSRQTNRIKDGFIHAKENIMGSP +EQHRHEPSLGDRAHGVIDDARASAYDAAGQAQDRLGDAGDRVSEWADDAQLALQQAPAQL +RGRTAGNPLAAGLIAFGAGLLLSSLIPASRVEQRAAEGLKEQAAPLVDEAKQAAQQLRED +LEPAAREAAGSVKESAAEAASHLKEQGTDTAQDLKAESQDAARQVKDTAKDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000236.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000236.fa new file mode 100644 index 0000000000000000000000000000000000000000..970e4fb6ebbeb653f319e799e053d41b490e1af7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000236.fa @@ -0,0 +1,25 @@ +>PROKKA_00091 +MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR +TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD +TGPKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTSARLAAPAAPARFLLAPP +APRDPAEPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD +>PROKKA_02104 +MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR +TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD +TGPKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTPARLAAPAAPARFLLAPP +APRDPAAPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD +>PROKKA_00300 +MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGDAGADPGAHSFRGR +TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD +TGLKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTPARLAAPARFLLAPPASR +DPAEPPIEVVTGPRVGVSGEGGSVRFPWRFNVAGHRSVSAFRRGRNVPD +>PROKKA_00245 +MTPERLAAAFDGPTPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR +TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD +TGLKLLSGPGNLGQGLGITLQMGHVPVEIVAAPPEVADDGGTPARLAAPARFLLAPPASR +DPAEPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD +>PROKKA_00086 +MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR +TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD +TGPKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTSARLAAPAAPARFLLAPP +APRDPAEPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000237.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000237.fa new file mode 100644 index 0000000000000000000000000000000000000000..568b0a9d74021da281c2419fda7814ece83582c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000237.fa @@ -0,0 +1,20 @@ +>PROKKA_00092 +MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD +VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTVV +SLTYDWTAVTDPELLAKNLFPMVSEEQMEESLAKLAAEVG +>PROKKA_02105 +MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD +VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTDV +SLTYDWTDVTDPELLEKNLFPMVSEEQMEKSLAKLAAEVG +>PROKKA_00299 +MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD +VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTDV +SLTYDWTAVTDPELLEKNLFPMVSEEQMEESLAKLASAVA +>PROKKA_00244 +MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD +VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTDV +SLTYDWTDVTDPELLAKNLFPMVSEEQMEESLAKLASEVG +>PROKKA_00087 +MTEMNKTAHGETQQTVTRTIDASAKDVFDFLTLPANHAKFDGSGMVQSDDKTQRIQKVGD +VFTMNMHAEHMGGDYQTDNHVVAYDPNKLVGWKTAPAGTEPKGWQWVYRLEDNGSGSTVV +SLTYDWTAVTDPELLAKNLFPMVSEEQMEESLAKLAAEVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000242.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000242.fa new file mode 100644 index 0000000000000000000000000000000000000000..f645ab53c4b26e2fa251d1744022e52ada51513b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000242.fa @@ -0,0 +1,50 @@ +>PROKKA_00097 +MTTQNSASAAVDHHDQQAVRAAKREQLLASGREAYPVQVPRTHALAEVRERFDGHEPDWT +SGETVSVTGRVVFLRNTGKLCFATLQESGADGEAVRLQVMVSLAAVGEESLAEWKKVVDL +GDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIVREE +ARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLVHGGALARPFETHLNAFDQPMTLRIA +TELYLKRAVVGGIDRVFEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQEIIL +NAADAVGAGRRLETAKGVIDLDGEWAWVAVYPGLSEAVGREITPETDAETLRAIAAEHEV +KVDPAWDAEKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPHRSDDRVIEAWDLIIGG +MERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGLGID +RLVMLFTDAGIRETILFPLLKPEA +>PROKKA_02110 +MTTQNSASAAVDHHDQQAVRAAKREQLLASGREAYPVQVPRTHALAEVRERFDGHEPDWT +SGETVSVTGRVVFLRNTGKLCFATLQESGADGEAVRLQVMVSLAAVGEESLAEWKKVVDL +GDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIVRDE +ARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLVHGGALARPFETHLNAFDQPMTLRIA +TELYLKRAVVGGIDRVFEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQEIIL +NAADAVGAGRRLETAKGVIDLDGEWAWVAVYPGLSEAVGREITPDTDAGTLRAIAAEHEV +KVDPAWDAEKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPHRSDDRVIEAWDLIIGG +MERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGLGID +RLVMLFTDAGIRETILFPLLKPEA +>PROKKA_00294 +MTSQNSANPQTSAVDHHDQQAVRAAKREQLLAAGREAYPVQVPRTHTLTEVREQFDGHEP +DWASGETVSVTGRVVFLRNTGKLCFATLQESGVDGEAVRLQVMVSLAAVGEDSLAQWKKA +VDLGDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIV +RDEARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLIHGGALARPFETHLNAFDQPMTL +RIATELYLKRAVVGGIDRVYEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQE +IILAAADAVGAGRRIETDRGVIDLDGEWAWVSVYPGLSEAVGREITPDTDAETLRAIAAE +HEVKVDPAWDAQKLVIELFGEIVEPTLMNPTFVHDYPPAAQPLARPHREDGRVIEAWDLI +IGGMERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGL +GIDRLVMLFTDAGIRETILFPLLKPEA +>PROKKA_00239 +MTPENPAPAAVDHHDQQAVRAAKREQLLTSGRQAYPVQVPRTHSLAAVRAKFDGKHEAGW +EEGPEVSVTGRVVFLRNTGKLCFATLQESGAAGEAVRLQVMVSLAEVGEESLGEWKKSVD +LGDFLSVTGRVIVSRRGELSIQAAAWEMASKALRPLPVLHADLNEETRVRQRYTDLIVRD +EAREMVYKRAKITSAVRRTLESHGYVEVETPILQLVHGGAQARPFETHLNAFDQDMTLRI +ATELYLKRAVVGGIERVYELGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMADRIKEII +LNAADAIGAGRRIETSRGVIDLDGEWAWVSVYPGLSEAVGREVTPDTDAETLRAIAAEHD +VKVDPKWDAQKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPNRDDDRVIEAWDLIIG +GMERGTAFSELIDPVIQRERLTEQSLKAADGDDEAMQLDEDFLRALEYGAPPMGGIGLGI +DRLVMLFTDAGIRETILFPLLKPEA +>PROKKA_00092 +MTTQNSASAAVDHHDQQAVRAAKREQLLASGREAYPVQVPRTHALAEVRERFDGHEPDWA +SGETVSVTGRVVFLRNTGKLCFATLQESGADGEAVRLQVMVSLAAVGEESLADWKKVVDL +GDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIVREE +ARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLVHGGALARPFETHLNAFDQPMTLRIA +TELYLKRAVVGGIDRVFEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQEIIL +NAADAVGAGRRLETAKGVIDLDGEWAWVAVYPGLSEAVGREITPETDAETLRAIAAEHEV +KVDPAWDAEKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPHRSEDRVIEAWDLIIGG +MERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGLGID +RLVMLFTDAGIRETILFPLLKPEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000246.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000246.fa new file mode 100644 index 0000000000000000000000000000000000000000..05a0af7e52641c2b3904e4203617ad988b4201b4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000246.fa @@ -0,0 +1,20 @@ +>PROKKA_00102 +MSVPRLDPMPADRPLTLRSARTQDVPVIQALVEPLARERVLLQKEAVAYYEAIQEFVVAE +EADGTLAGFGALHVMWQDIAEVRTLAVSEAHRGTGVGHLIIEELLDRARAVGVERVFCLT +FEVEFFRRHGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRRL +>PROKKA_02115 +MSVPRLDPMPADRPLTLRSARTQDVPVIQALVEPLARERVLLQKEAVAYYEAIQEFVVAE +EADGTLAGFGALHVMWQDIAEVRTLAVSEAHRGAGVGHLIIEELLDRARAVGVERVFCLT +FEVEFFRRHGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRRL +>PROKKA_00288 +MPADRQITLRSARTGDVPAIRALVEPLAQERVLLQKEAVAFYEAIQEFVVAEDADGSLAG +FGALHVMWQDIAEVRTLAVSRDHRGAGVGHLILEELLRRARVVGVERVFCLTFEVEFFRR +HGFAVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRTL +>PROKKA_00234 +MPAAPVVTVRPARTQDVPAIRALVSPLAERRLLLQKEAVAFYESIQEFMVAEAEDGSLAG +FGALHVMWQDIAEVRTLAVADAWLGAGVGHRILTALLERAREVGVARVFCLTFEVEFFRR +HGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRSL +>PROKKA_00097 +MSVPRLDPMPADRPLTLRSARTQDVPVIQALVEPLARERVLLQKEAVAYYEAIQEFVVAE +EPDGTLAGFGALHVMWQDIAEVRTLAVSEAHRGAGVGHLVIEELLDRARAVGVERVFCLT +FEVEFFRRHGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRRL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000247.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000247.fa new file mode 100644 index 0000000000000000000000000000000000000000..bcf2455641710356685993cd2936f5b00bf688fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000247.fa @@ -0,0 +1,35 @@ +>PROKKA_00103 +MPAPAPLVPPTVDVPHLHDAMLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL +PRWREWLERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAVVGRHDGRVPADPA +ALRALPGIGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA +LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA +GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR +DDDGGLTFPA +>PROKKA_02116 +MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL +PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA +ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA +LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA +GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR +DDDGGLTFPD +>PROKKA_00287 +MPAHETAVPPSVDVPRLHDAVLDWFAVHARDLPWRSPDCPPWGVLVSEIMLQQTPVARVL +PRWHAWLERWPTAADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHSGEVPADPA +ALRALPGIGEYTAAAVSSFAFGLPETVVDTNVRRVIARAVGGQALPGRSLTRAEMRRAHA +LMPEDPDRAQAWNAGVMELGALVCTARSPACERCPLADACAWVAAGSPPPEQAPRGQAWA +GTDRQVRGAVMAAVREHGRVAGDGLRAVVVAGGRLGAHRPGDAQWERCVAGLLADGLLAR +DDDGALAFPS +>PROKKA_00233 +MPAHDDAAPRPDLTALQDEVLDWFAAHGRDLPWRDPDCPPWGVLVSEIMLQQTPVVRVLP +RWRAWMERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHGGEVPADPAA +LRALPGIGEYTAAAVSSFAFGIPETVVDTNVRRVLARALRGEGLPGRTLTRAEMAAAHAA +LPADEHRANRWNAAVMELGALVCTARSPACDRCPIRARCAWVAAGSPAPEVARRGQAWVG +TDRQVRGAVMAAVREHGRVPRGGLREAVDGTGRLGAHTPDDAQWERAVAGLLGDGLLVAH +DDGALAFPA +>PROKKA_00098 +MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL +PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA +ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA +LMPEDPTRANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA +GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGWLGSHRPEDAQWARCVAGLVSDGLLAR +DADGGLTFPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000249.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000249.fa new file mode 100644 index 0000000000000000000000000000000000000000..bc05eb19eafa0e7b7982f6944a8aeec69dd4a9fb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000249.fa @@ -0,0 +1,40 @@ +>PROKKA_00106 +MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA +EAVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS +VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPTGTGGPFVRSQDAIVGGVLALLVTFL +SPQDVRRPAVRQLGGLYDSIATVLRDLSRALRENDSRTAWMALVASRGTHTTLEALRKEL +RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSVLDEGVFDDDDRER +LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL +VMLLRPMMVDLIEATGAEHDEARGYLPRV +>PROKKA_02119 +MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA +ETVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS +VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPIGTGGPFVRSQDAIVGGVLALLVTFL +SPQDVRRPAVRQLGGLYDSIATVLRDLSRALREDDSRTAWMALVASRGTHTTLEALRKEL +RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSALDEGVLDDDVRER +LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL +VMLLRPMMVDLIEATGAEHDEARAYLPRV +>PROKKA_00284 +MSDRFATATGTVPMVAPESRGARLRRFLRRRSRAGWSRVRSSVAHAALMAVCAVGAYWFA +ETVLGHHQPLFSSTALLIALGFQREPTLRKVAEVAVGCTVGILIGDLLLAALGRGLWQAT +VVVFVSVMVARFLDSGATFTMQMSLQSVLVVLLPAAQGGPFARSADALVGGLLALVVTFL +SPQDVRRGTARHLEGLYDSMATVLRDLSRALRQEDSRTAWMALVACRGTQGTLESIRAEL +KMAQEQATFNPLQRGSRSFVSDAANAADRSDLAVRSLRIVARRVVSVLDEGAFDDDHRER +LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASRLDPRELGGGSLHGEAL +VMLLRPMMVDLLEATGAPHDEARAYLPRV +>PROKKA_00225 +MTDRHATATGTLPAVPAAAGPSGVGRFLRRRARAGWSRLRSSVGHAALMAVCAVGAYWFA +ETVLGHAQPLFAATALLIALGFQREPRVRKVAEVAFGCTLGILIGDLMMAALGRGLWQAV +LVVFVSVLAARFLDSGATFTMQMSLQSVLVVLLPLNADGPFARSADALVGGLLALLVTLL +SPRDPTRLPARQLRGLYESMASVLRELSAALRAEESRTAWMALVECRRTQSTLEDVRKEL +KVTREQTVLNPLQRPARDAADVMAVAADRSDLAVRSLRIVARRVVSILDHGAVDGDHRER +LAAWFDDAADAVEILHRSLAEPQAEGRHRSLDVARDALGASASWLDPHELAGGTVHGEAL +VMLLRPMMVDLIEATGASHAEALTYLPRV +>PROKKA_00101 +MTDRFATATGTVPMVDPQTRGERLGRFLRRRARAGWSRVRSSVGQAALVAVCAVGAYWFA +EAVLGHQQPLFASTALLIALGFQREPKLRKVAEVAVGCTVGILIGDLLMVGLGRGLWQAS +VVLFVSVMVARFLDSGATFTMQMSLQSVLVVLLPTGTGGPFVRSQDAIVGGVLALLVTFL +SPQDVRRPAVRQLGGLYDSIATVLRDLSRALRENDSRTAWMALVASRGTHTTLEALRKEL +RVTHEQTVFNPLHRSSRSFVEDAVNAADRSDLAVRSLRIVARRVVSALDEGVLDDDVRER +LAAWFDDAADAVEILHRSLVEPQAEGRHRSLSVARDALGASASALDPHQLGGGSVHGEAL +VMLLRPMMVDLIEATGAEHDEARGYLPRV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000250.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000250.fa new file mode 100644 index 0000000000000000000000000000000000000000..aa08027fdef67469246e1d6f29c50fc2d8c97d18 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000250.fa @@ -0,0 +1,40 @@ +>PROKKA_00107 +MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS +QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKEN +CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL +PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS +QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES +GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM +ERIEAISVKG +>PROKKA_02120 +MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS +QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKKN +CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL +PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS +QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES +GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM +ERIEAISVKG +>PROKKA_00283 +MKALRFGRSAALLSVAALALTACGGNGGGDASSSAPAGGSSSAAAEGSGAAAASGTLIGG +GASSQEAAMTAWSEGVKATSPELTVQYSPDGSGAGREGFLGGAFSFAGSDAALKEDEAEQ +AKQICGDNGAFHVPAYISPIAIAYNLEGVDEVKMDAETIAKVFSKEITTWNDPAIAEQNE +GVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWKYDEVETWPSEITAESAQGTRGVV +GQAAQTDGAITYADASAVGELGTVAVKVGEEYVPYSSDAAAKTVSASVQNEDGSIELDRA +TTEAGVYPIVLVSYHIYCNQYQNQETADQVKAFASYVVSEDGQKAAEEAAGNAPIGAETR +DAAVERIEAITAG +>PROKKA_00224 +MKALRFGRSAALLSVAALALTACGGGNDSASSSSSAASSSAAGSSSASSSAAGSSSASSS +AAESSSASGSSSAAQGGYAIDVPTASGTLMGSGASSQEAAMTAWTEGVKATSPELQVQYS +PDGSGAGRKAFLSGAATFAGSDAALKDEEKTQAQEVCGPDGAFHVPAYVSPIAVAYNLEG +VDSLNLDADTIAKIFSKKITKWNAPEIAALNEGVELPDTAITVVHRADESGTTENFTAYL +DQVAPEAWTYGKVKEWPGDITAESAQGTKGVVSQAAATNGAITYADESGVGSLKTAKVGK +DGKFAEISPEAAAKIVADGKKQDDGSIELDRANAGEGVYPIVLVSYHIFCNQYGDQETVD +QVKAFASYVISEDGQKAAQEASKSAPLDAELAKEAKTRIDAIKVG +>PROKKA_00102 +MKAHRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEHASGSAGGEQGTTSEVQG +NLVGAGASSQEAAMTAWTQGVTEIAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKE +EEAESAKENCGDEGAFHVPAYISPIAVAYNLPGVDEVKMDAETIAKVFSGEIKNWNDEAI +AAQNEGVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQG +TKGVVGLASQTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSI +ELDRATDESGVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPI +SEDTRKKAMERIEAISVKG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000253.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000253.fa new file mode 100644 index 0000000000000000000000000000000000000000..140d1970a1bd6f79992afa311c574873eea151ee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000253.fa @@ -0,0 +1,30 @@ +>PROKKA_00110 +MSKRIQAIDVDVFYGKFKAVEGVNIDIAPRSVTAFIGPSGCGKTTFLRSINRMHEVLPGA +TVDGQLLLDGEDIYGPGVDPVRVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLNKS +RADELVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSIAVQPDVILMDEPCSAL +DPISTLAVEDLINELKEEYTVIIVTHNMQQAARVADKTAFFNIQGVGKPGKLIEYDDTNV +IFNNPSSQQTEDYVSGRFG +>PROKKA_02123 +MSKRIQAIDVDVFYGKFKAVEGVNIDIAPRSVTAFIGPSGCGKTTFLRSINRMHEVLPGA +TVDGQLLLDGEDIYGPGVDPVRVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLNKS +RADELVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSIAVQPDVILMDEPCSAL +DPISTLAVEDLINELKEEYTVIIVTHNMQQAARVADKTAFFNIQGVGKPGKLIEYDDTNV +IFNNPSSQQTEDYVSGRFG +>PROKKA_00280 +MSKRIQAKDVDVYYGKFKAVEGVNIDIAPRTVTAFIGPSGCGKTTFLRAINRMHEVLPGA +HVEGQLLLDGEDVYGPGVDPVTVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLSRS +RADEIVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSVAVSPDVILMDEPCSAL +DPISTLAVEDLINELKEQYTVIIVTHNMQQAARVADKTAFFNIQGIGQPGKLIEFDDTNV +IFNNPSNQQTEDYVSGRFG +>PROKKA_00221 +MSKRIQAKDVDVYYGKFKAVEGVSIDIAPRTVTAFIGPSGCGKTTFLRAINRMHEVLPGA +HVEGQLLLDGEDVYGPGVDPVTVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLTKS +RADEIVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSVAVEPDVILMDEPCSAL +DPISTLAVEDLINELKEDYTVIIVTHNMQQAARVADKTAFFNIQGIGQPGKLIEYAETNT +IFNNPSNQQTEDYVSGRFG +>PROKKA_00105 +MSKRIQAVDVDVFYGKFKAVEGVNIDIAPRSVTAFIGPSGCGKTTFLRSINRMHEVLPGA +TVDGQLLLDGEDIYGPGVDPVRVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLNKS +RADELVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSIAVQPDVILMDEPCSAL +DPISTLAVEDLINELKEEYTVIIVTHNMQQAARVADKTAFFNIQGVGKPGKLIEYDDTDV +IFNNPSSQQTEDYVSGRFG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000254.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000254.fa new file mode 100644 index 0000000000000000000000000000000000000000..66d7a5ddb68997e1e01ee8ddd8b14c05202fb75e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000254.fa @@ -0,0 +1,35 @@ +>PROKKA_00111 +MTAGLAVVLVLLCAVGALMGFRDAPNAAALPVRYRALTPRGALLLTGAVNTVGALLGIGL +ITLSVHYFTSPAVRSEIGPLAVGVSCAVTLVWGLLLWWRRLPGSSTHALISALAGSHLAV +RLSLHIDVAHTIFDLVRAEVLLSLLLSPLIAWALARLLTAPAMRLATRGTTVNVQHRARV +ALGISASAMAMGHGLQAGQRMGVLWAAVLVGSGSVLAPDALTAEFVGGAFLFALAVGLGT +LGGAWRIAWTLTERLVRLDPLRASVAAVIPAGLLFVGSLVFHLPLSSTHTATAAIVGAGQ +TQTYASVRWPTVLRVVGWWLLTPVACALLGLLGTLALLPLA +>PROKKA_02124 +MTAGLAVVLVLLCAVGALMGFRDAPNAAALPVRYRALTPRGALLLTGAVNTVGALLGIGL +ITLSVHYFTSPAVRSEIGPLAVGVSCAVTLVWGLLLWWRRLPGSSTHALISALAGSHLAV +RLRLHIDVAHTIFDLVRAEVLLSLLLSPLIAWALARLLTAPAMRLATRGTTVNVQHRARV +ALGISASAMAMGHGLQAGQRMGVLWAAVLVGSGSVLAPDALTAEFVGGAFLFALAVGLGT +LGGAWRIAWTLTERLVRLDPLRASVAAVIPAGLLFVGSLVFHLPLSSTHTATAAIVGAGQ +TQTYASVRWPTVLRVVGWWLLTPVACALLGLLGTLALLPLA +>PROKKA_00279 +MTPGLAVVALLLCALAAMMGFRDAPNAVALPVRFRALTPRLALVMTALINAVGALLGIGL +ITLSVHYFTSPAVRGDVGPLAVGVTAVVAVLWGLLLWWRRLPGSTTHAVLSALAGAHLAV +QLSLHDDLAGSILESVRVEVVLSLLLSPVIAWGLARLLTGPVVQVATTGTTVNVQRRARI +ALAVSAGAMAMGHGLQAGQRVGVLWAAVLVGSGAALSPDALTAEFVVGSVLFALAIALGT +LGGAWRIAWTLTERLVRLDPLRASVAAVVPAGLLFVGSLVLHLPLSSTHTATAAIVGAGQ +TQTYASVRWPTVLRVGGWWLLTPVVCAALGLLGTLALLPLA +>PROKKA_00220 +MTAPLLVPVLVLLLAVGGLMGFRDAPNAVALAVRFRALTPRVALILSALLNAVGVLLGAL +MLTLGLPLMVAGGTARPEVLALVGVAAAVTLGWGVLAWRFRAPTSTTHALLASLAAAHVA +SVSALGSGLDPAFENGARWEVAASLLLSPVLAWGLARLTARPVLRLATTGTTVNVQHRAR +IALAVSTGLIALGHGVQAALRLLPLAVLVATAAVGTGLPPGTELSAAFVAAAAVGIGTLG +GAWGIAWTLTERLVILDPLRAAVAAVVPAVLLFAGTMLLHLPLSSTHTGVAGIVGAGQTQ +SYASVRWGAVARVAVWWVATPLVCGSLAFAAGAVLLPLLG +>PROKKA_00106 +MTAGLAVVLVLLCAVGALMGFRDAPNAAALPVRYRALTPRGALLLTGAVNTVGALLGIGL +ITLSVHYFTSPAVRSEIGPLAVGVSCAVTLVWGLLLWWRRLPGSSTHALISALAGSHLAV +RLSLHIDVAHTIFDLVRAEVLLSLLLSPLIAWALARLLTAPATRLATRGTTVNVQHRARV +ALGISASAMAMGHGLQAGQRMGVLWAAVLVGSGSVLAPDALTAEFVGGAFLFALAVGLGT +LGGAWRIAWTLTERLVRLDPLRASVAAVIPAGLLFVGSLVFHLPLSSTHTATAAIVGAGQ +TQTYASVRWPTVLRVVGWWLLTPVACALLGLLGTLALLPLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000257.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000257.fa new file mode 100644 index 0000000000000000000000000000000000000000..f272d0db1daf321eb1b29aa7be18e2017d0726c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000257.fa @@ -0,0 +1,29 @@ +>PROKKA_00115 +MSPTPPPVTETISSGHSVVWSRPPAERAGTDLVLVFHGYGSNEVRAARRHFPMLPERCTG +LAVRGGFEIDETASEGPGDPGAHGWFLLDLLLQSDFAQVLAAAHRVFDVLSAEEVVAAGF +RTVSVLGFSQGMAMATTVLRLRPEAFTCGVGLSGFAVDNELLAMLDSPAEGPGPRPFFWG +RDAEDPVIHPDAVAHTRAWAEEHTRLTVRTYPGILHGTGPDEVRDVRIFLEHSLRAATPG +S +>PROKKA_02128 +MSPTPPPVTETISSGHSVVWSRPPAERAGTDLVLVFHGYGSNEVRAARRHFPMLPERCTG +LAVRGGFEIDETASEGPGDPGAHGWFLLDLLLQSDFAQVLAAAHRVFDVLSAEEVVAAGF +RTVSVLGFSQGMAMATTVLRLRPEAFTCGVGLSGFAVDNELLAMLDSPAEGPGPRPFFWG +RDAEDPVIHPDAVAHTRAWAEEHTRLTVRTYPGILHGTGPDEVRDVRIFLEHSLRAATPG +S +>PROKKA_00272 +MPTPPTTSIETLRSGHPVVWSRPAAERPGTDLVLVLHGYGSNEVRAANRFFPMLPERCTG +LAVRGGFEIDAAATEGPGDPGAHGWFLLDLMLQSDFAQVVAAAHRVFDVLASEEVAQARF +RTVSVLGFSQGMAMATTLIRLRPEAFACGVGLSGFVVDNELLAVLDSPPEGPGPRPFFWG +RDVEDPVIHPDAVAHTRAWAEEHTLLTVRTYPGVLHGIGPEAVRDVRIFLDHSLRAATPD +T +>PROKKA_00204 +MSTGSAPESEPLASGGHAVWSRPEHERAGTDLVLVLHGYGSNEVRAARRFFPMLPERCTG +LALRGPFEIDAAAVEGPDDPGAHGWFLLDVLLQSDFAQVIAAAHRVYDALADDAVADAGF +RSVSVLGFSQGMAMATTVIRLRPEAFACGVGLSGFAVDNELLAVLDSPAEGPGPRPFFWG +RDAQDPVIRPDAVAHTAAWAEEHTLLTARTYPGILHGTGPEEARDVRIFLEHVLGGA +>PROKKA_00120 +MSPTPTPVTETISSGHSVVWSRPPAERAGTDLVLVFHGYGSNEVRAARRHFPMLPDRCTG +LAVRGGFEIDETASEGPGDPGAHGWFLLDLLLQSDFAQVLAAAHRVFDVLSAEEVVAAGF +RTVSVLGFSQGMAMATTVLRLRPEAFTCGVGLSGFAVDNELLAMLDSPAEGPGPRPFFWG +RDAEDPVIHPDAVAHTRAWAEEHTRLTVRTYPGILHGTGPDEVRDVRIFLEHSLRAATPG +S diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000264.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000264.fa new file mode 100644 index 0000000000000000000000000000000000000000..4927c6b18a4c05e72ed480f2b365f953fb0dd32d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000264.fa @@ -0,0 +1,35 @@ +>PROKKA_00126 +MSAQTQPAATRREDAPLGVLVGVDGSDQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWG +YGADASGAVLDDSRLREGVQALLEEVAGKLDADGVRPELRVEIGDAAGVLVELSAEASLL +VSGARGRGGFMGRLLGSVAAALPGHAHCPVAIIPAGVEASRAGDRTAVVVGVDGSEQGRA +AALEAAEEARLRQAPLKLVCAVPPLGANAAWLAVSLDEEARERELRERLEAGAAWISSEF +PGLEVLTELVDGTPVDVLVDQTATARLTVVGTRGLGGFAGAIVGSTSRGVADHAKGPVLV +VPFREDVRLGRRASFGPVQDQSGS +>PROKKA_02140 +MSAQTQPAATRREDAPLGVLVGVDGSDQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWG +YGADAGGAVLDDSRLREGVQALLEEVAGKLDADGVRPELRVEIGDAAGVLVELSAEASLL +VSGARGRGGFMGRLLGSVAAALPGHAHCPVAIIPAGVEASRAGDRTAVVVGVDGSEQGRA +AALEAAEEARLRQAPLKLVCAVPPLGANAAWLAVSLDEEARERELRERLDAGAAWISSEF +PGLEVLTELVDGTPVDVLVDQSATACLTVVGTRGLGGFAGAIVGSTSRGVADHAKGPVLV +VPFREDVRLSRRASFGPVQDQPES +>PROKKA_00259 +MSAQTQPAAPREDAPLGVLVGVDGSEQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWGY +GADAGGTVLDDSRLREGVQVLLDEVAAKLDADGVRPELRVEVGDAAGVLVDLSKAASLLV +SGGRGRGGFIGRLLGSVASALPGHAHCPVAIIPAGVEASRAADGAAVVAGVDGSEQGRAA +ALVAAEEARIRQAPLKLVCALPPVGGNAAWLGVTLDEAAREQELRERLDAGAAWIASEFP +GLEVVTELVDGTPVDVMREQTATARLTVVGTRGLGGFTGALVGSTSRGVTDHAKGPVMVV +PFRKDARLGTRTKFGPVADQD +>PROKKA_00193 +MSAETTPSTLPAEAPLGVLVGVDGSDQSISAARWAQREAGLRNLPLTLATAYTVPAFWGY +AADGAGLLTDDGRLHAGVEALLREVAGKLDPAGVAPELRVEVGDAAGVLIDLSAQAELLV +SGSRGRGGFIGRLLGSVSSALPGHAHCPVAIIPAGVEASRADSGAPVVVGVDGSEQGRAA +ALVAAEEAQARKAPLHLISALPPISPNAAWLAVSLDEEAREQELRERLEDGARWLASEFP +GLEVTSELASGVPVDVMVEQTATARLTVLGTRGLGGFSGALMGSTSAGVANHAKGPVMVV +PFREDVRLGRRAEFGAVVDQDDPRV +>PROKKA_00134 +MSAQTQPAATRREDAPLGVLVGVDGSDQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWG +YGADAGGAVLDDSRLREGVQALLEEVAGKLDADGVRPELRVEIGDAAGVLVELSAEASLL +VSGARGRGGFMGRLLGSVAAALPGHAHCPVAIIPAGVEASRAGDRTAVVVGVDGSEQGRA +AALEAAEEARLRQAPLKLVCAVPPLGANAAWLAVSLDEEARERELRERLDAGAAWISSEF +PGLEVLTELVDGTPVDVLVDQSATACLTVVGTRGLGGFAGAIVGSTSRGVADHAKGPVLV +VPFREDVRLGRRASFGPVQDQPES diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000265.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000265.fa new file mode 100644 index 0000000000000000000000000000000000000000..4e46690bb0a9b8a6708ee907d973c2caec286319 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000265.fa @@ -0,0 +1,19 @@ +>PROKKA_00127 +MDHRPSPEQPAATWMSEQEFDDAVSAALTRIPDELARLLTNVVVVVEDEYEPQRWEDPAT +ELFGLYEGVPLTERAEFAWQMPDRIVVFRGPLTRHCTSRAELEDEITVTVMHEVGHFFGI +SEERLHELGWG +>PROKKA_02141 +MDHRPSPDQPAATWMSEQEFDDAVSAALARIPDELARLLTNVVVVVEDEYEPQRWEDPAT +ELFGLYEGVPLTERAEFAWQMPDRIVVFRGPLTRHCTSRAELEDEITVTVMHEVGHFFGI +SEERLHELGWG +>PROKKA_00258 +MSEQEFDDAVSAALTRIPDELARLLTNVVVVVEDEYEPQRWENPDTELFGLYEGVPLTER +AEMPWQMPDRIVVFRGPLTRHCTSRAELEHEITVTVMHEVGHFFGIDEERLHELGWG +>PROKKA_00192 +METWMSEEEFDAAVDAALLRIPDELARLLTNVVVIVEDEYEPQRWEDPDTELFGVFEGFS +LAERAEAAWQLPDRIVIFRGPLTRHCRSRAELEHEITVTVMHEVGHFFGISEERLHELGW +G +>PROKKA_00135 +MDHRPSPEQPAATWMSEQEFDDAVSAALTRIPDELARLLTNVVVVVEDEYEPQRWEDPAT +ELFGLYEGVPLTERAELAWQMPDRIVVFRGPLTRHCTSRAELEDEITVTVMHEVGHFFGI +SEERLHELGWG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000266.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000266.fa new file mode 100644 index 0000000000000000000000000000000000000000..2d44df32f86753c9ca5df323410c44693d064cfc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000266.fa @@ -0,0 +1,25 @@ +>PROKKA_00131 +MPDSPSARATGGETALVVIDVQHSYFEHPALAAQQAELTAAVVELLRTAREAGRPVFLVR +TEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA +ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRDE +MRQPLLGQDEALTLLRTGLVPDRG +>PROKKA_02145 +MPDSPSARATGGETALVVIDVQHSYFEHPALAAQQAELTAAVVELLRTAREAGRPVFLVR +TEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA +ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRAE +MRQPLLGQDEALTLLRTGLVPDRG +>PROKKA_00254 +MPDSAPAPEPIAGERPSGGETALVVVDMQYSYFEHPDLAARQAELTEAVVELVRTAVEAG +RPVVLVRTEHERDRSTWTLNMLEDGEGFAFPGTRQAAVLDEVARAARGAVEVVKTRDSAF +HRTDLDAQLRRRGVGRLLLCGVSTHSCVFQTATDAFARDFHAATAVDAIASEDPRLSAAM +LEFLRDEMRQPLLGREDALALLRTGLVPDQG +>PROKKA_00651 +MNTLQNPALIVVDVQRGFDDVEYWGSRDNPDCETNISSLLTHWRDRSWPIVFVRHDSTNP +ESTLAVGTPGNEFKEVITGDPDLLVSKTVNSSFHGTPDLDDWLRAEGIEQVVICGITTNH +CCETTARIAGNLGYDTYFAIDATHTFDRPALDGTVLPAATVSAMTAANLHGEFATVVSTR +TLIDGNSYAPRYEQEK +>PROKKA_00139 +MPDSPSARATGGETALVVIDVQHSYFEHPALAAHQSELTAAVVELLRAAHEAGRPVFLVR +TEHARDRSTWTLNMLADDEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSAFHGTGLAA +ELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIASEEPALAAAMLDFLRDE +MRQPLLGQDEALTLLRTGLVPDRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000270.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000270.fa new file mode 100644 index 0000000000000000000000000000000000000000..de9db6b420e233fcb5edab8e01ba9faaa1352133 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000270.fa @@ -0,0 +1,30 @@ +>PROKKA_00137 +MKIATWNVNSLRARADRVEAFLERHDIDVLAIQETKCRDENFPWELFERAGYEVVHNGTS +QWNGVAIASRVGLSDVQRGFPGQPHFGKGGVDPQEESRAIGATVGAEAADGVAPVRLWSL +YVPNGRGLENEHMGYKLEWLRVLQEHAAARLAEDPDTRLALTGDWNIAPQDEDVWDIELF +QREGYTHVSPPERAAFRAFEDAGLVDVVRPRHPGPGVYTYWDYTGLAFPKKKGMRIDFQL +CSPALARTVTDAWIDREERKGKGASDHAPVVVELG +>PROKKA_02151 +MKIATWNVNSLRARADRVEAFLERHDIDVLAIQETKCRDENFPWELFERAGYEVVHNGTS +QWNGVAIASRVGLSDVQRGFPGQPHFGKGGVDPQEESRAIGATVGAEAADGVAPVRLWSL +YVPNGRGLENEHMGYKLEWLRVLQEHAAARLAEDPDTRLALTGDWNIAPQDEDVWDIELF +QREGYTHVSPAERAAFHAFEDAGLVDVVRPRHPGPGVYTYWDYTGLAFPKKKGMRIDFQL +CSPALARTVTDAWIDREERKGKGASDHAPVVVELG +>PROKKA_00247 +MKIATWNVNSLRARADRVEAFLERHDIDVLAIQETKCRDENFPWELFERAGYEVAHHGTS +QWNGVAIASRVGLSDVQRGFPGQPHFGKGGIDPQEESRAIGATVGTEAGDGVAPVRLWSL +YVPNGRALDNEHMPYKLEWLRVLREHVAQRLAEEPQTRLALTGDWNIAPQDEDVWDIEMF +VREGYTHVSPPERAAFHAFEETGLVDVVRPRHPGPGVYTYWDYTGLAFPKKKGMRIDFQL +CSPALAETVTDAWIDREERKGKGASDHAPVVVELG +>PROKKA_00181 +MKIATWNVNSLRARADRVEAFLDRQDVDVLAIQETKCRDENFPWELFERAGYEVAHNGTS +QWNGVAIASRVGLSDVQRGFPGQPHFGKGGVDPQEESRAIGATVGAEAADGVAPVRLWSL +YVPNGRGLENEHMGYKLEWLRVLQEHAAARLAEDPDTRLALTGDWNIAPQDEDVWDIELF +QREGYTHVSPAERAAFHAFEDAGLVDVVRPRHPGPGVYTYWDYTGLAFPKKKGMRIDFQL +CSPALARTVTDAWIDREERKGKGASDHAPVIVELG +>PROKKA_00145 +MKIATWNVNSLRARADRVEAFLERHDIDVLAIQETKCRDENFPWELFERAGYEVVHNGTS +QWNGVAIASRVGLSDVQRGFPGQPHFGKGGVDPQEESRAIGATVGAEAADGVAPVRLWSL +YVPNGRGLENEHMGYKLEWLRVLQEHAAARLAEDPDTRLALAGDWNIAPQDEDVWDIELF +QREGYTHVSPAERAAFHAFEDAGLVDVVRPRHPGPGVYTYWDYTGLAFPKKKGMRIDFQL +CSPALARTVTDAWIDREERKGKGASDHAPVVVELG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000271.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000271.fa new file mode 100644 index 0000000000000000000000000000000000000000..f0332fc7959a16d672b768450899b7a61ef8bbb3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000271.fa @@ -0,0 +1,33 @@ +>PROKKA_00138 +MRELQQRIIAQQGVLPEIDPAAEVERRVAFLADYLAATGASGFVLGISGGVDSTVGGRLA +QLAVERRRAQLGVTDAVALGGPDTTPPGEAGVGADVVPSRENPRFTAVRLPYKVQHDEAD +ARAAMDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMTAQYAVAGA +HGQLVIGTDHAAEAVTGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEPLWNKVPTA +DLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTTPVTIHDDW +WR +>PROKKA_02152 +MRELQQRIIAQQGVLPEIDPAAEVERRVAFLADYLAATGASGFVLGISGGVDSTVGGRLA +QLAVERRRAQLGVPDAVALGGPGTTPPGEAGVGADVVPSRENPRFTAVRLPYKVQHDEAD +ARAAMDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMTAQYAVAGA +HGQLVIGTDQAAEAITGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEPLWNKVPTA +DLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTTPVTIHDDW +WR +>PROKKA_00246 +MRELQQQIIAEQGVRPQIDPAQEIERRVEFLVDYLEATGAAGFVLGISGGVDSTVGGRLA +QLAVERRRARLGAPDAVALGGPEAPRGAPAADEAPSPQRPQFTAVRLPYRQQKDEADARA +AMDFVDADREITLDIAAGVEGIASAFVEATGDEIADFDKGNVKARMRMVAQYALAGAHRQ +LVIGTDHAAEAVTGFYTKFGDGGADVLPLSGLNKRQVRALGRELGAPEHLWNKVPTADLL +DGNPGRTDEDELGMTYEHIDDYLEGGDIPEEAAEKLEGIWLRSRHKRTMPVTVHDDWWR +>PROKKA_00180 +MPEPYAGAMRELQQQIIAEMGVRPEVDPAAEVEARVRFLVDYLEATGASGFVLGISGGVD +STTAGRLAQLAVERRRAELGTEAGDDAAPSRENPRFTAVRLPYRVQADEADATAAMDFVG +ADGRVTLNIAEAVAGMASAFQEATGEPISDYNQGNVKARMRMVAQYAIAGAHGQLVIGTD +HAAESITGFFTKFGDGGADVLPLAGLDKRQVRAVAKELGAPEHLWAKVPTADLLDGSPGR +ADEDELGLSYEHIDDYLEGREIPEEAAEKLEGVWRRSRHKRTTPVTIHDDWWR +>PROKKA_00146 +MRELQQRIIAQQGVLPEIDPAAEVERRVAFLVDYLAATGASGFVLGISGGVDSTVGGRLA +QLAVERRRAQLGVTDAVALGGPGTTPPGEAGVGADVVPSRENPRFTAVRLPYKVQHDEAD +ARAALDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMTAQYAVAGA +HGQLVIGTDQAAEAITGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEPLWNKVPTA +DLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTTPVTIHDDW +WR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000273.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000273.fa new file mode 100644 index 0000000000000000000000000000000000000000..21a54d221606c554c10672a5c606e3aabd4156de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000273.fa @@ -0,0 +1,25 @@ +>PROKKA_00140 +MGGMTDAQTPTVPTPEQDRERLKQLIQDLAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA +PLIGRVMLRLLEENGIGCDAVGGLTMGADPVATAMMHQAGAAGRALDAFVVRKAQKSYGM +GRQVEGPGVDGRRVVVLEDTSTTGGSALTAVEGVRNAGGDVQAVAVIVDRATGAAERVAE +EAGVPYLYAFGKDELGLD +>PROKKA_02154 +MGGMTDAQTPTVPTPEQDRERLKQLIQELAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA +PLIGRVMLRLLEENGIEFDAVGGLTMGADPVATAMMHQAGTVGRALDAFVVRKAQKSYGM +GRQVEGPGVDGRRVVVLEDTSTTGGSALTAVEGVRNAGGDVQAVAVIVDRATGAAERVAE +EAGVPYLYAFGKDELGLD +>PROKKA_00244 +MGGMTDAQTPTVPTPEQDRERLKELIQELAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA +PLIGRVMLRLLEENGVQFETMGGLTMGADPVATAMMHQAGAQGRALDAFVVRKAQKSYGM +GRQVEGPGVDGRDVVVLEDTSTTGGSALTAVEGVRRAGGRVQAVAVIVDRATGAAERVAE +EADVPYLYAFGKDELGLD +>PROKKA_00178 +MTAEHTSVAPTPEQDRERLRELIKELAVVHGRVTLSSGAEADYYVDLRRVTLHHEAAPLI +GRVMLRLLEENGIEFETMGGLTMGADPVATAMMHQAGAQGRALDAFVVRKAQKSYGMGRQ +VEGPGVEGRRVVVLEDTSTTGGSALTAVEGVRKAGGDVQAVAVIVDRATGAAERVAEEAG +VPYLYAFGKDELDLD +>PROKKA_00148 +MGGMTDAQTPTVPTPEQDRERLKQLIQDLAVVHGRVTLSSGKEADYYVDLRRVTLHHEAA +PLIGRVMLRLLEENGIGCDAVGGLTMGADPVATAMMHQAGAAGRALDAFVVRKAQKSYGM +GRQVEGPGVDGRRVVVLEDTSTTGGSALTAVEGVRNAGGDVQAVAVIVDRATGAAERVAE +EAGVPYLYAFGKDELGLD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000277.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000277.fa new file mode 100644 index 0000000000000000000000000000000000000000..6dbed9684840a8d20284dbc6fad4c1118a99c196 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000277.fa @@ -0,0 +1,30 @@ +>PROKKA_00144 +MRAEQVTDPIAYHGEGPVWAASWGAAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV +GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC +GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTLAYYNDTPTRQV +AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV +VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG +>PROKKA_02158 +MRAEQVTDPITYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV +GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC +GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV +AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV +VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG +>PROKKA_00240 +MRAEQVTDPITYHGEGPVWAEHWGTAASGLAAGGGLRWVDMLAGDVLSLRADGAVERTHV +GDVAAVVRPRAGGGAVLAVERGFALMSPEGELTTLPELWGPEAGLRMNEGGCDPDGRFHA +GTMAYAKTPGAASLHRLSPGPDGGAGEVDVVLTGATTSNGLEWSPGGSLAYYNDTPTRQV +AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV +VEVPVQKTTACTFGGEDLGTLYITTSWENMERGEDPLAGALFAVRPGVTGLPARPFAS +>PROKKA_00174 +MRADQVTDPLCYHGEGPVWAESWGGLRWVDMLAGDVLSLGADGGVTRRNVDPKVCAVVRP +RVGGGAVFAVERGFALEDPDGTLHRLPPLWDDAAGLRMNEGGCDPDGRFYAGSMAYAKTP +GAASLHRLSPAPEGGAGEVDVVLEGVTTSNGLAWSPDGSLAYYDDTPTRQVAVFDYSREE +GLTNRRVLVDVLDGEGKPDGLCVDAEGGIWVAVISHGRIHRYTPEGVLDEVVEVPVQKTT +ACTFGGDDLGTLYITTSWEGMERGEDPLAGALFSVRPGVAGLPTLPFAG +>PROKKA_00152 +MRAEQVTDPIAYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRTDGTVDRTHV +GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC +GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV +AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV +VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000280.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000280.fa new file mode 100644 index 0000000000000000000000000000000000000000..c41601d6a1a45ee25838da75a00edf43f91396ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000280.fa @@ -0,0 +1,45 @@ +>PROKKA_00148 +MTTQPHHSTPASAEQLQHDWDNNPRWAGVERSFTAEDVVRLRGRIQEEHTLARRGAEKLW +TQLKDENARGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP +ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT +AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA +ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL +ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA +LNHSMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS +STVALAGSTESGQFH +>PROKKA_02162 +MTTQPHHSTPASAEQLQHDWDNNPRWAGVERSFTAEDVVRLRGRIQEEHTLARRGAEKLW +TQLKDENARGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP +ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT +AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA +ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL +ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA +LNHSMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS +STVALAGSTESGQFH +>PROKKA_00235 +MTTQPHHSTPASAEQLQHDWDHNPRWAGIERTYSPDDVVRLRGRIQEEHTLARRGAEKLW +TQLKDENARGDFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP +ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT +AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA +ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL +ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA +LNHSMFDLAKGYHERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS +STVALAGSTESGQFH +>PROKKA_00820 +MTEQTVQQIAQEIQKDWDTNDRWTHIERTHTAEDVAKLRGRVQEEHTLARRGSEKLWEQL +TSEHAKGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYPANS +VPAVVRRINNALLRADQIEWSEGIKTVEDYLVPIVADAEAGFGGPLNAYELMKGMIASGA +SGVHWEDQLASEKKCGHLGGKVLIPTGQHVRTLNAARLAADVAGVPSVIIARTDAEAATL +ITSDVDERDAEFITGERTAEGFYKVKNGVEPCIARAKAYAPYSDLIWMETGTPDLELARK +FAEAVKSEFPDQMLSYNCSPSFNWKKNLDDATIAKFQRELGAMGYTFQFITLAGFHALNH +SMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAISTAVNPESSTV +ALKESTEAGQFH +>PROKKA_00156 +MTTQPHHSTPASAEQLQHDWDNNPRWAGVERSFTAEDVVRLRGRIQEEHTLARRGAEKLW +TQLKDENARGEFTNALGALTGNQAVQQVKAGLRAIYLSGWQVAADANLSGHTYPDQSLYP +ANSVPQVVRRINNALLRADQIEHAEGVSSVEDWLVPIVADAEAGFGGPLNAYELMKSMIT +AGASGVHWEDQLASEKKCGHLGGKVLIPTGQHIRTLNAARLAADVADVPSVIIARTDAEA +ATLITSDVDERDAEFITGERTAEGFYKVRNGVEPCIARAKAYAPHADLIWMETGTPDLEL +ARKFAEAVKAEFPDQMLAYNCSPSFNWKKNLDDDTIAKFQRELGAMGYTFQFITLAGFHA +LNHSMFDLAKGYNERQMSAYVELQEREFADEARGYTATKHQREVGTGYFDAVSTAINPDS +STVALAGSTESGQFH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000281.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000281.fa new file mode 100644 index 0000000000000000000000000000000000000000..933d5a108b80b9c647524ed6f14fd83ea3ec476c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000281.fa @@ -0,0 +1,55 @@ +>PROKKA_00149 +MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT +DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP +GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDQID +FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE +LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI +LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH +RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF +DAVLGEAPNQIRTRRREDVEPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG +AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG +PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFASQDDAAAKA +>PROKKA_02163 +MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT +DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP +GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDRID +FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE +LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI +LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH +RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF +DAVLGEAPNQIRTRRREDVVPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG +AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG +PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFAGQDDAAAKA +>PROKKA_00234 +MTTTTVTSGRHHAAPALHHTDEPVDTAAHTPLPHDVSTQALPVVAPAGAAPVVTVHGPVT +DRQAEILTEDALAFLGRLHRVAEDRRRRLLEEREFTRQRITEGWDPHFLRATKRVREDDS +WRVAPLAPGLKDRRVEITGPVDRKMTVNALNSGATGWLADFEDSSTPSWERMLDGQVNLY +DAIRGRIDFTSPEGKEYRLRGAELTDRPTIIVRPRGWHLTDDHLRVDGEPMAGGLVDFGL +YFFHNAAELVRRGHGPYFYLPKLESHLEARLWNCVFVAAQDALGIPQGTIRATVLIETIT +AAFQMEEILYQLRNHAAGLNAGRWDYIFSLIKNYRDRGPAYVLPDRAEVTMTQPMMRSYT +EQLVRACHRRGASAIGGMSAVIPDRRDQAANEVAFAKVREDKTREARDGFDGSWVAHPDL +VPVAREVFDEVLGEAPNQIRTRRREDVEPDEAGLLDVAATTGSVTEAGVRRNIEVAMRYV +ESWLRGQGAAAIHGLMEDAATAEISRSQIWQWAHNRTAVALEDGGTRTASREWMEQLVRE +EHARILAGPLPEGHRFEDARRVFCESALPPEYPAFLTLGAYRRHFSAERA +>PROKKA_00819 +MMTLQTTHSDTTVNGVRVLGEPVPGQDRVLTSAALEFLAALHRGVEGRRRELMDERAARR +RRIAEGETLDFLPATRKVREDDSWHVAPLAPGLRDRRVEITGPVDRKMTINAMNSGAKCW +LADFEDSSTPSWENVIAGQVNLQDAIRRTISLTTPEGKEYTLGGVQLVDRPTIIVRPRGL +HLMEDRILVDGQPVSGALADFALYFFHNAKELLRRGRGPYFYLPKTESHLEARWWNCVFV +RAQDLLEIPQGTIRATVLIETITAAFEMEEILYQLRNHAAGLNAGRWDYIFSVIKTFRER +GEDFVLPDRSEVTMTQPMMRAYTELLVRTCHRRGASAIGGMAAQIPNRKDPEANAAALEK +VRSDKTREAGDGFDGSWVAHPDLVPVAMEVFDAVLKDLPNQIRTRRREDVVPDAAALVDI +KSTTGSITEQGLRMNIEVGIRYVESWLRGNGAAAIHNLMEDAATAEISRSQIWQWIRTGS +TARLTDGGERTVTREWVEQVTEEEFGRIERTEGDRFDDAREIFTSVALAEDFPDFLTLPA +YERFLSAEARRRAGHGA +>PROKKA_00157 +MSPQTTTPTLHEIHADDVREHTPLPHDVSTQAIPVVIPEGAAPVVTVHGPVDGRQAEILT +DEALAFLGRLHRLAEDRRRRLLEEREYTRRRITDGWNPHYLRSTRRVREDDSWRVAPLAP +GLQDRRVEITGPVDRKMTINALNSGASGWLADFEDSSTPSWDRMLDGQVNLFDAIRDQID +FTSPEGKEYRLRERELTDRPTIIVRPRGWHLLEDHIRVDGEPMAGALVDFGLYFFHNADE +LIRRGHGPYFYLPKLESHLEARLWNCVFVAAQDELGIPQGTIRATVLIETITAAFQMEEI +LYQLRNHAAGLNAGRWDYIFSIIKNFRDRGAEFVLPDRSEVTMTQPMMRAYTEQLVRACH +RRGASAIGGMSAVIPDRRNEEANAAALEKVRADKAREAGDGFDGSWVAHPDLVPVAREEF +DAVLGEAPNQIRTRRREDVVPDEAALLDVAATTGSVTEAGVRMNIEVGIRYIESWLRGNG +AAAIHGLMEDAATAEISRSQIWQWAHNGTGVQLTEGGVRTANRGWMEQLIREEHARILAG +PLPEGHRFEDAVRVFCESALPPEYPAFLTLGAYRRHFAGQDDAAAKA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000286.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000286.fa new file mode 100644 index 0000000000000000000000000000000000000000..801ca84b3c0803ffc2a7c566752526b97c04f248 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000286.fa @@ -0,0 +1,24 @@ +>PROKKA_00168 +MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR +LADRWERQLEIACGKPTAEATSMERLTAYILTCSTAASRAEFQMILDSQHTQHMAIWEDL +IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV +HESEAKPNG +>PROKKA_00359 +MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR +LADRWERQLEIACGKPTAEATPMERLTAYILTCSTAASRAEFQLILDSQHTQHKAIWEDL +IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV +HESEAKPNG +>PROKKA_02333 +MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR +LADRWERQLEIACGKPTAEATPMERLTAYILTCSTAASRAEFQMILDSQHTQHKAIWEDL +IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV +HESEAKPNG +>PROKKA_00676 +MAKTTEQLLDDAIAVLRRGGVVTIDSVASEAGMSKAGVVHHFSSKEALMVGVVNRVMDLW +EGQLAATIGEVTDPVERLRAYVDFEVLSDFDGGDLALLADVKLRDTLAAQWRERLRPWFG +EDAPGDAGQKAALQSARLIADGAWTDQALGLLSMTGEQRALVRGIAQRLIDEGVQK +>PROKKA_02011 +MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR +LADRWERQLEIACGKPTAEATPMERLTAYILTCSTAASRAEFQMILDSQDTQHKAIWEDL +IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV +HESEAKPNG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000288.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000288.fa new file mode 100644 index 0000000000000000000000000000000000000000..08433ab1f5150639845f775eec19d3997273eecd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000288.fa @@ -0,0 +1,45 @@ +>PROKKA_00179 +MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL +SPNAVPVIGNGVVVNLEALFEEIDGLESRGHSCEHLKISANAHLVAPYHQTMDKVTERFL +GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV +TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS +NPTAGGAAVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT +GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ +TEFHHAKPVYEHFDGWTEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV +VQVRDLIQD +>PROKKA_02175 +MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL +SPNAVPVIGNGVVVNLEALFEEIDGLESRGHSCEHLKISANAHLVAPYHQTMDKVTERFL +GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV +TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS +NPTAGGAAVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT +GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ +TEFHHAKPVYELFDGWTEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV +VQVRDLIQD +>PROKKA_00222 +MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL +SPNATPVIGNGVVVNLEALFEEIDGLESRGHSCAHLKISANAHLVAPYHQTMDKVTERFL +GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV +TVDEVAEYFLGYAERLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS +NPTAGGASVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT +GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIESIPVCVAYDVDGVRHDRMPMTQ +TEFHHAKPIFEHFDGWTEDISGAREFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV +VQVRDLIDG +>PROKKA_00168 +MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL +SPNAVPLIGNGVVINLEALFEEIDGLEARGHSCANLKISANAHLVAPYHQTMDKVTERFL +GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV +TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATFLDVDHGTYPFVTSS +NPTAGGASVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRMTGGEFGVNT +GRPRRTGWYDAVLAHYAARVNGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ +TEFHHAKPIFEHFDGWTEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDEV +VQVRGLIED +>PROKKA_00176 +MPAIAIVGAQWGDEGKGKATDLLGGRVDYVVKPNGGNNAGHTVVVNGEKFELKLLPAGIL +SPNAVPVIGNGVVVNLEALFEEIDGLESRGHSCEHLKISANAHLVAPYHQTMDKVTERFL +GKRAIGTTGRGIGPTYMDKVARLGIRVQDIFDESILRQKIEGALRQKNELLVKLYNRRAV +TVDEIAEYFLGYADRLRPMVVDSVNLLNDALDEGKVVLMEGGQATYLDVDHGTYPFVTSS +NPTAGGAAVGAGIGPTRFSRTIGIVKAYTTRVGAGPFPTELFDEMGEQLRTTGGEFGVNT +GRPRRTGWYDAVMAHYAARINGFTDYFLTKLDVLTGIEKIPVCVAYEVDGVRHDRMPMTQ +TEFHHAKPVYEHFDGWAEDISGARAFTDLPLNAQRYVEALEKLSGCRISAIGVGPGRDQV +VQVRDLIED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000291.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000291.fa new file mode 100644 index 0000000000000000000000000000000000000000..2f8bff27179252ea64e3de5dcc5cc1a8e98eead6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000291.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000294.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000294.fa new file mode 100644 index 0000000000000000000000000000000000000000..ea44890e9b6da4f9467182d480a985ced77978c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000294.fa @@ -0,0 +1,45 @@ +>PROKKA_00185 +MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD +HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF +GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR +VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL +GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPEQAVTRDRFRVARRA +AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL +FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLGARFVIGVVCVSAIIFFSAVVPAI +LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT +>PROKKA_02181 +MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD +HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF +GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR +VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAAGFSTVSATFMVIVAKTL +GLMDIWLWYFFGTLVVTFAVTAITVRIPPLSRIPDEVYPGAVHSPELAVTRDRFRVARRA +AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL +FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI +LATDIPIPLWKLVVIWAERVALTILLAMPVAHLVAALT +>PROKKA_00216 +MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD +HLVTWVRGLLGPADRWVGLAIIATGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF +GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR +VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL +GLMDIWLWYFFSALVVTFVVTAITVCIPPLSRIPDEVYPGAVHSPEQAVTRDRFRVALRA +AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGMIFYPL +FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI +LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT +>PROKKA_00161 +MTHAHPADGELHTDTTAMAAIEADSPRPPARWRMVVYSLIGIVMFFVPVTINGASSIPLD +HLVTWVRGLLGPADRYVALALIAAGAVFPFATGRWRQSVTTTVFAFLGVVGLLTACMVVF +GFGPSWVLDKGIGPFLLDKLVIPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR +VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL +DLMDHWLWYFFGTLVVTFVVTAITVRIPPLSRIPDEPFPGAVHVPEEAVTQDRFRVARRA +AEQTLAEAPSLGRNVWLNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWVGLIFQPV +FWALGFSDPALMASASATSIAEMFIPATMLAGHEDFVARFVIGVVCVSAIIFFSALVPAI +LATDIPVKLWHLVVIWVERVVLTVLLATPLGHLVAALTS +>PROKKA_00182 +MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD +HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF +GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR +VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL +GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPELAVTRDRFRVARRA +AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL +FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI +LATDIPIPLWKLVVIWAERVALTILLATPVAHLVAALT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000302.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000302.fa new file mode 100644 index 0000000000000000000000000000000000000000..a85297ac2333e31227a82b2c0c6c3fa53419977f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000302.fa @@ -0,0 +1,30 @@ +>PROKKA_00197 +MPHPPRPTPDDVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW +GVDGRPDAWEDASFGTVATGPLIGLGVTGFLALVSAMVTVLVPTDPGLSPWRRVRQAGVH +RGVQECLGWSCVLIVLVLAPTTAEVLAAGAWTMPWWILPLTLTVLMVGVFPAMRASTRRW +TRWSDRVAAELGYRPTAAERAEDEVWTPLGLKRDPDDPAVFPTKRPGYGVGVTVNLATPA +GRWLVRGFVVVVIVGLPLALWLGAFAAR +>PROKKA_02193 +MPHPSRPTPDDVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW +GVDGRPDAWEDTSFGTVATGPLIGLGMTGFLALVSAMVTALVPTDPGLSPWRRVRQAGVH +RGVQECLGWPCVLIVLVLAPMTAEVLAAGAWTMPWWLLPLTLTVLMVGVFPAMRVSTRRW +TRWSDRVAAELGYRPTAAELAEDEVWTPLGLKRDPDDPAVFPAKRPGYGVGVTVNLATPA +GRWLVRGFVAVFIVGLPLALWLGAFAAR +>PROKKA_00202 +MARYVPAPAPEPVPAAEEAALRQGRARPWWPYLLTAAVSVALLVWTVVAYPGLPEQVPVR +WGIDGRPDRWEDTTFGTVAFGPIFGLGMTAFLALIAAMIPAMTGVHGATSAWRRVRQEGV +NRGVREGMGWIALLSLLMTAPTTAEVLSAGAWRMPWWLMPLLLTALMVGVFGALRATLGR +WTRWADGVAADLGHRPTPEELAEDKTWTPLGMKDDPEDPTVFPAKRPGYGVGTTINIGTR +AGRLLVYGFVAVFMVALPLATWIGAYLAR +>PROKKA_00150 +MPHPPRPTPDDVPAAERAALRRGRWIPWLPYLLTAAVSAGLLVWAIVALPGLPDRVPVHW +GIDGRPDAWEEKSFGTVAFGPLLGLGMTALLAFCAALTPAMTATPQDASPWRRVRQEGVN +RGVREALGWLTLLIALATAPSTVEVLSNGAWRPAWWLMPLVLTLVMLGTVGVFGPALRRW +TGWADRTAQDLGYRADFAELAEDAKWTPLGLKNDPEDPSAFPAKREGYGVGATVNLATTT +GRLLVYGFVALFVIGLPAALWIGAFLNR +>PROKKA_00197 +MTHPPHPVPADVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW +GVDGRPDAWEDASFGTVATGPLIGLGMTGFLALVSAMVTALVPMDPGLSPWRRVRQPGVH +RGVQACLGWSCVLIVLVLAPTTAEVLAAGAWTMAWWLLPLTLTVLMVGIFPAMRAGTRRW +TRWADRVAADLGHRPTAAELAEDEVWTPLGLKRDPEDPAVFPAKRPGYGVGVTVNLATPA +GRWLVRGFVAVFIVGLPLALWLGAFAAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000303.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000303.fa new file mode 100644 index 0000000000000000000000000000000000000000..c84ad8c23b66685d48e73f624c5af844107cddc1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000303.fa @@ -0,0 +1,70 @@ +>PROKKA_00202 +MTAGDDGGRGAVVGVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA +ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAEADRLAFWEAAGRRLSWER +PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR +AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF +SAEALRFRVEDTGAKLLVTTDGQFRRGAAVPVKANADEAVSGDNAIEHILVLDRTGHRDI +PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW +THDFLFSHPNPARRDDDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH +FEVIERYRVTSYYTAPTLIRSLKGWHPDGIPAHADGGPDLSSIRLIGTVGESVNPEAWTW +ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP +TPEGLQGRIVVTRTSPAMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV +WILGRVDDVINISGHRLSTIEIESALVAHPEVIEAGVCPVPHETTGHAAVAFVVAHESWL +AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT +ALGDTTSLQNEPCVGQIAEVLRAGRRAQDAGTGAVRSASSAST +>PROKKA_02197 +MTPTEDPARPDPAEEGASGAVRGPNDGVPAAALATLPGPLPQALVDAADPDVHPGRPADR +LHGGRGDGRPVAEADRLAFWEAAGRRLSWERPFTRTRSLTAPDPAAERGPEIRWYEDGTL +NVAVNCVDRHVAAGRGEKVALYFEGEPGDRRAVTYAQLQREVAQAANALEELGIEAGDRV +VVYLPVLVETIVITLACARIGAVHSLVFGGFSAEALRFRVEDTGAKLLVTTDGQFRRGTA +VPVKANADEAVSGDNAIEHVLVLDRTGHRDIPWTEGRDLWWHDVVDRQPDTHTPRAFDAE +HPLFIMYTSGTTGQPKGLVHTSGGYLAAASWTHDFLFSHPDPARRDDDVHWCTADLAWVT +AHTYEIYGPLSNGVTQVIYEGVPNAPHPGRHFEVIERYRVTSYYTAPTLIRSLKGWHPDG +IPAHADGGPDLSSIRLIGTVGESVNPEAWTWARTQIGRDTPDLPMVDTWWQSETGATVLS +PRPTDTAFKPGCGSRPLPGVDVAVVDDDGTPTPEGLQGRIVVTRTSPSMARTVWQNPARY +FHSYWEDYADQSEAGWFLAGDGAKRDEDGDVWILGRVDDVINISGHRLSTIEIESALVAH +PEVIEAGVCPVPHETTGHAAVAFVVAHESWLAGDDGPGASAADRAEELRRHVGRVIGPVA +KPAEVVFVPDVPKTRSGKIMRRLLTQLHQGTALGDTTSLQNEPCVGQIAEVLRAGRRAQD +AGPGAVRSASSAST +>PROKKA_00190 +MTPSPLDAATRARSSAPASPGDAPTAPDAPVRRPNDGVPAEALATLPGPLPQAVVDAADP +DVHPGRAEDLAHGGRGDGRPVAEEDRLAFWAAAGRRLTWDREFTRVSTGTPADPAAERGP +ALRWYEDGRLNVAVNCVDRHVAAGRGEKVALYFEGEPGDREAVTYADLQRRVAQAAHALE +DLGIGPGDRVVVYLPVLVETIVIALACARIGAVHSLVFGGFSADALRFRVEDTGAKLLVT +TDGQHRRGQVVPVKENADAAVAGDNAIEHVLVIARCGLTGAGEIPWTEGRDLWWHDVVET +KPTEHAPASFDAEHPLFVMYTSGTTGRPKGLVHTSAGYLAAASWTHDFLFSHPDPARRHE +DVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRHFEVIDRYRVTSYYTAP +TLIRSLMGWHPDGIPAEHSLESIRLIGTVGEAVNPEAWTWARTQIGRAALARTGEPVPMV +DTWWQSETGSTVLSPRPTDHTFKPGCGSRPLPGVEVAVVDDDGAPVPAQTQGKIVVTRTS +PSMARTVWGDPARYFHSYWEDCAEQGWFLAGDGAKTDEDGDVWILGRIDDVINISGHRLS +TIEIESALVAHPHVVEAGVCPVPDARTGHAAVAFVVPGREWAPGPEGDEAAAALAAERAE +ELRRHVGTVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHTGTALGDTTNLQNEVCVG +QIAQVLADRPGR +>PROKKA_00144 +MTAGDDGGRGAVIVVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA +ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAEADRLAFWEAAGRRLSWER +PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR +AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF +SAEALRFRVEDTGAKLLVTTDGQFRRGAAVPVKANADEAVSGDNAIEHVLVLDRTGHRDI +PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW +THDFLFSHPDPARRDGDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH +FEVIERYRVTSYYTAPTLIRSLKGWHPDGIPAHADGGPDLSSIRLIGTVGESVNPEAWTW +ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP +TPEGLQGRIVVTRTSPSMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV +WILGRVDDVINISGHRLSTIEIESALVAHPHVVEAGVCPVPDPKTGHAAVAFVVAHESWL +AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT +TIGDTTSLQNEWCIPQIAEVVAARR +>PROKKA_00204 +MTAGDDGGRGAVVGVPTLVGPADQEEPPPMTPTEDPARPDPAEEGASGAVRGPNDGVPAA +ALATLPGPLPQALVDAADPDVHPGRPADRLHGGRGDGRPVAESDRLAFWEAAGRRLSWER +PFTRTRSLTAPDPAAERGPEIRWYEDGTLNVAVNCVDRHVAAGRGEKVALYFEGEPGDRR +AVTYAQLQREVAQAANALEELGIEAGDRVVVYLPVLVETIVITLACARIGAVHSLVFGGF +SAEALRFRVEDTGAKLLVTTDGQFRRGVAVPVKANADEAVSGDNAIEHVLVLDRTGHRDI +PWTEGRDLWWHDVVDRQPDTHTPRAFDAEHPLFIMYTSGTTGQPKGLVHTSGGYLAAASW +THDFLFSHPDPARRDDDVHWCTADLAWVTAHTYEIYGPLSNGVTQVIYEGVPNAPHPGRH +FEVIERYRVTSYYTAPTLIRSLKGWHPDKIPAHADGGPDLSSIRLIGTVGESVNPEAWTW +ARTQIGRDTPDLPMVDTWWQSETGATVLSPRPTDTAFKPGCGSRPLPGVDVAVVDDDGAP +TPEGLQGRIVVTRTSPSMARTVWRNPARYFHSYWEDYADQGEAGWFLAGDGAKRDEDGDV +WILGRVDDVINISGHRLSTIEIESALVAHPEVIEAGVCPVPHETTGHAAVAFVVAHESWL +AGDDGPGASAADRAEELRRHVGRVIGPVAKPAEVVFVPDVPKTRSGKIMRRLLTQLHQGT +ALGDTTSLQNEPCVGQIAEVLRAGRRAQDADTGAVRNASSAST diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000304.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000304.fa new file mode 100644 index 0000000000000000000000000000000000000000..b1565a144a1fb5e36c3bf291fe7b58de7cb5a339 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000304.fa @@ -0,0 +1,40 @@ +>PROKKA_00203 +MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALGELQAAGFGKVGVPEDAGGEGGGS +ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRERWLRHIVDGDWAGSALAERA +GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG +AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV +LMEATLLALQAGIGRAALTEGTQLLRQRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA +ELMVREIGRLLDEGQDGADGAGPAEADVVAASAEAMAAAYRAQAVVPEAVLEVCTRIFDT +LGASATSATLRLDRHWRNARTLATHDPAAFKVRMAGDWLVNGTPPTAYTSAGEVPEGD +>PROKKA_02198 +MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALAELQAAGFGKVGVPEDAGGEGGGS +ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRERWLRHIVDGDWAGSALAERA +GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG +AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV +LMEATLLALQAGIGRAALTEGTQLLRQRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA +ELMVREIGRLLDEGQDGADGAGPAEADVVAASAEAMAAAYRAQAVVPEAVLEVCTRIFDT +LGASATSATLRLDRHWRNARTLATHDPAAFKVRMAGDWLVNGTPPTAYTSAGEVPEGD +>PROKKA_00188 +MTSYADLAARFADAFDAVGHGERAREAGRHLPFAVQRGLQEAGFGRVSVPEVAGGDGASH +ETALRLLMDLAARDVNTAHLWRSHLVFVATVLDQVPAAAEPWLERVVAGDWAGSALAERG +TAAPGRAATMAERDEGGTWVVTGEKYYATGSAFATWTIATVGVDGDGLVSRRNSKRAGGV +VREPGRAVAVVRVRQPRVRVKDDWDGFGQRLTATGSVVLDGAAAEALLEVPRREGPVPVL +QEASLLALQVGVGRAALAEGVELLRARRRTFNTGTEALPAQDPQLLEIMGRLAGQLAAAE +ALVRQVGGLMDEAEERGTAGDDDGAARLMEEAMVAAYRAQAVVPDAVLGVCTGIFDTLGA +SATSAALQLDRHWRNARTLATHDPAAFKVRMAGDHLVNGTPPTAYTSAGVVDDD +>PROKKA_00143 +MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALGELQAAGFGKVGVPVDAGGEGGGS +ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRDRWLRHIVAGDWAGSALAERA +GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG +AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV +LMEATLLALQAGIGRAALTEGTQLLRKRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA +ELMVREIGRLLDEGEDGADGAGLAEADVVAASAEAMAAAYRAQAVVPEAVLEVCTRIFDT +LGASATSATLRLDRHWRNARTLATHDPAAFKVRMAGDWLVNGTPPTAYTSAGDAQD +>PROKKA_00205 +MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALGELQAAGFGKVGVPVDAGGEGGGS +ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRERWLRHIVDGDWAGSALAERA +GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG +AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV +LMEATLLALQAGIGRAALTEGTQLLRQRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA +ELMVREIGRLLDEGEDGADGAGPAEADVVAASAEAMAAAYRAQAVVPEAVLEVCTRIFDT +LGASATSATLRLDRHWRNARTLATHDPAAYKVRMAGDWLVNGTPPTAYTSAGEVPEGD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000305.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000305.fa new file mode 100644 index 0000000000000000000000000000000000000000..0e89395556da6159bf5c1fb072f14275ee2adf68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000305.fa @@ -0,0 +1,30 @@ +>PROKKA_00204 +MSAALTTPAATTGPEARERSGHDDGDTGARRRQRPRVLDRPGARAVVGLAAPAVLLVLWW +AVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHVGISTQRVLLGFLLGAALGLAVGSA +LGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQIGEESKVTLIAIGAFFPVFTTVYAA +LRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVFSGLRLALAQAWLFLVAAELIASSM +GLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLLGLLERRALRRWA +>PROKKA_02199 +MLDRPGTRAAVGLAAPAVLLVLWWAVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHV +GISTQRVLLGFLLGAALGLAVGSALGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQI +GEESKVTLIAIGAFFPVFTTVYAALRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVF +SGLRLALAQAWLFLVAAELIASSMGLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLL +GLLERRALRRWA +>PROKKA_00198 +MTVLDRPGGRTAVGLIVPALLLLLWWALTAAGVFSGVQLPPPAWVAEAAVDLAARGTLWH +HIAISVQRVLVGFLIGGALGLLVGSVLGLSRWADALLAPTIGALRAVPSLAWVPLLILWM +QIGEESKVTLIAIGAFFPVFTTVYAALRHVDPHLVEAGRAYGYHGVRLLGTVQLPAVVPA +MFSGLRLALAQAWLFLVAAELIASSMGLGFLLTDSQNNGRTDRLILAIILLAVLGKISDW +LLGFVERWAVRRWA +>PROKKA_00140 +MSTALTTPAATTGPEARERSGHDDGGTGARRRQRSRVLDRPGARAVVGLAAPAVLLVLWW +AVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHVGISTQRVLLGFLLGAALGLAVGSA +LGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQIGEESKVTLIAIGAFFPVFTTVYAA +LRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVFSGLRLALAQAWLFLVAAELIASSM +GLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLLGLLERRALRRWA +>PROKKA_00206 +MLDRPGTRAAVGLAAPAVLLVLWWAVTAAGLLSAVQLPSPGAVLSAGVNLLERGDLWLHV +GISTQRVLLGFLLGAALGLAVGSALGLSRWADALFAPLIGALRAVPSLAWVPLLILWMQI +GEESKVTLIAIGAFFPVFTTVYAALRHVDPHLVEAGRAFGYHGLSLLRTVQLPAVVPAVF +SGLRLALAQAWLFLVAAELIASSMGLGFLLTDSQNNGRTDRLILAIILLAVLGKLTDWLL +GLLERRALRRWA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000308.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000308.fa new file mode 100644 index 0000000000000000000000000000000000000000..096e33b2f996dd9157dc0f52ed77de295462ca30 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000308.fa @@ -0,0 +1,19 @@ +>PROKKA_00210 +MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK +KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNITSAARHGAEPDTISDPSTPLGD +EGPLTR +>PROKKA_02203 +MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK +KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNITSAARHGAEPDTISDPSTPLGD +EGPLTR +>PROKKA_00181 +MRLITLGLGAALGYLLGSAEGRRNLEKMSQNAQKFWNDPKTQQKVGNLQETAQQKFADVK +NSEQVQKATAKVEDTMNKNGSKDQVRDDRVTESNNENTTTASAHGADPDIVSDPSTPLGD +EGPQTR +>PROKKA_00127 +MRWFTLAVGAAAGYLLGSAEGRQNLQKMTANAQKVWNDPKTQDKVGVVKDKAQVVASDAK +DKAASAASDAKQAVQEKTSSNQPSPASNNETVTTGNAHGADPDVVSDPSTPLADEGPAA +>PROKKA_00210 +MRLITLGLGAALGYLLGSAEGRKNLEKMTQNAQKLWNDPKTQEKVGQVQETAQQKFAEVK +KSDPVQKATTKVEDAMQGNDKKNDVREDRVTESNNDNVTSAARHGAEPDTVSDPSTPLGD +EGPLTR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000312.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000312.fa new file mode 100644 index 0000000000000000000000000000000000000000..880b669c47d267ad06c3635d515cfacfd5b2c0c3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000312.fa @@ -0,0 +1,17 @@ +>PROKKA_00214 +MRSRYTAFARLGEAGPAEAQAMADYLAATWAPEHRPPAAELLPAAGEQAPRFTRLAVLDV +RDGGPFQDAGTVEFVAVGAGAEGRFRLHEVSRFRREDGVWRYVDGDVR +>PROKKA_02207 +MRSRYTAFARLGEAGPAEARAMADYLAATWVPEHRPTAAELLPTEGEQAPRFTRLAVLDV +RDGGPFQDAGTVEFVAVGTGAEGRFRLHEVSRFRREDGIWRYVDGDVR +>PROKKA_00169 +MTDPCPCGAGLPLAECCGRLHARFAADGALTAPTAEALMRSRYAAFALLGEAGADDDGTQ +GTDGASGPGGTGPGHAGPGHAGPDRARAMAAYLAATWAPEHRPAVEDLLPEAGERAPRFT +RLAVTDVRDGGPFQDRGIVEFTALGHGEEGRFRLRERSRFRREDGAWLYVDGDVA +>PROKKA_00120 +MTEAPCPCGLGLPYPECCGRLHAAHAADGSLTAPTAEALMRSRYTAFARLGEVEGAGATG +AADVAATVAYLRATWAPEHRPSTAELTPGPGDPAPAFTRLAVLAVEGGGPFQDVGEVEFA +AVGRGPEGRFRLHERSRFRRESGVWLYVDGDVTA +>PROKKA_00214 +MRSRYTAFARLGEAGPAEVRAMADYLAATWAPEHRPTAAELLPAAGEPAPRFTRLAVLDV +RDGGPFQDAGTVEFVAVGTGAEGRFRLHEVSRFRREDGIWRYVNGDVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000313.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000313.fa new file mode 100644 index 0000000000000000000000000000000000000000..8cc2c0b24260daf3e28f7b0d600fd7c86dc18ed0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000313.fa @@ -0,0 +1,10 @@ +>PROKKA_00215 +MDRELRTPPELEGVDWHDDAPRRPRPIVTLVAWIAILGLVLSVGAGIFSAF +>PROKKA_02208 +MDRELRTPPELEGVDWHDDAPRRPRPIVTLVAWIAILGLVLSVGAGIFSAF +>PROKKA_00166 +MDRSNEIPPELQGLDWGEDDAPRRRRPLITLVAWLCIIGLVLGVAAGLFSIL +>PROKKA_00119 +MADLPPELEFAEFDDDPRPSAPSPWVRVLAVVVLLGLVGSLAAGLFGGI +>PROKKA_00215 +MDRELRTPPELEGVDWHDGAPRRPRPIVTLVAWIAILGLVLSVGAGIFSAF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000314.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000314.fa new file mode 100644 index 0000000000000000000000000000000000000000..2319f2db2dec758862e985925bbce6e9bf8e110e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000314.fa @@ -0,0 +1,34 @@ +>PROKKA_00218 +MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGVVGAAIYPDRPDAFV +CGLDEDELAGAGLRVRREPGDPSDPHSAEFPHVYPDEAVSGHIPCSMLTPVTDPRADARV +HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAAAEARGIEVRRLTAVDL +PALRALDEEAAPRFPRTDGSRHEPLPDDLEARLSTPAGLAVGAFEGGVLIGFTLTFRSPD +RWEVDRTAVASEHENRGVAKAVKAATLLATHARGGRQWGTGGAEANAASLRMNTALGFRL +EPAWLGLTPPMTWEEFARAPASSSLDDKVT +>PROKKA_02212 +MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGMVGAAIYPDRPDAFV +VGLDEDELAGAGLRVRREPGDPSDPHSAEFPHIYPDEAVSGHIPCSMLTPVTDPRADARV +HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAVAEARGIEVRRLTAVDL +PALRALDEEAAPRFPHTDGSRHEPLPDDLEARLSTPEGLAVGAFQGGVLIGFTLTFRSPD +RWEVDRTAVASEHENRGVAKAVKAATVLATHARGGREWGTGGAESNAASLRMNAALGFRL +EPAWLGLTPPTTWEEFARAPASSSLDDKVT +>PROKKA_01604 +MILHIALPEDWAAARAAGHYTVSTRGATVDRVGFLHASEDAAQVGIVGPAVYADRPDAVV +LAMDEAALEAAGLTVRREPGVPGDPHSPLFPHVYGGPVPVGLMTPLPRADVDPRVVREDD +AEAIRLQDAGWTPASTSWGARLHLADDADLAPYERRVAAVRAAGFQVRRLTPDDVGQVRR +LDGETAADYPATAASSHSPLPEDLAVRLTLPGHRGYGAFRDGVLAGFTLLDRLDDRWDVD +RTAVHPTGRRRGLAAAVKALSVLETHREDGARTWGTGGAGANAGSLAMNRKLGFELEPLW +LALVPALTWPEAAATSGTP +>PROKKA_00616 +MILHLTLPEDWAAARAAGVYTASTRGAGIAEVGFLHASEDERQAGAVAAAFYADRPDAFL +VALDEDALAAAGLEVRREPGNPADPQSELFPHVYGGPIPVALMRPLRPSLTLRPYAPDDA +AATLDVFRAAVTGTAAAHYTPEQIRAWCPADVDADAWAARRAAAWTVVAVDGAGRVLGFA +DLTADGVLDMLFVHPEAGGRGASHLLVGAVLAEARRRGLLRVDVRASRSARPVLEALGFT +VDGEDPGNTVRGVVVPNTRMHADLAGSAGSPAPPGLWS +>PROKKA_00219 +MILHITLPEDWAAARRTGRYTASTRGASIDDVGFLHASDDAAQVGMVGAAIYPDRPDAFV +VGLDEDELAGAGLRVRREPGDPSDPHSAEFPHIYPDEAVSGHIPCSMLTPVTDPRADARV +HREDSAEAAALLDAGWSVRSRSWGARLHLDDDADLAPYRGHVAVAEARGIEVRRLTAVDL +PALRALDEEAAPRFPHTDGSRHEPLPDDLEARLSTPEGLAVGAFQGGVLIGFTLTFRSPD +RWEVDRTAVASEHENRGVAKAVKAATVLATHARGGREWGTGGAESNAASLRMNAALGFRL +EPAWLGLTPPTTWEEFARAPASSSLDDKVT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000315.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000315.fa new file mode 100644 index 0000000000000000000000000000000000000000..eadda90592b3d2e62b80a656b26ed7e1bdba9128 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000315.fa @@ -0,0 +1,34 @@ +>PROKKA_00220 +MPEPHTAPAPSETLPPAVVALPADVWRAHARAHRERIARRTDPLVALRMRGQKHPVQDFL +FGYYTHSPAALQRWHPGPGVLLADDDGAAARAEAAELGATPRGEWKHYRRVEAGEVAGAV +VDGRPVGGWLVDVAAVLADRASGVAFTRELLARTAERAPRLGCFGLHEWAMAYRSDVHGV +RHSQLPLRLGAEGTDAVVEGSRIRCTHFDAFRFFAPEARDRNEGDDGVLPTRAGMRKMEQ +PGCLHAGMDLYKWAYKLVPVVDSDLLADCFDLAWDIRRLDMEASPYDLTGVDDLSDGRGG +YAAVRIEEPAGRAEYARRQREFAARGQSLRVRLLAVLDAAAGAAPGARPDTEWTSSARP +>PROKKA_02233 +MPEPRTDPAPPPTAVVALPADVWRAHARAHRERIARRTDPLVALRMRGEKHPVQDFLFGY +YTHSPAALQRWHPGPGVLLADDDGAAARAEAAELGTTPRGEWKHYRRVEAGEVAGAVVDG +RPVGGWLVDVAAVLADRASGVAFTRDLLARTAERTPRLGCFGLHEWAMAYRSDVHGVRHS +QLPLRLGAGGTDAVVEGSRIRCTHFDAFRFFAPEARDRNEGDDGVLPTRAGMREMEQPGC +LHAGMDP +>PROKKA_00160 +MAGTCLHTPPPSPAAPRTAPTDPTAVVVLRPEEWLARSAAHRERIEARTAPLLELHGRGE +RHPVQDFLFGYYTHSPAALARWHPGAGVVLADPDGAAAAAEAERDGAPHRGGWRHLRATE +PGEIPGAEPDGRPTVGWTVDADAFAADRATGIAFTAELLERTAARPARLGCFGLHEWAMA +YRSDLHGVRHSRLPLRLGAEGTDAVVESQRIRCTHFDAFRFFAPEARGLNEGADGVLPTR +AGMRDMEQPGCLHAGMDLYKWAYKLLPWVSSDLVADCFDLAWDIRALDMRASPYDLRGVT +DLAGGDYPPVRIETPEGRAEYVRAQRGFADRGQALRARLLAALAPLLGDDARG +>PROKKA_00118 +MTSAAPSPVPLVLAPEDWRARARAHRERIAARTAPLMARRTRGEPHPVQDFLFGYYTLTP +GALQRWHPGAGVVLADDDGAAATAEAAELGTAPRGEWRHWRRVEPGEVVGVVLDGREVGG +WTVDVPAFLADRASGVAFTRELLERTAGRPARLGCFGLHEWAMAYRSDVHGVRHSQLPLR +LGAAGTDAVVEDQRIRCTHFDAFRFFAPEAVPLNEGAEGVQPTRAGMRDMEQPGCLHAGM +DLYKWAHKLLPLVDSDLVADCFDLAWDIRRLDMEASPYDLTGVDDLSDGLGGYTPVRIET +PEGRAEYARRQRGFAERGQALRARLLAALEAGARAAGDRRPTEDPSTPDPEEHHG +>PROKKA_00221 +MPEPRTAPAPPPTAVVALPADVWRAHARAHRERIARRTDPLVALRMRGEKHPVQDFLFGY +YTHSPAALQRWHPGPGVLLADDDGAAARAEAAELGTTPRGEWKHYRRVEAGEVAGAVVDG +RPVGGWLVDVAAVLADRASGVAFTRDLLARTAERTPRLGCFGLHEWAMAYRSDVHGVRHS +QLPLRLGAEGTDAVVEGSRIRCTHFDAFRFFAPEARDRNEGDDGVLPTRAGMREMEQPGC +LHAGMDLYKWAYKLVPVVDSDLLADCFDLAWDIRRLDMEAAPYDLTGVDDLSDGRGGYAA +VRIEEPAGRAEYARRQREFAERGQALRARLLAVLDAAVGAAPGTGPDAEWTSSSARP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000318.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000318.fa new file mode 100644 index 0000000000000000000000000000000000000000..9ca77995c279b234e118360064771ccc2ca54ea2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000318.fa @@ -0,0 +1,25 @@ +>PROKKA_00225 +MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF +NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ +LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE +YADEVTLGRAFEGRRLISG +>PROKKA_02238 +MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF +NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ +LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE +YADEVTLGRAFEGRRLISG +>PROKKA_00155 +MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDKVRLCSVCF +NVSEDEVCSLCRDERRDASQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ +LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE +YADEVTLGRAFEGRRLISG +>PROKKA_00113 +MYEGAVQDLIDELGRLPGIGPKSAQRIAFHVLEADAADMLRLADAIRTVKDKVRLCSVCF +NVSEQEVCHLCRDARRDDSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ +LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE +YADEVTLGRAFEGRRLISG +>PROKKA_00226 +MYQGAVQDLIDELGRLPGIGPKSAQRIAFHMLEADREDMLRLADAIRTVKDRVRLCSVCF +NVSEDEVCSLCRDERRDRSQICVVEESQDVMAMERTRAFQGRYHVLGGAINPIAGIGPEQ +LHVRELLTRLQDEAVQEVILATDPNLEGEATATYLGRLLGATGIRVTRLASGLPVGGDLE +YADEVTLGRAFEGRRLISG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000319.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000319.fa new file mode 100644 index 0000000000000000000000000000000000000000..ccdc41bae790d5731d8881e99f4119e9d08f74d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000319.fa @@ -0,0 +1,107 @@ +>PROKKA_00226 +MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC +LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR +YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP +PEPLIAYLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV +RLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL +PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADITNLALTDMVGATSPRLHLELLMA +RLLLPASDETHRGLAARLEALERRLELGGAAPVEDGAPEGTTTPARSGTPAKDGGGSAGD +ADGSGPLTGAALARAAMRRPEEPAPTAPTAPPERWTPPAPQSVAEAPEGDAAAGATGSER +PQQPPQPKRPEPAEVGARSGDTRRPEAGSRAEPEGRPEGRPQAQDRTGAAPSSPAPAPAA +SQVEMIRRAWPDILTALEDASRLVWMLVKDNASVAGYDGSLLTIGFQQDGPRQSLLGRGG +DRVLGEAVHQVLGIRPRLDLILGGDAPTGDARAQSGARPAGPARTDRPERPAPQQGRPDR +PTAQPNRPAPAPGQAPREPESSRPTPPRSAAPSTAEDDPAPPAAPPRATQQRQTPEPSPA +WTPAAPATSWGPTPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPEEDPWDSLPAFDPDA +EQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAPAPGGAAPDAGQDSP +VQPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELRAEFAKRFGATRPAG +FDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSSDEQRRPTGAPTADA +TPDPGVPADDADATPRTAAGPTGSDFPGSGHPASMYPRLMERLRAGGPLEPPVNAGSSGG +GGTGGGPGAPGGPDPDASPGSPAGGRPSAASLGARPADVEPAGGASAPPSLDARAAAIHA +AREAAQGRGPTRPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLVGRAVVERVLGGRLL +EERPNDA +>PROKKA_02239 +MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC +LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR +YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP +PEPLIAYLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV +SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL +PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA +RLLLPTSDETHRGLAARLEALERRLELGGAAPVEEGAPEGTTTPARSGTPAADGGGSAEN +AEGSGTLTGAALARAAMRRPEEPAPTASTAPPERWTPPAPQSVAEAPEGDAAAGATGSER +PQQAPQPKRPEPAEVGARSGDARRPEAGSRPEPEGRPEPEGRPQAQERTGAAPAPAHGPE +ETAAPSSPTPAPAASQVEMIRRAWPDILAALEDASRLVWMLVKDNASVAGYDGSLLTIGF +QQDGPRQSLLGRGGDRVLGEAVHQVLGIRPRLDLILGGDAPTGDARAQSGARPAGPARTD +RPERPAPQQGRSDRPTAQPNRPAPAPGQAPREPESSRPTPPRSAAPSTAEDDPAPPAVPP +RATQQRQTPQPSPAWTPAAPATSWGPAPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPE +EDPWDSLPAFDPDAEQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAP +APGGAAPDAGQDSSVRPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELR +AEFAKRFGATRPAGFDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSS +DEQRRPTGAPTADATPDPGVPADDADAAPRAASGPTGSDFPGSGHPASMYPRLMERLRAG +GPLEPPVNAGSSGGSGTGGGPGAPGGPDLDATPGSPAGGRPSAASLGARPADAEPAGGAS +ALPSLDARAAAIRAAREAAQGRGPARPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLV +GRAVVERVLGGRLLEERPNDA +>PROKKA_00154 +MSTALYRRYRPDRFEEVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC +LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR +YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP +PEPLIAHLEQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQDGGVSYELAV +SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL +PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA +RLLLPASDDTHRGLAARLEALERRLELGGVPVASADESAGGTTTSARPGAPAAAGGGSAG +SGGAGGGEPLTGAALARAAMRRPEVQEAPTPPAQETARSEKAPAQPEPTPMPSPVGQAAP +PAQPAQSEHPRPERWAPPAAASSPEADAPAQRPDAARPEQPAQQDRPQRQTPPPAPAGQP +EQRQQQTAQAERPTTTERPAERPAAGAPEASPASTRPQAAERAAERPQAEADAAGSAVPS +SAAPAPTPSQVEKVRRAWPDILAALEDASRLMWMIVKDNASVAGYDGSLLTIGFQQDGPR +QMLLGRGGDRVLAEAVHQVLGIRPQLDLILGGDAPQGGSRHAQGQAQTPSAPRAESRADA +PTSRPDAGEAAPTRQDRPQQQGGEPDRGQQQDRGQQQGRGQASDLGPAQGGSPSGRPTGQ +AAAPTPGRGPSSPAPAQRPTAPQAASTTPPGAPPSDGWGRADEEPPAWDDAPPPEEDPWD +SLPEFDPDADMDDSDGPEGWTPPAAGQDDAPVGAAGWDGPVPAAEDWGAPPQGGAPAPDG +RRDERPAAAQGSDAPSEQPTPQGSADAGPAAETDAEPSAEEVRRAYDPGPLVREEEHTIP +VFARPEAELRAEFAQRFGATRPAGFDDGAGAGADAESTRAAAPSPGPDDLPPGQGDDPDA +TARRDTHPAASASGPSSAADHGSSGEPTADGTPDPGVPAEDHEHTSASDADDDGSPERAA +GSGHPASMFPRLMERVRAGGPLEPPVNAAPPGGATPPGGGPGGGAGPSGPGSAPGSDQGP +RPGGAPSDAQGPGAPGPDAPRGGRPSAAALGARPGGETGSPAGASAPPSLDARAAAIRAA +REAAQGRGPARPAGNGPAAPSAPAVGWEDEVASDDDVALEDSGLVGRAVVERVLGARLLE +ERANSA +>PROKKA_00112 +MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC +LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR +YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP +PEPLIAYLERLCQEEGVRVEPGVLPLVVRAGTGSVRDTLSVLDQLIGGAQQGQVSYDLAV +SLLGFTPEALLDDVVDAIAADDTPTVFRVADRVVQSGQDPRRFVEDLLERFRDLVIARAL +PDEASSILHGMPEDQVRRLAAQASQLSRAELSRLADVTNLALTDMVGATSPRLHLELLMA +RLMLPATDDTHRGLAARLEALERRVAGGAAFSPDDDASSGAEGPAAGGAGQGGAALSGAA +LARAAARRAEPEQAREQEPGAGSDKRAAEPATPKPATPEPVAAAPAPERPVERPAEAPAP +SSSAPAAPAAPTAHTPSQVEKVRRAWPDILAALESDSRLMWMLVKDNATVAGYDGELLTV +AFPQEGPRRTLQSRNGEQVLGEAVHRVLGIRPRLDLILGGDTPRGEERPKAEGRPAAAVS +EAPAAPSTSAPPPAPQGQPTQAQPPRAQPSPEDGRRPAASAPRPQDVAVATSWDQAPAPS +AAPWQPAPSRPAAASPAPQTGPAAPSTPDPRQDAHPGTRPGPADTTPPAAPPSDGWGHVD +EEPPAWDDAPPPPEDPWDSLPEFDPDADMEDSPGPEGWTPGAGDDAVHGSAGSAPTSAPE +AWGGAVPTPQDWGAPRPQDPVESPAPQGPEAGTQGTAPDAAAQGAPSPAAPAEAVPEDPE +TARRAYDPGPLVREEELTIPVFAKPEAQLRAEFAARFGGTRPAGFDSTAASDAAAPDAQG +PGAAARAAAHGEPVRGGQDAAEPAADREAEPEEDPQAAASAPEHPVRPSPARPTADDTPD +PGVPQEDHAEDAAPPSATAPDDRGSGHPDSHYPALMERLRASGPLEPPVNARPAGQGGAR +EEQVPAPVDAAPSPGRPSAASLGRPTGDPQAAIAPPAEDPRASGARAAAIQAAREAARGA +GPRPADGAPGGPATASGPSVDWQDEVASDDDVALEDSGLVGRPVVERLLGARLLEERPLE +PGL +>PROKKA_00227 +MSTALYRRYRPDRFEDVIGQDHVTVPLRTALAKDRVNHAYLFSGPRGCGKTTSARILARC +LNCAQGPTPTPCGECDSCRDLATGGPGSLDVLEIDAASHGGVEDARGLRERATFAPVRDR +YKILIIDEAHMVTAAGFNALLKIVEEPPEHLKFIFATTEPEKVIGTIRSRTHHYPFRLVP +PEPLIAYLVQLCAEEGVSVEKGVLPLVVRAGTGSVRDTLSVLDQLIAGAQEGQVSYELAV +SLLGFTPEALLDDVIDAVAADDTPTVFRVVDRVVQSGQDPRRFVEDLLDRFRDLVIARAL +PEEAGAILHGMPEDQVRRLSAQAAQLSRAELSRLADITNLALTDMVGATSPRLHLELLMA +RLLLPASDETHRGLAARLEALERRLELGGAAPVEDGAPEGTTTPARSGTPAPDGGGSAEN +AEGSGPLTGAALARAAMRRPEEPAPTAPTAPPERWTPPAPQPVAEAPEGDAAAGATGSER +PQQPPQPGRPEPAEVGARSEDARRPEAGSRPEPEGRPEPEGRPQAQDRTGAAPAPAHGPE +ETAAPSSPTPAPAASQVEMIRRAWPDILAALEDASRLVWMLVKDNASVAGYDGSLLTIGF +QQDGPRQSLLGRGGDRVLGEAVHQVLGIRPRLDLILGGDAPTGDTRGQSGARPAGPARTD +RPERPAPPQGRPDRPAAQPNRPAPAPGPAPREPESSRPAPPRSAAPSTAEDDPAPPAAPP +RATQQRQTPQPSPAWTPAAPATSWGPTPTSSTTPAPAPPADGWGGPDEEPPAWDDAPPPE +EDPWDSLPAFDPDAEQDDSDGPEGWTPPARDAEERPVGAAGWDGPVPSVEDWGAPPQAAP +APGGAAPDAGQDPPVRPDAPTPGESEPSAEEVRRAYDPGPLVREEEHSIPVFARPEAELR +AEFAKRFGATRPAGFDDGAGAAADGDSARPATPSPAPDDDAAATERRDPHPAASGAGPSS +DEQRRPTGAPTADATPDPGVPADDSDATPRAAAGPTGSDFPGSGHPASMYPRLMERLRAG +GPLEPPVNAGSSGGPGAPGGPDPDASPGSPAGGRPSAASLGARPADVEPAGGASAPPSLD +ARAAAIHAAREAAQGRGPTRPADTGPAAPATSGVGWEDEVASDDDVPLEDSGLVGRAVVE +RVLGGRLLEERPNDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000321.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000321.fa new file mode 100644 index 0000000000000000000000000000000000000000..90b076714a978653e6e555534797a1e4b8465de9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000321.fa @@ -0,0 +1,50 @@ +>PROKKA_00230 +MSFADLITAVNDVIWSPALIWLCLIVGLYFTIRTMFLQFVNIPDMVKQLREGQDSADGTS +SLQSLMMSLAGRVGMGNIGGVATAIAFGGPGAVFWMWVMALLGAATSFIESTLGQIYKER +DPDTGEYRGGPAYYFEKAYKHTAAAPAFKVYAILFAVVTVFATSYFLPGVQANGVAAAAG +EAWAVPAWVVALAMVILLAFIVLGGVKRIATFAVYVVPVMAALYIILALIVLFLNFDQIP +EVFGSIFASAFGVHAVFGAILGLAIQWGVKRGIYSNEAGQGTGPHAAAAAEVSHPAKQGF +VQAFAVYIDTLFVCSATAFIIISTGAYRVYSDESGSGLLFEGIVAPTASEGPAFVQTGFD +AMFTGFGPTFVAVALAFFAFTTIVAYYYMAEVNIVFLTRNLRNGMVRRVVLRFLQALILV +SVAYGAVATTGAAWGLGDIGVGSMAWLNILGILVLQGPALKALKDYRAQKRQGLDPQFDP +RPLGIRNADFWEHRADGLITQGVAGTAEHPIVAEGGAHRA +>PROKKA_02243 +MSFADLITAVNDVIWSPALIWLCLIVGLYFTIRTMFLQFVNIPDMVKQLREGQDSADGTS +SLQSLMMSLAGRVGMGNIGGVATAIAFGGPGAVFWMWVMALLGAATSFIESTLGQIYKER +DPDTGEYRGGPAYYFEKAYKHTAAAPAFKVYAILFAVVTVFATSYFLPGVQANGVAAAVG +EAWAVPAWVVALAMVILLAFIVLGGVKRIATFAVYVVPVMAALYIILALIVLFLNFDQIP +EVFGSIFASAFGVHAVFGAILGLAIQWGVKRGIYSNEAGQGTGPHAAAAAEVSHPAKQGF +VQAFAVYIDTLFVCSATAFIIISTGAYRVYSDESGSGLLFEGIVAPTASEGPAFVQTGFD +AMFTGFGPTFVAVALAFFAFTTIVAYYYMAEVNLVFLTRNLRNGMVRRVVLRFLQALILV +SVAYGAVATTGAAWGLGDIGVGSMAWLNILGILVLQGPALKALKDYRAQKRQGLDPQFDP +RPLGIRNADFWEHRADGLITQGVAGTAEHPIVAEGGAHRA +>PROKKA_00151 +MTFEDLIGTLNDVIWSLPLIYLCLAVGLYFTVRTMFLQFVNIPDMIRQLREGEDSKDGTS +SLQSLMMSLAGRVGMGNIGGVATAIAFGGPGAVFWMWAMALLGAATSFIESTLGQIYKER +DRDTGEYRGGPAYYFTKAYSHKPWGKALVVYGVLFAIVTIFATSYFLPGVQANGVAAAVE +QAWNVEPWIVAVAMVILLAFIVLGGVKRIATFAVYVVPVMAVLYIVLALIILVLNADQIP +VVFGSIFSSAFGMDAVFGAIVGLAIQWGVRRGVYSNEAGQGTGPHAAAAAEVSHPAKQGF +VQAFAVYIDTLFVCSATAFIIISTGAYRVYEGESEAGAVIFEGGSLPATASVGPAYVQSG +FDAMFSGFGPTFVAVALAFFAFTTIVAYYYMAEVNLVFITRNFSNPLFRRVALRALQGLI +LVSVAYGAVATTGAAWGLGDIGVGSMAWLNIIGILLLQGPALKALKDFRAQKRQGLDPQF +DPRPLGIHNATFWEERADGRITPGVAGTAPTPVVDADGGSPRA +>PROKKA_00108 +MSFADLVTEINDVIWSPALIWLCLIVGLYFTVRTMFLQFVNIPDMVKQLREGEDSADGTS +SLQSLMMSLAGRVGMGNIGGVATAIAFGGPGAVFWMWVMALLGAATSFIESTLGQIYKER +DPDTGEYRGGPAYYFEKAYRHTAAGGAFKVYAILFAIVTVFATSYFLPGVQANGVAAAME +QAWSLPPWVAAVGMVILLAFIVLGGVKRIATFAVYVVPIMAIAYIILALVVLFMNWEQIP +EVFGTIFSSAFGTHAVFGAILGLAIQWGVKRGVYSNEAGQGTGPHAAAAAEVSHPAKQGF +VQAFAVYIDTLFVCSATAFIIISTGAYRVFEGESETGRVLFEGGTLPVTASVGPAFVQSG +FDAVFAGFGPTFVAIALAFFAFTTIVAYYYMAEVNLVYLTRTLRNGTVRRVALRLLQALI +LVSVAYGAVATTGAAWGLGDIGVGSMAWLNILGILVLQGPALKALKDYRAQKKQGLDPQF +DPRPLGIKNADFWEHRADGLITQGVGGLSTDVRADTADGAGSHRA +>PROKKA_00231 +MSFADLITAVNDVIWSPALIWLCLIVGLYFTIRTMFLQFVNIPDMVKQLREGQDSADGTS +SLQSLMMSLAGRVGMGNIGGVATAIAFGGPGAVFWMWVMALLGAATSFIESTLGQIYKER +DPDTGEYRGGPAYYFEKAYKHTAAAPAFKVYAILFAVVTVFATSYFLPGVQANGVAAAVG +EAWAVPAWVVALAMVILLAFIVLGGVKRIATFAVYVVPVMAVLYIILALIVLFLNFDQIP +EVFGSIFASAFGVHAVFGAILGLAIQWGVKRGVYSNEAGQGTGPHAAAAAEVSHPAKQGF +VQAFAVYIDTLFVCSATAFIIISTGAYRVYSDGSGSGLLFEGIVSPTASEGPAFVQTGFD +AMFSGFGPTFVAVALAFFAFTTIVAYYYMAEVNIVFLTRNLRNGMVRRVALRFLQALILV +SVAYGAVATTGAAWGLGDIGVGSMAWLNILGILVLQGPALKALKDYRAQKRQGLDPQFDP +RPLGIRNADFWEHRADGLITQGVAGTAEHPIVAEGGAHRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000322.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000322.fa new file mode 100644 index 0000000000000000000000000000000000000000..c631e939964d1ec85c3db012b36771c2c3d1369f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000322.fa @@ -0,0 +1,55 @@ +>PROKKA_00231 +MATVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRSHGGIQWVHTRHEETAAFAASAES +QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF +RECSVYVEHVSSADQMPRMLRTAMRAAVEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR +VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHALRGKDRIEYD +NPYDVGLTGLLGFASGYHALKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVA +VDVPLVGGVKETAQALLPLLRGNSSSAFLDKALKHYAKTRKDLDQLASPGRGRVHPQYVA +RLLDELADDDVVFLPDVGSPVIWASRYLTMNGRRRIIGSLSHGSMANAVTQAVGAQAVDP +TRQVVAMAGDGGLAMMLGELMSFVQNGLPVKTLVFDNDSLNFVELEMMAAGFVPYGTSLE +NPDFAAIAEAIGIKGFRADHTTDLPAVMREFLAHDGPALLVVKTERQELTIPPSIEFEQA +KGFALYAMRTVLDGKGTKLLDLAKANLRQLF +>PROKKA_02244 +MATVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRSHGGIQWVHTRHEETAAFAASAES +QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF +RECSVYVEHVSSADQMPRMLRTAMRAAVEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR +VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHALRGKDRIEYD +NPYDVGLTGLLGFASGYHALKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVA +VDVPLVGGVKETAQALLPLLRGNSSSAFLDKALKHYAKTRKDLDQLASPGRGRVHPQYVA +RLLDELADDDVVFLPDVGSPVIWASRYLTMNGRRRIIGSLSHGSMANAVTQAVGAQAVDP +TRQVVAMAGDGGLAMMLGELMSFVQNGLPVKTLVFDNDSLNFVELEMMAAGFVPYGTSLE +NPDFAAIAEAIGIKGFRADHTTDLPAVMREFLAHDGPALLVVKTERQELTIPPSIEFEQA +KGFALYAMRTVLDGKGTKLLDLAKANLRQLF +>PROKKA_00150 +MANVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRTHGGIEWVHTRHEEAAAFAASAES +QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF +RECSVYVEHVSSADQMPRMLRTAMRAALEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR +VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHAMRGKDRIEYD +NPYDVGLTGLLGFSSGYHALKDAETLLILGSSLPYRQFYPEDATVIQVDVRGDQIGRRVA +VDVPLVGGVKETAQALLPLLRGNASSSFLKKARRHYAKTRKDLDELAAPDRRTVHPQYVA +RVLDEAASEDAVFLPDVGSPVVWAARYLTMNGRRRIIGSMTHGSMANAVTQAIGAQAVDR +TRQVVAMAGDGGLAMMLGELLTFVQNGLPVKTLVFDNDSLNFVELEMKAAGLVPYATDLQ +NPDFAAVAEAMGLKGFRVERSKDLPAVMAEFLAHEGPALLVVKTERQELTIPPSIEFEQA +KGFALYALRTVLDGKGTQLVDLAKANLRQLF +>PROKKA_00107 +MATVAKHIVETLSASGVRRMYGVPGDSLNALTEALRQHTDMEWVHTRHEEAAAFAASAES +QLTGELAVCAGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQELF +RECSVFVEHVSDVSQMPQLLRIAMRAAVEQRGVAVLVIPGDVALQDLDAKPEVIRATRSH +VVPDEDSLREAAEALNSCKRITILAGSGAAGAHDEVVALADRLQAPVVHALRGKDHIEYD +NPFDVGLTGLLGFASGYHAMKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVS +VDIPLVGGVRETAQALMPLLKGNSSSAFLKKALKHYDKSRKGLDSLATPSRGTIHPQYVA +RLLDEAADDDAVFIPDVGSPVIWASRYLTMNGRRRIIGSMVHGSMANGITQALGAQAIDR +SRQVVVMAGDGGLAMMLGELLSFVQNRLPVKTVVFDNDSLNFVELEMKAAGFVPFGTGLQ +NPDFAQVAEAIGIKGFRVDRAKDLPDVMREFLAHDGPALLLVKTEPQELTIPPSIELEQA +KGFALYALRTVLDGKGTQLIDLAKANLRQLF +>PROKKA_00232 +MATVAQNIVETLHASGVRRMYGVPGDSLNGLTEALRSHGGIQWVHTRHEETAAFAASAES +QLTDELAVCVGSCGPGNLHLINGLFDAQRSRTPVLAIAAHIPSEEIGSGYFQETHPQDLF +RECSVYVEHVSSADQMPRMLRTAMRAAVEQRGVAVLVIPGDVALTELSAKPEVIRHTPSR +VIPADSVLREAAEALDSSKRITILAGAGAAGAHDEVVALAERLQAPIVHALRGKDRIEYD +NPYDVGLTGLLGFASGYHALKEAETLLILGSSLPYRQFYPEDATVIQVDVRGEQIGRRVA +VDVPLVGGVKETAQALLPLLRGNSSSAFLDKALKHYAKTRKDLDQLASPGRGRVHPQYVA +RLLDELADDDVVFLPDVGSPVIWASRYLTMNGRRRIIGSLSHGSMANAVTQAVGAQAVDP +TRQVVAMAGDGGLAMMLGELMSFVQNDLPVKTLVFDNDSLNFVELEMMAAGFVPYGTDLQ +NPDFAAIAEAAGIKGFRADHTTDLPAVMREFLAHDGPALLVVKTERQELTIPPSIEFEQA +KGFALYAMRTVLDGKGTKLLDLAKANLRQLF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000323.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000323.fa new file mode 100644 index 0000000000000000000000000000000000000000..be104533284f03b00ab00703a15d8c3efddfeee1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000323.fa @@ -0,0 +1,30 @@ +>PROKKA_00232 +MRTSSPIGLLLDVDAPVASTETRTVPEGIIDVLVRLARRGVPVGFNTGRSTDFLLHNLIA +PLRDAGLPDDAPFHAICEKGAVWFPFSAVPSGDLPDVTVDGTAPDWLRTDPDMAIDADTR +DAIWALNDERAGDLQFTDRTKLAMVSLEKTVGADQTEYERVRDDVAAGVEDLLAERGLAE +EVRVAPSVISVDVEHRSSGKDLGVERCFDLLAEAGTPVPERWLTAGDSRSDYAMADRLHE +RGLAVEHMDVRPADGVPEKPYGVVTAAILAERGIGDADDVHERAGESLLRWVERDLLR +>PROKKA_02245 +MRTSSPIGLLLDVDAPVASTETRTVPEGIIDVLVRLARRGVPVGFNTGRSTDFLLHNLIA +PLRDAGLPDDAPFHAICEKGAVWFPFSAVPSGDLPDVTVDGTAPDWLRTDPDMAIDADTR +DAIWALNDERAGDLQFTDHTKLAMVSLEKTVGADQTEYERVRDDVAARVEDLLAERGLAE +EVRVAPSVISVDVEHRSSGKDLGVERCFDLLAEAGTPVPERWLTAGDSRSDYAMADRLHE +RGLAVEHMDVRPADGVPEKPYGVVTAAILAERGIGDADDVHERAGESLLRWVERDLLR +>PROKKA_00147 +MSTPSPIGLLLDVDGPVASTQTRTVPDGIVATLVRLAGRGVPVGFNTGRSADFLLHSVIG +PLRAAGLPADAPFFAVCEKGAVWFPFSAVPAGTLPEVTVDAPAPAWVRTDPAMALDPGLR +ERIWELNRERAGDLQFVDRTKLAMVSLEMRVGADQAAYEAVRDDVAAGVEEMLAERGLAD +EVRVDPTVISVDVEHRSSGKDLGVDRCRALMAEAGVPVPGRWFTAGDSRTDYAMADRLHA +IGLAVEHLDVRPADGIPATPYPVLTAADLAGRGVGNAEDVHERAGESLLRWVERDLLD +>PROKKA_00105 +MTSPSPIGLLLDVDGPVASTETRAVPEGIVTTLVRLAAARVPVGFNTGRSADFLLHSVIG +PLRAAGLPEDAPFFAICEKGAVWFPFSDVPAGDLPAVTVDAPTPGWVRTDPAMAVDADVR +DAIWEINGERAGDLQFVDRTKLLMVSLEKTVGADQDAYVQVRDDVAAGIEDLLRERGLAE +DVRVDPTVISIDVEHRTSGKDLGVDRCLGMLAEVGVAVPERWFTAGDSRTDYAMADALHA +MGAPVEHMDVRPADGIPERPYRVLTAADLAERGVGQAEDVHERAGESLLRWVERDLLA +>PROKKA_00233 +MRTPSPIGLLLDVDGPVASTETRTVPEGIIDVLVRLARRGVPVGFNTGRSTDFLLHSVIA +PLRDAGLPDDAPFHAVCEKGAVWFPFSAVPSGDLPDVTVDGTAPDWLRTDPDMAIDADTR +DAIWALNDERAGDLQFTDHTKLAMVSLEKTVGADQTEYERVRDDVAAGVEGLLAERGLAE +EVRVAPSVISVDVEHRSSGKDLGVERCFDLLAEAGTPVPERWLTAGDSRSDYAMADRLHE +RGLTVEHMDVRPADGVPEKPYGVVTAAILAERGIGDAEDVHERAGESLLRWVERDLLR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000324.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000324.fa new file mode 100644 index 0000000000000000000000000000000000000000..26e78bb89a5d81d3cfeae9b09e5428f36e859a2b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000324.fa @@ -0,0 +1,35 @@ +>PROKKA_00233 +MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAVVAAFLGSGVVGGLT +PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLLAYAVWQFLASAQSARHDRLRPWILV +SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL +GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA +WGLMWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD +GGGDPIDGRR +>PROKKA_02246 +MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAVVAAFLGSGVVGGLT +PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLLAYAVWQFLASAQSARHDRLRPWILV +SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL +GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA +WGLVWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD +GGGDPIDGRR +>PROKKA_00138 +MSTATDLGPHRSTFGPDAAGRVPSSGTGLASTGGRVAMLLVVLAALVAAFLGAGVVAGFT +PVAEASGGWLGPDATWVAPASPAFSIWSVIYAGLLAYAVWQFLPSAQSARHDRLRPWILV +SVLLNAAWIWTVQLGLLGLSVVVIVLLLASLCRILMLLESARAHSWGERILLDGVQGLHL +GWVSIATVANVAAWLASTGWTGDPFQPTTWAKIMIVVAVLVGAFTAVYDGGRPAPAFALA +WGLVWIGVGRADGSGLLSGSLAVLAWGGAAIVLLCWVAALLLSRRSATGEARDLVLDALD +GGDDPVDGRR +>PROKKA_00103 +MSTAIDAGPQGTVPIDAAQAPSSGRGLASPGGRWAMLAVVVLGLVGAFLGAGVLPGMTPT +SDAAGGWLGADSTWIAPATPAFRIWSVIYLGLLAYGVWQLAGSAQSARHDALRTWIMASI +VLNVAWLWVVQVGWLGLSVVVIFLLLAVLCRILVLLETGRPRGWAARILLDGVQGLHLGW +VSIAAVTNVAAWLASLGWFGAPLEPTRWAQIMIVVAVLVGAFTAVYSGGRFAPAAALAWG +LLWVGVGRSDGSGLLSGAVALTAWGAAAIVMLCWLVSLWLSSRSATGEARDLVLDALDGG +GDPVDGVR +>PROKKA_00234 +MSTATDLGPSRSPFGPDAAARVPSSGTGLSSTGGRVAMLVVVILAIVAAFLGSGVVGGLT +PVAEAAGGWLGPDATWVSPATPAFGIWSVIYAGLFAYAVWQFLPSGQSARHDRLRPWILV +SVLLNAAWIWTVQAGLLGLSVVVIALLLACLAWILVLLESVRAHSWGERILLDGVQGLHL +GWVSIAAVANLAAWLASTGVVGDPGQSSLWAKVMLVVAVLIGAFTAVYNGGRPAPAFALA +WGLVWIGVGRADGTGLLSGSLALLAWGGAAIVLLCWLAALLLSRRSATGEARDLVLDALD +GGGDPIDGRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000326.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000326.fa new file mode 100644 index 0000000000000000000000000000000000000000..4f13d3d207a5096b3e02101042a57c35ee07cbe2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000326.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000327.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000327.fa new file mode 100644 index 0000000000000000000000000000000000000000..e1f74794c4fc7b303e68b2a01a7af5ef4167fbe4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000327.fa @@ -0,0 +1,35 @@ +>PROKKA_00237 +MSPAAPPTAPPAAEDRPRVPAVPASSLVLVRPGAGGEISVFTVRRAGTMAFSAHATAFPG +GRVDPADDLSDRLWEGTDLADWGRRLGLPHEPADAHGTLAELDPAEGAGRVLAAAVRETF +EETGVLLARDAVTGTPVDPARVAAFPDELRDAVERHEVDFGELLDREGLRPDAGALVPWS +RWITPHGGPRRYDTFFFAVHLPQGQSPERMSSEAASHGWASPAELLRRFRVGKVNLMAPT +WWQLRTLVDAGEDVHAGRSRFEPLEGVMLVAGQGPVFPHADEYLRDLTAFRAAAQVEESK +DNIL +>PROKKA_02250 +MSPAAPPTAPPAAEDRPRVPAVPASSLVLVRPGAGGETSVFTVRRAGTMAFSAHATAFPG +GRVDPADDLPDRLWEGTDLADWGRRLGLPHEPVDAHGTLTELDPAEGAGRVLAAAVRETF +EETGVLLARDAVTGTPVDPARVAAFPDELRDAVERHEVDFGELLDREGLRPDAGALVPWS +RWITPHGGPRRYDTFFFAVHLPHGQSPERMSSEAASHGWASPAELLRRFRAGEVNLMAPT +WWQLRTLVDAGEDIHAGRSRFEPLEGVMLVAGQGPVFPHADEYLRDLMAFRAAAQVEESK +DNIL +>PROKKA_00134 +MSPAAPSADPADGDRPDVPAVPASSLMLVRPEQDGDTSVFALRRAGSMAFSAHATAFPGG +RVDPADDLPDALWEGTDLAAWGRRLGLPHEPVDALGTLAALDPAEGAGRVLAAAVRETFE +ETGVLLARDTATGAPVDPDRVAALPEDLRDAVERHEVDFGDLLRDEGLRPDAGALVPWSR +WITPHGGPRRYDTFFFAVHLPAGQSPERMSSEAAEHGWASPAELLRRFRAGEVNLMAPTW +WQLRTLDDAGEDVHAGRSRFEPLEGVMLVAGQGPAFSHADEYLRDLAAFRAAAHVEESKD +NIL +>PROKKA_00099 +MDAAQTSSSETLPVEATPARAAASLLLLRDGAAGLEVFHVHRAGTMAFSAHATAFPGGRV +DPSDDALPVPGADLAAWARRLGLEDRPVETQPEDDPARVAARFLAAVVRETFEETGVLLA +RAADGGPVPPEAAAALAGRREDVEAHAADLGALLAEHGLAADVSGLRAWQRWITPLSVPR +RYDTAFFLVAVPAGQDPDRLTTEATEHGWARPADLITAFQAGDVNLMAPQWAQLRALMDL +PDVEAALRAGAAAEPVPVVQLASEASPEERTREFSHAAEYREHLRSFRTHDRVQDTPDNV +L +>PROKKA_00238 +MSPAAPPAEPSAAEDRPRVPAVPASSLVLVRPGAGGEISVFTVRRAGTMAFSAHATAFPG +GRVDPADDLPDRLWEGTDLAEWGRRLGLPHEPVDAHGTLTELDPAEGAGRVLAAAVRETF +EETGVLLARDAVTGTPVDPARVAAFPDELRDAVERHEVDFGELLDREGLRPDAGALVPWS +RWITPHGGPRRYDTFFFAVHLPQGQSPERMSSEAASHGWASPAELLRRFRAGKVNLMAPT +WWQLRTLVDAGEDIHAGRSRFEPLEGVMLVAGQGPVFPHADEYLRDLTAFRAAAQVEESK +DNIL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000331.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000331.fa new file mode 100644 index 0000000000000000000000000000000000000000..bd5c1e3f3f2896d1536cdeec51bd04111886ef64 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000331.fa @@ -0,0 +1,35 @@ +>PROKKA_00241 +MICRVATGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA +AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA +AAVTAGDEDGPLLECWTRPLAWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA +EFVAAGRLPRGAETRVPMPGLLAARPESLPTADPDVRPAVDAAATAGARFAPKPELANPS +GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVD +VDLVPVGADGVPVADKPMVQVQVTFRAARS +>PROKKA_02254 +MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA +AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA +AVAAGDEDGPLLECWTRPLSWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMAE +FVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPSG +AVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVDV +DLVPVGADGVPVADKPMVQVQVTFRATRS +>PROKKA_00128 +MRWHGDRAAASGVTALTNILGHPIICDAAGRGRSASVLTVQNSLRPAADSPTGPRAHASG +RTEQLFGIRRHAAMPERDGALNPAAFEAGPWCLDLDGRPTGAAATVIMDNATAVAVHHAA +PGVETVVTTELQINVLAPLPAFDAAAITEGRAEGPLLECWTRPLSWDAGGGVGRAWLEDA +EGRRIVEATGWFQAVPTGAPEHRAAFTAAADLPRGPETRVPMPGLLAARPETLPPAARAG +RPAVTAAVAPGARFAPKPELANPSGAVHGGAMTLRAVVAAQAAMPDRELYDVQAVRVVFT +RPGHGEMVALTRVRHAGRSLRLVDVDLVPVGEDGAPVAEKPMVQVQVTFRAAR +>PROKKA_00095 +MDEITLNPDADARWRGPRRLLLGRPEQLAGLRRRETAEIQGDTLHPGDWEVGPWVRDLDG +RPTGAAACVAADNLTAVALHWAAAEAYDAMVTTQLQVNVLRPLPVFDPADPADRPRLRML +GTPLSTDALGGCARGVIVDDDGTAYVEATGWFQATPGPMSLALEAFREHAALPVAEADRA +DLPAVTAVVADSVPAPRPGERPAVSQEMTAGLRFRAEPLLDNPGGMTHGGIQCLRAVLAA +QAALPDRLEYDVQAVQVVFARPGLGEQVALTRVRHAGRSLRIVEVELVGVDPETGAPQAG +RPSILAQVSFRAAQG +>PROKKA_00242 +MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA +AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA +AAVTAGDEDGPLLECWTRPLAWDAGGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA +EFVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPS +GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVHVVFVRPGHGEMVALTRVRHAGRSLRLVD +VDLVPAGADGVPVADKPMVQVQVTFRAARS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000332.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000332.fa new file mode 100644 index 0000000000000000000000000000000000000000..e067083df79337117d387b0cf0c6626de1c83072 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000332.fa @@ -0,0 +1,40 @@ +>PROKKA_00244 +MSDAQSTATTAPAAARDGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW +AADPAVRGVLIRGAGEKGLCAGGDVVSLRASLLAGRFAEAEEFFRDEYAMNERIAAYPKP +YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH +LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD +EVLARFAVAEDAQPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE +AIRTKSPTAVAVAHEAQRRLAARGADLTVADALRQEFTIATHLMREPDMAEGIRALLVDK +DKDPTWSPARLEDVSTEDVAGHFEPVSGVDPLQLG +>PROKKA_02256 +MSDAQSTATTAPAAARDGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW +AADPAVRGVLIRGAGEKGLCAGGDVVSLRASLLAGRFAEAEEFFRDEYAMNERIAAYPKP +YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH +LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD +EALARFAVAEDARPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE +AIRTKSPTAVAVAHEAQRRLAARGADLTVADALRQEFTIATHLMREPDMAEGIRALLVDK +DKDPTWSPARLEDVSAEDVAGHFEPVPGVDPLQLG +>PROKKA_00125 +MSDAQTTTTAGSAPQAGEGGDVLLEVRDGLARITLNRPRALNALTHVMVQEIDAALVAWA +ADPAVRGVLIRGAGEKGLCAGGDVVSLHASLTGGRFEEAAQFFRDEYRMNHRISAYPKPY +VAFMDGIVLGGGMGVSVHGSHRVATERTRAGMPETAIGFTPDVGGSYHLARAPFHAGRHL +AATSAHASGADAVALGLADAFVESARLDELEQAMADALGSLEAPSGDAGRDGVRDEAAFA +AADEVLARFAMAEGERPDSALAAGREWIEDAYGRQTAAEVLAALDERAAGGGEHADAARS +AAEAIRAKSPTAVAVAHEAQNRLAAHGQDLTVAEALRQEFTVGAHLMRAPDMPEGIRALL +VDKDKDPKWSPARLEDVTADAVATHFEPVEGVARLELS +>PROKKA_00094 +MSEQTSTPQAAAEDEVLFEAADGVGVITLNRPKALNALSHGMVVAVREQLAAWEEDPAVR +AVVVRGAGERGLCAGGDVVSLHGMITTGRAAEAMGYFEDEYAMNHAISVYPKPYVAFMDG +FVLGGGVGVSAHGSHRVVTERTRIGMPETGIGFTPDVGGSWLLARAPRNLGRHLGLTSAF +ATGADALELGFGDVLVDSGDLDAIVAELRAEVGSAGDDADAAHAAVDAVLARHARPASEA +PLLADAEWLEPAYAHDRVEDVFAALEATAADHADEGVRTRAAEAAETVRAKSPTAVKVTL +EALRRLGDRAGGTGRREGVAAALEQEHTLASHLTRGHDMAEGIRAQLVDKDRNPQWSPAT +VEEVSDEAVAAHFGPGEDAPLRLR +>PROKKA_00244 +MSDAQTTATTAPAAAQEGAAGEVLLEVRDGLGRITLNRPRALNALTQDMVRAIDAALTDW +AADPAVRGVLIRGAGEKGLCAGGDVVSLRSSLLAGRFAEAEEFFRDEYAMNERIAAYPKP +YVAFMDGVVLGGGMGVSAHGSHRVATERTRAGMPETAIGFTPDVGGSFHLARAPFQAGRH +LAATSAHASGSDAVALGLADVFVESARLDELEQALAAAFGALGPAADAGARDEAAFAAAD +EVLARFAVAEDARPASALVAGREWIEDVYDRETAAEVLAALDERAAAGGEHAEAAGQAAE +AIRTKSPTAVAVAHEAQRRLAARGADLAVADALRQEFTIGTHLMREPDMAEGIRALLVDK +DKDPTWSPARLEDVSAEDVAGHFEPVPGVDPLELG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000334.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000334.fa new file mode 100644 index 0000000000000000000000000000000000000000..eafcb1b505c23f6496f4e4c3803890014bc5d8eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000334.fa @@ -0,0 +1,30 @@ +>PROKKA_00248 +MDLSNQSAIVTGGASGLGHATARRLADAGAAVVVVDLPDRERETVRADAVAALGPRARFV +TGDVTAEDTAREAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLSAEVLSRVLAINTVG +TVAMMAQAAAAMKAQEPLGEDRGVIVNTASVAAYDGQIGQIAYSASKGAVVALTLPAARE +LASSQIRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGRPEDHALLVEQIVSNPF +LNGEVIRLDGAVRLEPR +>PROKKA_02260 +MDLSNQSAIVTGGASGLGHATARRLADAGAAVVVVDLPDREGETVRADAVAALGPRARFV +TGDVTAEDTAREAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLSAEVLSRVLAINTVG +TVSMMAQAAAAMKAQEPLGEDRGVIVNTASVAAYDGQIGQIAYSASKGAVVSLTLPAARE +LASSQIRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGRPEDYALLVEQIVSNPF +LNGEVIRLDGAVRLEPR +>PROKKA_00122 +MDLSNQSAIVTGGASGLGHATARRLAEAGAAVVVVDLPDREGETLRADAVAALGPRARLV +TGDVTAEATAEEAVAAALEAGPLRVLVNCAGVATPGKLVGRGGPLSAEVLTRVLAINTVG +TVNFMSRAAAAMQGQEPQGEDRGVIVNTASVAAYDGQIGQIAYAASKGAVVSLTLPAARE +LAASQIRVVTIAPGLMETPMMAGLPEAAREALATKTPHPARLGRPEDYALLVEQIVANPF +LNGEVIRLDGAVRLEPK +>PROKKA_00090 +MARRESLDLQGASAIVTGGASGLGHATARRLAAAGAAVVVVDLPDREGESLRADAVASLG +ERARFITGDVTAEATAEQAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLAAEALSRVL +AINVVGTVTMMARAAAVMKDQELWGEDRGVIVNTASVAAFDGQIGQIAYSASKGAVAALT +LPAARELAASQVRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGAPDDYALLVEQ +IVSNPFLNGETIRLDGAVRLEPR +>PROKKA_00248 +MDLSNQSAIVTGGASGLGHATARRLADAGAAVVVVDLPDREGETVRADAVAALGPRARFV +TGDVTAEDTAREAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLSAEVLSRVLAINTVG +TVSMMAQAAAAMKAQEPLGEDRGVIVNTASVAAYDGQIGQIAYSASKGAVVALTLPAARE +LASSQIRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGRPEDYALLVEQIVSNPF +LNGEVIRLDGAVRLEPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000335.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000335.fa new file mode 100644 index 0000000000000000000000000000000000000000..91ba60fa906fc24ccc54211e576b7e713a41429d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000335.fa @@ -0,0 +1,24 @@ +>PROKKA_00249 +MKKPPLAQDPIREAARNWERHGWGDVARPMAAITSIMRAQQILLGRAQAALKPYGLTFAR +YELLALLNFSRENRMRMSKASALLQVHPTSVTNAVDRLEAAGLVERTPHESDRRALVLAL +TDEGRRVAVAATETLNAEVFGRSGFGPADVDTLIDVLGRFRAEAGDFQVDGPDAGAPATA +EHTSS +>PROKKA_02261 +MKKPPLAQDPIREAARNWERHGWGDVARPMAAITSIMRAQQILLGRAQAALKPYGLTFAR +YELLALLNFSREKRMRMSKASALLQVHPTSVTNAVDRLEAAGLVERTPHESDRRALVLAL +TDEGRRVAVAATETLNAEVFGRSGFDPADVDTLIDVLGRFRAEAGDFEADGPDAGAPATA +EHTSS +>PROKKA_00121 +MKNAPLPQDPIREAARNWERHGWGDVARPMAAVTSIMRAQQILLGRTQAALKPFGLTFAR +YELLALLNFSREKRMRMSKASALLQVHPTSVTNAVDRLESAGLVERTPHESDRRALVLAL +TDEGRRVAVAATETLNEEVFGRTGFDEADVDALIDVFGRFRAGAGDFEADGADTTTERPS +A +>PROKKA_00089 +MSTRDPLPQDPIREAARNWEHHGWGEVAAPMAAVTAIMRTQAILLARTQAVLKPFGLTFA +RYELLALLNFSRERRQLMSKAGALLQVHPTSVTNAVDRLEAAGLVERQPHETDRRALLLA +LTDEGRRVADAATEALNAEVFGATGFTDDDVAALNEILGRFRAGSGDFEA +>PROKKA_00249 +MKKPPLAQDPIREAARNWERHGWGDVARPMAAITSIMRAQQILLGRAQAALKPYGLTFAR +YELLALLNFSREKRMRMSKASALLQVHPTSVTNAVDRLEAAGLVERTPHESDRRALVLAL +TDEGRRVAVAATETLNAEVFGRSGFDPADVDTLIDVLGRFRAEAGDFEADGPDAGAPATA +EHTSS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000337.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000337.fa new file mode 100644 index 0000000000000000000000000000000000000000..5dd02c615b73013b74677e26a0c922d35fa9839d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000337.fa @@ -0,0 +1,90 @@ +>PROKKA_00255 +MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAV +PAGIRQPKPLELPAPLTESAVLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENP +AWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANASLLDEASAAAEAVLLMHRANR +RRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPEDVRAEVEEKGLCGVVLQ +QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLF +FGGPHAAYMAVKEGLQRSMPGRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQ +ALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAGGVEVAEEHFFDTITVRVPGR +AEQVLQAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGSLPASAHEGAVA +TPAVPESLRRSSAFMMHPVFNTHHSETKMLRYLRRLSGYDLALDRTMIPLGSCTMKLNAT +AEMEAISWPEFCSIHPFAPDHQTEGWRFLIADLEAKLAEITGYAGVSVAPNAGSQGEFAG +LWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKVVVVATADDGTIDAADLDAKI +AANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGEFGG +DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYI +HLMGAEGLRSATAHALLGANYISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTA +EDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLEEIERFIEAMEAIHAEITAVTPETV +ADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS +CPPPEAFEGAVADTADED +>PROKKA_02269 +MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAV +PAGIRQPKPLELPAPLTESAVLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENP +AWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANASLLDEASAAAEAVLLMHRANR +RRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPEDVRAEVEEKGLCGVVLQ +QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLF +FGGPHAAYMAVKEGLQRSMPGRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQ +ALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAGGVEVAEEHFFDTITVRVPGR +AEQVLQAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGSLPASAHEGAVA +TPAVPESLRRSSAFMTHPVFNTHHSETKMLRYLRRLSGYDLALDRTMIPLGSCTMKLNAT +AEMEAISWPEFCSIHPFAPDHQTEGWRFLIADLEAKLAEITGYAGVSVAPNAGSQGEFAG +LWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKVVVVATADDGTIDAADLDAKI +AANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGEFGG +DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYI +HLMGAEGLRSATAHALLGANYISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTA +EDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLEEIERFIEAMEAIHAEITAVTPETV +ADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS +CPPPEAFEDAVADTADED +>PROKKA_00114 +MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAV +PAGIRQPKPLELPAPLTESAVLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENP +AWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANASLLDEASAAAEAVLLMHRANR +RRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPEDVRAEVEEKGLCGVVLQ +QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLF +FGGPHAAYMAVKEGLQRSMPGRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQ +ALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAGGVEVAEEHFFDTLTVRVPGR +AEQVLQAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGALPASAHEGAVA +TPAVPEALRRSSAFMTHPVFNTHHSETQMLRYLRRLSGYDLALDRTMIPLGSCTMKLNAT +AEMEAISWPEFCSIHPFAPDHQTEGWRFLIADLEAKLAEITGYAGVSVAPNAGSQGEFAG +LWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKVVVVATADDGTIDAADLDAKI +AANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGGFGG +DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYI +HLMGAEGLRSATEHALLGANYISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTA +EDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLQEIERFIEAMEAIHAEITAVTPETV +ADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS +CPPPEAFEDAVADTADED +>PROKKA_00082 +MTSPLTPTEPRDTASAPFVARHIGPRGEDVRHMLQTLGLGSVDELVDTAVPSVIRQSAPL +DLPAPLTEAAALEQLREIAGRNVVKTQMIGQGFYDTVTPGVILRKVLENPAWYTAYTPYQ +PEISQGRLEALLNYQQMVEDLTALPIANASLLDEASAAAEAVLLMHRANRKKADGITLLD +ADLFPQTLTVAQMRAEAVGLEVRVADLSAGIPEDVRAEVEEKGLCGVVLQQPGDSGRLHD +HSAVIAQAKEAGALITVAADILSLALITPPGEQGADIAIGSTQRFGVPLFFGGPHAAYLA +VREGLQRSMPGRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQALLAITASMY +AVYHGPAGITAIARHAHAQAHRLAIALAGAGVEVAHAEYFDTLTLNVPGRAEEVVRAAEE +AGVNLRLVDADIVRVACDETTVDEDLAAVLTAFGADPASLPAAPHEGAVQTPAVPEAQRR +TSAFMTHPVFNTHRSETQMLRYITRLANRDLALDRTMIPLGSCTMKLNATTEMEAISWPE +FCAIHPFAPDHQTEGWRFLISDLEERLAEITGYAGVSVAPNAGSQGEFAGLWAIRQYHLA +HGDGERDVCLIPASAHGTNAASAVLAGLRVVVVATADDGTIDSADLDAKIAAHEGRVAAI +MITYPSTHGVFDGDVTEVCDKVHAAGGQVYIDGANLNALVGLARPGAFGGDVSHLNLHKT +FCIPHGGGGPGVGPVAVGEHLVPFLPSAERLVTAAPHGSAGVLPISWAYIAMMGGEGLKD +ATEQALLNANYISRRLADHYPTLYTGEGGLVAHECILDLRELTAQTGVTAEDVCKRLIDY +GFHAPTLAFPVAGTLMVEPTESEDLAELDRFIDAMISIHAEITATTPETVEQSVLRRAPH +TLGATTGEDWDRPYTRAQALYPLPSLVDDKYLPPVGRIDGAYGDRNLVCSCPPPEAFEEA +AASPESTEPVSAADTASTSH +>PROKKA_00254 +MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAV +PAGIRQPKPLELPAPLTESAVLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENP +AWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANASLLDEASAAAEAVLLMHRANR +RRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPQDVRAEVEEKGLCGVVLQ +QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLF +FGGPHAAYMAVKEGLQRSMPGRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQ +ALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAGGVEVAEEHFFDTITVRVPGR +AEQVLKAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGSLPASAHEGAVA +TPAVPEALRRSSAFMTHPVFNTHHSETKMLRYLRRLSGYDLALDRTMIPLGSCTMKLNAT +AEMEAISWPEFCSIHPFAPDHQTEGWRFLIEDLEAKLAEITGYAGVSVAPNAGSQGEFAG +LWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKVVVVATADDGTIDAADLDAKI +AANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGEFGG +DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYI +HLMGAEGLRSATAHALLGANYISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTA +EDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLEEIERFIEAMEAIHAEITAVTPETV +ADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS +CPPPEAFEGAVADTADED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000338.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000338.fa new file mode 100644 index 0000000000000000000000000000000000000000..1762732482729aef691cd0beb638ab63607185e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000338.fa @@ -0,0 +1,40 @@ +>PROKKA_00256 +MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV +TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV +PNAGNIAAVHTALNQRASGWDAVVEDESSTTALVAVQGPQAERILARAMPEAAAQLAELK +YYGHLTLTVPTDAGDVTAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE +AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG +RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDLAA +EGTSLQVDLRGRGEPFTVVATPFYRRER +>PROKKA_02270 +MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV +TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV +PNAGNIAAVHTALNQRASGWDAAVEDESSTTALVAVQGPQAERILARAMPEAAAQLAELK +YYGHLTLTVPTDAGDVIAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE +AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG +RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDLAA +EGTSLQVDLRGRGEPFTVVATPFYRRER +>PROKKA_00113 +MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKHGSELAEHKAVRTAAGLFDLSHMGEVRV +TGPQAGAMLDYALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEDGSEPDFMVV +PNAGNIAAVHTALNQRASGWDATVEDQSSTTSLVAVQGPKAEAILAQAMPEAAEQLAALK +YYGHLTLTVPTEAGDVTAVVARTGYTGEDGFELFLPASSTQEAGDRGSAVWNAVLKAAEA +ADVELTLCGLASRDSLRLEAGMPLYGNELDTAHQPHASGVGFAVPASKEADFVGKAALVG +KDDAEEVLVGLRGEGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDVAA +EGTSLQVDLRGRGEPFTVVATPFYRRER +>PROKKA_00081 +MTESTRNSPLHPVHEAAGASFTDFGGWNMPLKYGSELAEHKAVRESAGLFDLSHMGEVRV +SGPESGAMLDHALSSSISVLKPGRAKYALCLTDAGTVLDDLIVYRTDSGAEGEDQEFLVV +PNAGNISAVVTALTQRASGWDVEVHDESSTTALVAVQGPQSEAILARLMPASAQELAELK +YYGHVTLTVPTAAGDVQAVVARTGYTGEDGFELFLPASSTAEAGDRGSAVWSAVVKAAEE +AGIALTPCGLASRDSLRLEAGMPLYGNELDTAHQPHASGVSFAVPASKEGDFVGKAALVG +KDEVEEVLVGLKGEGRRAARHGYSVLDADGAVIGEVTSGAPSPTLGHPVAMARIRREHAA +EGTSVQVDLRGRGEPFTVVPLPFYTRAR +>PROKKA_00255 +MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV +TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV +PNAGNIAAVHTALNQRASGWDAVVEDESSTTALVAVQGPQAEKILARAMPEAAAQLAELK +YYGHLTLTVPTDAGDVIAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE +AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG +RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDVAA +EGTSLQVDLRGRGEPFTVVATPFYRRER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000339.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000339.fa new file mode 100644 index 0000000000000000000000000000000000000000..12bc4a09671ef0973d84c474d6203e2baae14f67 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000339.fa @@ -0,0 +1,30 @@ +>PROKKA_00257 +MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG +GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYAWLRDRLPQGATASMTTSDEGAPEGM +ESAVISIGGGTVNVAMAEAGMAAPTDVAVGKRLAEEIAQANQEAVGRGVGLYDIEEPCTY +QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEVRALDPENGTFADLA +YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG +>PROKKA_02271 +MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG +GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYAWLRDRLPQGATASMTTSDEGAPEGM +ESAVISIGGGTVNVAMAEAGMGAPTEVAVSERLAEEIAQANQEAVGRGVGLYDIEEPCTY +QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEIRALDPENGTFADLA +YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG +>PROKKA_00112 +MTHVAARARVPKKGLLVFLVVAAVLLLLGALTVVRGIAADAARVNIVSVVDGNTVVVNQG +GTQRTLVLAGVTSAGRNPEGLKVGPELCMGEQSYAWLRDRLPQGAVASVDTSREGAPEGM +ESALVHIGGKTVNVDMAEAGMTAPTGIGVDDDMAEEIAAANRVAVGRGVGLYDVEEPCTY +QNRLYEAQFALDQIPKDAEDSIRRIDERSVEYAAGLDQVRLVQQEIQALDPENGTFEDLA +YGPARESLLAEADPVVEEGLQVLRDLNARRNEIAARG +>PROKKA_00080 +MTHVAAQARVPKKGLIVFLVVAGVLLALGAASAVRGLVVARDTVEVVRVVDGNHVVVNAD +GEERTLTLAGVRSAIRNPEGLRVGPEYCMGEEAYAWLRDRLPQGATVRVDRSDEGAPEGE +QSAVFTVAGKEVNVDMAKAGMAAPTGLGVSGDLEEQIAQANQQAQTAGGRNNGVGLYNRD +ETCTLGYQLYAAQTELEKVPTAPAANTVVEIDKKSVEYANALDAVRLVQQRIEGLDASSG +DFTGLAYAPAKDRLLARANPVVDEGMQVLRDLNAQRNALAGG +>PROKKA_00256 +MTHVAARARVPLKGLLVFLAVAAVLLLLGIVTVLRGVAADAARVDIVTVLDGNTVVVNQG +GTERTVVLAGVTSAGRNPEGLKVGPNLCMGEESYSWLRDRLPQGATASMTTSDEGAPEGM +ESAVISIGGGTVNVAMAEAGMAAPTEVAVGKRLAEEIAQANQEAVGRGVGLYDIEEPCTY +QNRLYEAQFALEQIPEDAEASLTKIDERAVEYAAGLDQVRLVQQEIRALDPENGTFADLA +YGPAKESLLAEADPVVEHGMQVLKDLNTRRNEIAARG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000342.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000342.fa new file mode 100644 index 0000000000000000000000000000000000000000..f40b43e87ad5319fbb0893d5c1d3771306c3fefe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000342.fa @@ -0,0 +1,30 @@ +>PROKKA_00263 +MPQTAHSPQHSASAPALALTIAGSEATGGAGAQADLKTFQELGVFGIVALTCIVSFDPED +DWNHRFFPVPTEILQQQLDAIQGDYPERLRTVKLGMQGSPEVIRTSAAALRRAEWDHVVL +DPVLICKGQEPGHALDTDQALKAELLPLATFTTPNHFETEQLSGMTVRSVEDLTAAARRI +HEISGAAVLAKGGMHLPGPDAVDVFVDGDTVEVLSAPKIGQSGVSGAGCSLAAAVTAELA +KGATTLEAARRAKEFVRAGIAQAVEGRTPFAALWQGGLRSA +>PROKKA_02276 +MPQTGHSPQHSASAPALALTIAGSEATGGAGAQADLKTFQELGVFGIVALTCIVSFDPED +DWNHRFFPVPTEILQQQLDAIQGDYPERLRTVKLGMQGSPEVIRTSAAALRRAEWDHVVL +DPVLICKGQEPGHALDTDQALKAELLPLATFTTPNHFETEQLSGMTVRSVEDLTAAARRI +HEISGAAVLAKGGMHLPGPDAVDVFVDGDTVEVLSAPKIGQSGVSGAGCSLAAAVTAELA +KGATTLEAARRAKEFVRAGIAQAVEGRTPFAALWQGGLRSA +>PROKKA_00100 +MSQTAPASQNHDAVPALALAIAGSEATGGAGAQADLKTFQELGVFGIIALTCIVSFDPKD +DWNHRFFPVPTEVLEHQLEAVQQDYPELLRTVKLGMQGSPEVIRTSAAALRRQEWDHVVL +DPVLICKGQEPGHALDTDQALKAELLPLATFTTPNHFETEQLSGMTVHSVDDLVAAARRI +HEVSGAAVLAKGGMHLPGPDAVDVFVDADTVEVLSAPKIGEAGVSGAGCSLAAAVTAELA +KGATPLEAARRAKEFVRSGIEQAVAGRTPFAALWQGGLRGA +>PROKKA_00071 +MTTTTTTPRSVAPALALAIAGSEATGGAGAQADLKTFQELGVFGILSLTCIVSFDPADDW +NHRFFPVPQDVQAAQLEAILADYPDELRAVKLGMQGSPETIRTTAEALRGHAWDHVVLDP +VLICKGQEPGHALDTDQALKAELLPLATFTTPNHFETEQLSGMAVRTVEDLTAAARRIHE +ISGAAVLAKGGMHIEGLDAVDVFVDADHEEVLATPKIGDSGVSGAGCSLAAAVTAELAKG +AEPVEAARRAKAFVTAGIAQAVEGRTPFAALWQGGLRETPEAGR +>PROKKA_00261 +MPQTAHSPQHSASAPALALTIAGSEATGGAGAQADLKTFQELGVFGIVALTCIVSFDPED +DWNHRFFPVPTEILQQQLDAIQGDYPERLRTVKLGMQGSPEVIRTSAAALRRAEWDHVVL +DPVLICKGQEPGHALDTDQALKAELLPLATFTTPNHFETEQLSGMTVRSVEDLTAAARRI +HEISGAAVLAKGGMHLPGPDAVDVFVDGDTVEVLSAPKIGQSGVSGAGCSLAAAVTAELA +KGATTLEAARRAKEFVGAGIAQAVEGRTPFAALWQGGLRSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000343.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000343.fa new file mode 100644 index 0000000000000000000000000000000000000000..59118d220cd38339f26af8312742b1623562633f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000343.fa @@ -0,0 +1,22 @@ +>PROKKA_00264 +MLEFLTGTGLATSAGLNAYIPLLALGLLDRFTGLVDLPAGWTWLSADASLWILGALLALE +LVADKIPGVDAVNDVVQTVVGADTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLV +VAVVVGLWLLARRFRARRTRGRAAAVPGGPEWTA +>PROKKA_02277 +MLEFLTGTGLATSAGLNAYIPLLALGLLDRFTGLVDLPAGWTWLSADASLWILGALLALE +LVADKIPGVDAVNDVVQTVVGADTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLV +VAVVVGLWLLARRFRARRTRGRAAAVPGGPEWTA +>PROKKA_00099 +MLEFLTGTGLATSAGLNAYIPMLALGLLDRFTGLVDLPAGWTWLSADASLWILGVLLLLE +VVADKFPGVDAVNDAVQTVVRPAAGGIVFASGVGTETTAVHDPGTLFGGSGWVSVLIGAG +IALAVHLAKAGTRVGANTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLVVAVVVG +LWLLARRFRARRTRGRAAAAAGGSEWTA +>PROKKA_00070 +MLALGLLDRFTPLVDLPPAWAWLSSDVALWVVGILLVLEVVADKIPAVDAVNDVVQTVVR +PAAGGITFASGVGAQTVTVQRPDTLLDSQVWVPTLIGAAMALLVHLTKAGTRAAANTVTM +GTAAPLLSTAEDASAVVLTAAALFLPVLVLVVLLAVLVGLWAVPRRFRAGRRGGRRATMA +S +>PROKKA_00262 +MLEFLTGTGLATSAGLNAYIPLLALGLLDRFTGLVDLPAGWTWLAADASLWILGVLLALE +LVADKIPGVDAVNDVVQTVVGADTVTVGAAAPVLSAAEDVSAAGLVAAALFLPVLVAVLV +VAVVVGLWLLARRFRDRRTRGRAAAVPGGPEWTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000345.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000345.fa new file mode 100644 index 0000000000000000000000000000000000000000..ff37519c94757a33b7d8d1d8192a617113399636 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000345.fa @@ -0,0 +1,25 @@ +>PROKKA_00266 +MSAEQNSTQTPGHRTAHVPAGQDLGHRWSTREADHDDPADRRAVRQIAELAFASTAEADL +VEALADGAEGWLPQYSLVAMTAAIPGTDLQSDPMGYGTLVRAHIDDAEVLALAPHGVLPE +HQGEGAGTALVNALLQKAQADGEEVVVVYGWPEYYAKFGFHQASEHGVHAAFARQPEALQ +ILTLQDGAEVPAGEFRYPPAFGAENAQVAGR +>PROKKA_02279 +MSAEQNSIQTPGYRAAHVPAGQDLGHRWSTREADHDDPADRRAVRQIAELAFASTAEADL +VEELAGGAEGWLPQYSLVAMTAAIPGTDLQSDPMGYGTLVRAHIDDAEVLALAPHGVLPE +HQGEGAGTALVNALLQKAQADGEEVVVVYGWPEYYAKFGFHRASEHGVHAAFARQPEALQ +VLTLQDGAEVPAGEFRYPPAFGAENAQVAGR +>PROKKA_00097 +MSTEQNSTQTPAYRAAHVPAGQDLGHRWSTRVADHEDPADRRAIRQIAELTFESSAEADL +VEELAGGGEGWLPQYSLVAMTASIPGTDLQSDPMGYGTLVRAHVGEAEVLALAPHGVLPE +HQGEGAGTAIVNALLQKAQGDGEKVVVVYGWPEYYAKFGFRPGVEHGVTAAFADQPEALQ +VLTLQDDAEVPSGEFRYPPAFGAENAQVAGRA +>PROKKA_00068 +MSTEKGSTATPTYRAAHVPEGQDLGHRWSTRLAHHDDPADRRAVRQIAELTFESSAEADL +VEELVASGEGWLPQYSLMAMTASIPGTDLYSDPMGYGTLVRAHIDDAEVLALAPHGVLPE +HQGEGAGTALVNALLEKAQKDGEQAVVVYGWPEYYAKFGFRPAAEHGVTAAFATQPEALQ +VIALQEGAEIPSGEFRYPPAFGAENAQVAGR +>PROKKA_00264 +MSAEQNSTQTPGHRAAHVPAGQDLGHRWSTREADHDDPADRRAVRQIAELAFASTAEADL +VEELAGGAEGWLPQYSLVAMTAAIPGTDLQSDPMGYGTLVRAHIDDAQVLALAPHGVLPE +HQGEGAGTALVNALLQKAQADGEEVVVVYGWPEYYAKFGFHRASEHGVHAAFARQPDALQ +VLTLQDGAEVPAGEFRYPPAFGAENAQVAGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000346.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000346.fa new file mode 100644 index 0000000000000000000000000000000000000000..2b48b86c35d8c6424319db9af71e53c97a579f59 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000346.fa @@ -0,0 +1,25 @@ +>PROKKA_00267 +MARMTTPAEDTLTALIHLLDREGYDAVTADQLARQAGMSRASFFRHLGGKEEVVFADHAA +LLARLDDFLRGTSLGVREALEEAVLQVFRHHTADPDRARARSRLLRGSQSLRTRELLTSH +RYTELFSGWLATALPDTPARGGVAVGLAAAVVAVHNRALRAWLHAPADDAEAGLRADLAE +VIARLTAEPAEAERTLAAVRRLLG +>PROKKA_02280 +MARMTTPAEDTLTALIHLLDREGYDAVTADQLARQAGMSRASFFRHLGGKEEVVFADHAA +LLARLDDFLRGTSLGVREALEEAVLQVFRHHTADPDRARARSRLLRGSQSLRTRELLTSH +RYTELFSGWLATALPDTPARGGVAVGLAAAVVAVHNRALRAWLHAPADDAEAGLRADLAE +VIARLTAEPAEAERTLAAVRRLLG +>PROKKA_00096 +MARMSTPAEDTLTALIHLLDREGYDAVTADQLAREAGMSRASFFRNLGGKEEVVFADHAT +LLAHLEELLRGTGLGVREALDEAVLQVFRHHTRDPERAQARARLLRGSQALRTRELLTSH +RYEELFSAWLADALPDTPARGGVAVGLAAAVVAVHNRALRAWLHSPDDDAEAGLRADLAE +VVARLTAEPSAAERTLEAVRRLLG +>PROKKA_00067 +MNPMTAVPEDTLTALIHLLDRQGYDDVTVDQLAREAGMSRASFFRHVGGKEEVVFADHEQ +LLPRLEDLLHSTSLPLPTALREAGLQVFRHHVQHPERARARARLLRGSRALRTRELLASH +RYEQLFSRWLAERLPDTPTRGSVAVGLAAAVVAVHNAALRGWLHAEAPDPTAAEAALGAQ +LDEVILRLTREPGEAEVRLAAVRALLD +>PROKKA_00265 +MARMTTPAEDTLTALIHLLDREGYDAVTADQLARQAGMSRASFFRHLGGKEEVVFADHAA +LLARLDDFLRGTSLGVREALEEAVLQVFRHHTADPDRARARSRLLRGSQSLRTRELLTSH +RYTELFSGWLATALPDTPARGGVAVGLAAAVVAVHNRALRAWLHAPADDAEAGLRADLAE +VIARLTAEPAEAERTLAAVRRLLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000348.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000348.fa new file mode 100644 index 0000000000000000000000000000000000000000..02e707feb022e429a4149aaa62591186099153e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000348.fa @@ -0,0 +1,30 @@ +>PROKKA_00269 +MVAPPPHHDAAPSPVFPVAAGLQAGLTASQLRGPRFDAPHHGLRHTAGGQPSLADVVRAL +QRTNPGTAATHATAARLWGMWLPRQWERGPIHLARTRAEGGAPRRSGVVGHELHPQDPVL +VRARVRITTPAATWAALAQLGLPLADVVAAGDSLLQRADGPAGRRRPGDHPRCTVRDLEA +EVLRVRGRRGTRTLRAALPLLRDGADSRAETLLRLALADAGVPEPEVNPLLMLSDGSTVR +PDLVWREAHVCVQYEGDHHRTDPRQWRRDIERDRRMQAEGWIVLRVTASVFTRRGLDALL +RDLAAHLRLPLPA +>PROKKA_02282 +MVAPPPHHDAAPSPVFSVAAGLQAGLTASQLRGPRFDAPHHGLRHTAGGQPSLADVVRAL +QRTNPGTAATHATAARLWGMWLPRQWERGPIHLARTRAEGGAPRRSGVVGHELHPQDPVL +VRARVRITTPAATWAALAQLGLPLADVVAAGDSLLQRADGPAGRRRPGDHPRCTVRDLEA +EVLRVRGRRGTRTLRAALPLLRDGADSRAETLLRLALTDAGVPGPEVNPLLLLSDGSTVR +PDLVWREAHVCVQYEGDHHRTDPRQWRRDIERDRRMQAEGWIVLRVTASVFTRRGLDALL +RDLAAHLRLPLPA +>PROKKA_00444 +MWLPAEAEQRVHLSRVRPGAQPRIAGVAGHRIRIDPVTGLTVLGVGDKAYTVTTPERTWT +DLASMGLTREDLIVAGDALLHRRDGPGGEVAAGRQHPLSSLADLGVAVAEARGVTGWRLL +GEALPHLRERSDSPQETRLRVRLVGAGFPEPQVNPEVPLVWDAWGRILRSTPVDLYFAAA +KVALQFEGEHHFSRARQYRRDMRRDEELRDVGVETVRVDSAVFGAGEWARFMARLQRLLT +TRGGA +>PROKKA_00397 +MDGPRDLVWREARVAIEYEGAHHFEDADQYRRDMRRDEELRALGWVVLRVDRDVWTPQGW +EVFLGRLGAALARWSC +>PROKKA_00267 +MVAPPPHHDAAPSPVFPVAAGLQAGLTASQLRGPRFDAPHHGLRHTAGGQPSLADVVRAL +QRTNPGTAATHATAARLWGMWLPRQWERGPIHLARTRAEGGAPRRSGVVGHELHPQDPVL +VRARVRITTPAATWAALAQLGLPLADVVAAGDSLLQRADGPAGRRRPGDHPRCTVRDLEA +EVLRVRGRRGTRTLRAALPLLRDGADSRAETLLRLALADAGVPEPEVNPLLMLSDGSTVR +PDLVWREAHVCVQYEGDHHRTDPRQWRRDIERDRRMQAEGWIVLRVTASVFTRRGLDALL +RDLAAHLRLPLPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000351.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000351.fa new file mode 100644 index 0000000000000000000000000000000000000000..0294213882be272572e34d5373d11e4d5af297a6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000351.fa @@ -0,0 +1,31 @@ +>PROKKA_00277 +MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV +KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH +GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS +LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR +DAEAEYQWRRARFGQLLYLRARGGSETLTDADLDSRIARELGALRTLADELEAKAATRR +>PROKKA_02292 +MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV +KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH +GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS +LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR +DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR +>PROKKA_00076 +MAPMTGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV +KIAHGSVIRVRTDRQEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH +GLNLRSGSQLEDLFGMAERLYLLHEDVEGTLAALGLLTNLPWDGAVGRWKSIQAGLALAS +QILRDEGEHIVAANLGKRLHEADEVPSEPGRAARVLEVRQRQLNEPQLYDREISRALQAR +DAEAEYRWRRARFAQLLYLRGRGGSETLTDADLDSRIARELGTLRGLARDLDAKAAARS +>PROKKA_00061 +MSDGGAEVAPIAGGYLRHLKAQDVRPGDSFLTRRGEPAPAVASTRVVRDDFGTPALVIAT +LVGGREVKIAHGSVIRVRTDRPEEVKAAADTAFSPVDAGSPESRIVAVGQRHLDDAELTA +TAARLSHGLNLRSGAQLEDVFGMAERMYLLHEDVEGTLTTLGLLTNLPWDGAVGRWKSIQ +AALGLAALILREDGDHITAANLGSRLKEADEVPSEPGRAARVLEVRQRQLDEPQLYDREI +SRALQARDAEAEFRWRRARFAQLLYLRGRGGSQTLTDQDLDSRIHRELGTLRQLAKRLAA +QAARA +>PROKKA_00276 +MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV +KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH +GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS +LILREEGEHIAAANLGRRLLEADEVPSEPGRAARVLEVRQRQLNEPPLYDREISRALQAR +DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000352.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000352.fa new file mode 100644 index 0000000000000000000000000000000000000000..1838b5f0bf28fa2e1696a1cf60695f63eb46664b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000352.fa @@ -0,0 +1,20 @@ +>PROKKA_00278 +MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR +TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH +AVALVYVVPVTGECQPRQNALELTWLTPEEALGEDIQAEFIGGRGDLVRQALAHVGWGR +>PROKKA_02293 +MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR +TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH +AVALVYVVPVTGECQPRQNALELTWLTPEEALGEDIQAEFIGGRGDLVRQALAHVGWGR +>PROKKA_00075 +MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR +TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH +AVALVYVVPVTGECQPRQNALELTWLTPEEALGQDIQAEFIGGRGDLVRQALAHVGWGR +>PROKKA_00060 +MSVRTPDPNPGWLNEEDLYEARRRLPMVYVEAIPVRVDALGYVSEIGLLYVADEEGQFQR +TFVSGRVMYRETIRGALMRHLEKDLGPLAFPQLPPSLVPCAVAEYFPAPSETGLTDDRQH +AVSLVYVVPVSGECSPRQDALELTWLTPQEALGEDVQAEFIGGRGNLVRQALAHVGWGR +>PROKKA_00277 +MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR +TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH +AVALVYVVPVTGECQPRQNALELTWLTPEEALGEDIQAEFIGGRGDLVRQALAHVGWGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000355.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000355.fa new file mode 100644 index 0000000000000000000000000000000000000000..1490afa1e3e0faa0e651d44e5ab080cb388fc443 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000355.fa @@ -0,0 +1,35 @@ +>PROKKA_00283 +MAVPSPLPPRNGVNATRLRLPTSGWPTAQDYVLHRFGHVDPEGIRARFARGEVVAADGTA +LTPTTPLGVHDDLWYYRDVPDEAPLPVTHTLLHRDEHLVVIHKPHFLPTTPGGRFVQETA +LVRLRNELGLDDLVPLHRLDRATAGVVMFSANPATRGAYHLLFERRAVAKTYEAVALLPD +APDDGARGPGAPTDPILGRFPLTVRSRIRKDKGVLRSVVEEIPAAASGRRAGAPVRTRRS +NRPHAGANAESRVELLGVGVSAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFDP +FYPDLLDLAPDDVARPLQLLSRSLRFTDPVTGEEREFTSPAELQERPR +>PROKKA_02298 +MAVPSPLPLRNGVNATRLRLPASGPWASVQEYVLDRFGHVDPDGIRRRFASGQVVAADGA +PIPADTPLGVHDDLWYYRDVPDEAPLPVTHTLLHRDEHLVVIHKPHFLPTTPGGRFVQET +ALVRLRNELGLDDLVPLHRLDRATAGVVMFSANPATRGAYHLLFERRAVAKTYEAVVLLP +EAPDDGARGPGAPADPVLGRFPLTVRSRIRKDKGVLRSVVEEIPAAASGRRAGAPVRTRR +SNRPHAGANAESRVELLGVGVSAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFD +PFYPDLLDLAPDDVTRPLQLLSRSLRFTDPVTGEEREFTSPAELQERPR +>PROKKA_00070 +MAVPSPSPARNGVNATRLRLPASGWDTAQDYVLHRFGHVDPDGIRARFAAGEVVAADGTA +LTPTTPLGVHDDLWYYRDVPHEDPLPVAHTLLHRDEHLVVIHKPHFLPTTPGGRFVQETA +LVRLRNELGVDDLVPLHRLDRATAGVVMFSVDPATRGAYHLLFERRAVAKTYEAVSALPP +DADDDGLVLGRFPLTVRSRIRKDKGVLRSVVEEVPAAASGRRAGAPVRTRRSNAAHAGAN +AESRVEVLGVGESAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFDPFYPDLLDA +APDDFSRPLQLLSRSLRFTDPLTGREREFVSPAQLQERPR +>PROKKA_00056 +MAAPSPLPPRNGVNATRLRLPASGWDTAQDYVLHRFGHVDPDGIRARFARGEVVARDGSP +LTPTTPLGVHEDLWYYRDVPHEAPLPFQHTLIHRDERLVVIHKPHFLPTTPGGRFVQETA +LVRLRNELGIDDLVPLHRLDRATAGVVMFSADPATRGAYHLLFERRAVTKRYEAISALPP +ARDHADDDAAAWLDRFPLVMRSRIRKDKGVLRSLTEEIPAAASGRAAGARVRTRKSNLSH +AGANAETRIEVLDVGRSAGTLAGAPVVRFRLSPRTGRTHQLRLHLAALGLGIAFDPFYPD +LLDAAPDDLARPLQLLSRSIAFTDPVTGEHREFVSPAELQERPA +>PROKKA_00282 +MAVPSPLPLRNGVNATRLRLPASGPWASVQEYVLDRFGHVDPDGIRRRFASGQVVAADGA +PIPADTPLGVHDDLWYYRDVPDEAPLPVTHTLLHRDEHLVVIHKPHFLPTTPGGRFVQET +ALVRLRNELGLDDLVPLHRLDRATAGVVMFSANPATRGAYHLLFERRAVAKTYEAVALLP +DAPDDGARRPGAPADPVLGRFPLTVRSRIRKDKGILRSVVEEIPPAASGRRAGAPVRTRR +SNRPHAGANAESRVELLGVGVSAGTLAGRRVAHLRLTPRTGRTHQLRIHLAALGLGIAFD +PFYPDLLDLAPDDVTRPLQLLSRSLRFTDPVTGEEREFTSPAELQERPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000358.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000358.fa new file mode 100644 index 0000000000000000000000000000000000000000..be0df39e9f1457bf0ff097d1cd457cf873791db8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000358.fa @@ -0,0 +1,40 @@ +>PROKKA_00289 +MTSTARSPRVSRRAALGLGVGALAVGGVAVVTDLAGAPAGPLGANATALYGMRSSTGHTY +ATLPGRAGRIDVYRPPGQGPFPVLVWNAGSGWRSDRGYSDGVDVARGLVPHGYAVAAFSV +RSSKQGTFPAQVEDATAAVRWVRRNAPGLQLDAGRVAVAGSSSGGWNALMAGLTGGQDLD +REQVPLPGREVPDGGHAIPEEDRVQAIVDFFGPTDFLTMNRQMLPGACADYNRANRLKHC +HLDDRSTKSDMLGVPVLASGGLTRLASPIAHVRPDSPPLLVVHGRKDVTVPWGQSLELYR +AAETAGLRTAFYSVAEGSHDLGMMTAKTRSAEVLRNGVPASAVHATISWSAVASFLDAVL +PR +>PROKKA_02311 +MTSTARSPRVSRRAALGLGVGALAVGGVAVVTDLAGAPAGPLGANATALYGMRSSTGHTY +AALPGRAGRIDVYRPPGQGPFPVLVWNAGSGWRSDRGYSDGVDVARGLVPHGYAVAAFSV +RSSKQGTFPAQVEDATAAVRWVRRNAPGLQLDAGRVAVAGSSSGGWNALMAGLTGGQDLD +REQVPLPGREVPDGGHAIPEEDRVHAIVDFFGPTDFLRMNRQMLPGACADYNRANRLEHC +HLDDHSTKADMLGVPVLASGGLTRLASPIAHVRPDSPPLLVVHGRKDVTVPWGQSLELYR +AAEAAGLRTAFYSVAEGGHDLGMMTAKTRSAEVLRTGVPASAVHASISWSAVASFLDAVL +PR +>PROKKA_00065 +MATSGRRGRLTRRAVLGLGAGALALGGGAAVANLAGVPPAPVGPDVNALFGMRSSTGHRY +ADLPGRAGRVDVYRPQGPGPFPVVVWNAGSGWRDDRGYHDGQTVARGLVPHGYAVAAFSV +RSSKQGRFPAQVEDATAAVRWVRAHAVELDLDASRLTVAGTSSGGWNALMAGLTGGRDLD +RAHVPPPGREVPPGGHAIPEEDRVQAILDFFAPTDFLAMNAQMPPGACADYNRQRRLEHC +HLDDHSTKSAMLGVPVLASYGLTRLASPIAHVRPDSPPMMIVHGLKDPTVPWRQSLELYE +AAEAAGVRAAFYSVADAGHDLGMMGGGWGSAEVLRSGVPLSAVHATISWAAVAAFLDTVL +PG +>PROKKA_00044 +MGGDTSTARAPRVRRRTLLGLGLGALAVGGTATALGHGSPVDSPALRQTMGALFGTTVIS +GIVYADLPGAAGRMDLYLPEGEGPFPVLAWNAGSGWRSDRGFQGGDAVARGLVPAGHAVA +AFSVRSAREDAFPAQVLDATAAVRHLRENAGELRVDPGRIAVGGNSSGGWNALMAGLTGG +RDLDRSAVPAPGDEVPEGGHAIPEEDRVQAIVDCFAPVDFLQMNVQMPRGACEEYDRRNH +TRHCHLDDASTKSRMLGAPVMARPELARLANPAVHVTPAAPPTLIVHGRADREVPYVQSR +GLYQAYVGAGVPVAMYSVEGAGHDLQMMARRVGRTDVVRSGLPRQAVHGSISWSAVAAFL +DVAMPRPRR +>PROKKA_00295 +MTSTARSPRVSRRAALGLGVGALAVGGVAVVTDLAGAPAGPLGANATALYGMRSSTGHTY +AALPGRAGRIDVYRPPGQGPFPVLVWNAGSGWRSDRGYSDGVDVARGLVPHGYAVAAFSV +RSSKQGTFPAQVEDATAAVRWVRRNAPGLQLDAGRVAVAGSSSGGWNALMAGLTGGQDLD +REQVPLPGREVPDGGHAIPEEDRVHAIVDFFGPTDFLRMNRQMLPGACADYNRANRLEHC +HLDDHSTKADMLGVPVLASGGLTRLASPIAHVRPDSPPLLVVHGRKDVTVPWGQSLELYR +AAEAAGLRTAFYSVAEGGHDLGMMTAKTRSAEVLRTGVPASAVHASISWSAVASFLDAVL +PR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000363.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000363.fa new file mode 100644 index 0000000000000000000000000000000000000000..0e88c80132a164cd67a58d0a3f48bcbe98d57aab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000363.fa @@ -0,0 +1,60 @@ +>PROKKA_00296 +MADNATTSFADRALADAPTDYAQLREWVAQIAELTQPDSVQWVDGSEEERDRLADELVAA +GTLTRLAEDKFPNSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPAKMHGILDDA +FTGAMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA +FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR +IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG +DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV +WWEGMTDEVPEHLTDWRGNDWTPEFGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA +ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA +GDYLAHWVRESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAE +AEETPIGLVPAAGSLDLSGIEVSAEDLEDALKVDAAEWAEENELIEQWLGRFGESLPAVV +RERFEAQKARFAQA +>PROKKA_00004 +MADNATTSFADRALADAPTDYAQLREWVAQIAELTQPDSVQWVDGSEEERDRLADELVAA +GTLTRLAEDKFPHSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPAKMHGILDDA +FTGAMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA +FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR +IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG +DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV +WWEGMTDEVPEHLTDWRGNDWTPESGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA +ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA +GDYLAHWVRESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAE +AEETPIGLVPAAGSLDLSGLEVSAEDLEDALKVDAAEWAEENELIEEWLGRFGESLPQAI +RDRFEAQKQRFAQA +>PROKKA_00058 +MADNATTSFADRALQDAPTDYAQLREWVAQVAELTQPDAVQWVDGSEEEYARLADELVAA +GTLTRLAEDKFPNSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPEKMHGILDDV +FAGSMRGRTMYVIPFVMGHLDAEDPKYGVELTDSAYVVLSMRIMARIGQDVLDKMSREQA +FYVPAVHSVGAPLEPGQEDVPWPCNSTKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR +IASVMARDEAWLAEHMLILKLTSPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG +DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAIAKGNSIFTNVALTDDGGV +WWEGMTDEVPEHLTDWRGNDWTPASETPAAHPNSRFCTPIEQTDMLADEYRDPKGVKLDA +ILFGGRRKTTVPLVTESFDWEDGILKAATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA +GDYLAHWVEESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGRAD +AVETPIGHVPSPEALDLTGIDVSAEDLEDALKVDAEEWAKENELIEEWLGRFGESLPAMV +RERFEAQKERFARA +>PROKKA_00036 +MADNATTSFTELATKDAPTDYAQLREWVAGIAELTQPDAVHWVDGSQEEYDRLAAELVAA +GTLTKLNEKKLPNSYAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPKEMHGILDDA +FAGSMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA +FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR +IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG +DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV +WWEGMTDEVPEHLTDWRGNDWTPESGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA +ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA +GDYLAHWVKESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAG +AEETPIGLVPAAGSLDLSGIEVSAEDLEDALKVDAAEWAEENELIEEWLGRFGESLPQAI +RDRFEAQKARFAQA +>PROKKA_00303 +MADNATTSFADRALADAPTDYAQLREWVAQIAELTQPDSVQWVDGSEEERDRLADELVAA +GTLTRLAEDKFPNSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPAKMHGILDDA +FTGAMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA +FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR +IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG +DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV +WWEGMTDEVPEHLTDWRGNDWTPESGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA +ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA +GDYLAHWVRESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAE +AEETPIGLVPAAGSLDLSGLEVSAEDLEDALKVDAAEWAEENELIEEWLGRFGESLPQAI +RDRFEAQKQRFAQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000364.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000364.fa new file mode 100644 index 0000000000000000000000000000000000000000..e6f7058d1c1256de5c99fea7e61a95759c3a2a53 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000364.fa @@ -0,0 +1,20 @@ +>PROKKA_00298 +MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADRIQVPYNHVIKAVAELRRRGTIQVARGR +LGGARITEAGLDQRVGELVRDLSPRAEVLDCAGHETGVPCPFAADCRLREALARAREAFM +AELDLLTVRDLVRPGRAGATGPVSLGLPAMGSHAATV +>PROKKA_00006 +MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADEIHVPYNHVIKAVAELRRRGTIEVLRGR +HGGAMIAAAGLDQRVGELVRTLSSRDEVIDCAGRDSGVACPYAGDCRLRGALHRAREAFL +AELDTLRIRDLVSAGPVGGPVLLGLPEIPVTH +>PROKKA_00056 +MKLNAYTDVCLRVLMTLAGDEGERLTSQQIADRIQVPYNHVIKAVAELRRRGAIDVARGR +LGGATIAEAGLELRVGALVRDLAGWDEVIDCTGRESGVACPLAGDCRLRGALHRAREAFL +AELDAVRVRDLVAAGPAAGPVLLGLPEIPLPADPRPRRRTCPAGA +>PROKKA_00034 +MKLTAFTDVCLRVLMTLGRDAGAKMTSQEIADRIGVPYNHVVKAVGELRRRGLVDVARGR +AGGAVITEAGLDQRVGELVRALSGRPEVVDCEGLESGTPCPLLEACSLRGALARAREAFF +AELDRQRVRDLVSLPAEFLGLRRLPGA +>PROKKA_00305 +MKLSAYTDVCLRVLMTLAAAEGERLTSQQIADRIQVPYNHVIKAVAELRRRGTIEVLRGR +HGGAMIAAAGLDQRVGELVRSLSSRDEVIDCTGRDSGVACPYAGDCRLRGALHRAREAFL +AELDTVQIRDLVSAGPVGGPVLLGLPEIPVAH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000366.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000366.fa new file mode 100644 index 0000000000000000000000000000000000000000..90723fd01b9d3037bca40b0607810595277fd7da --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000366.fa @@ -0,0 +1,50 @@ +>PROKKA_00300 +MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS +PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAQA +GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETAGTVTEEDILPGYAAYLRSLVDLTGVRR +LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ +AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAITALVARREIARAKADGEQTPVVIH +NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM +LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPAVGEGVG +EGQAVHEDFAGVATTVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR +DAVLAIVRAER +>PROKKA_00008 +MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS +PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAQA +GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETAGTVTEEDILPGYAAYLRSLVDLTGVRR +LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ +AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAITALVARREIARAKADGEQTPVVIH +NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM +LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPAVGEGAG +EGRAVHEDFAGVATTVTRMDGTTIAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR +DAVLAIVRAER +>PROKKA_00054 +MTTSTSSLDLHESFKAYDVRGIVGETITADSVRAVGAAFVDVLGLAGETVLVGGDMRPSS +PAFMAAFAEGATRRGADVVDLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAKA +GAVPVSSDTGLYEIRDAAQALLDAGEIPAAEAVGTVTQQDILPAYAEYLRSLVDLSGVRP +LTVVVDAGNGMAGKTTPAVLGDAALDALPLRIEPLYFELDGTFPNHPANPLEPENLRDLQ +AAVVEHGADIGLAFDGDADRCFVVDEKGAPVSPSAITALVARREIARAKGEGEETPVVIH +NLITSRAVPELVAADGGRAVVTRVGHSFIKAVMAEESAVFGGEHSAHYYFRDFFNADTGM +LAAMHVLAALGEQDQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPTVGEGAG +EGRAVHEDFAGVDTAVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEAIR +DAVLAIVRAER +>PROKKA_00032 +MVTLRPGRIIDRVTTAADAINLRDSFKAYDVRGIVGETITAETVRAVGAAFVDVLGLAGQ +TVLVGGDMRPSSPEFIEAFAEGATRRGGNVQRIGLISTDMLYYAAGVEQAAGVMFTASHN +PAAYNGMKMAKAGAVPVSSDTGLYEIRDVAQGYLDAGEIPAADAQGSVTESDILTGYAEY +LRSLVDLSGIRPLKVVVDAGNGMAGKTTPAVLGGEVLEALPLEITPLFFELDGTFPNHPA +NPLEPENLRDLQRAVVEHGADIGLAFDGDADRCFVIDEQGEPVSPSAVTALVARREIARA +KASGEETPVIIHNLITSRAVPELVSADGGRAVQTRVGHSFIKAVMASEGAVFGGEHSAHY +YFRDFFNADTGMLAAMHVLAALGEQDGPLSTLGAEYEPYVASGEINSQVEDKDAAVAAVL +ARFAPQAADGGESGTAVEDAVAGTSTSVLRMDGTTVSAADGSWWFNLRPSNTEPFLRYNG +EAKDRATMETVRDAVLAIVRAPR +>PROKKA_00307 +MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS +PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQASGVVFTASHNPAEYNGMKMAQA +GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETTGTVTEEDILPGYAAYLRSLVDLTGVRR +LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ +AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAVTALVARREIARAKADGEQTPVVIH +NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM +LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVEDKDAAVAAVVAQFAPAVGEGVG +EGQAVHEDFAGVATTVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR +DAVLAIVRAER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000369.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000369.fa new file mode 100644 index 0000000000000000000000000000000000000000..41a4195ec58384535f4cd4298a4920e3862c98e0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000369.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000370.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000370.fa new file mode 100644 index 0000000000000000000000000000000000000000..c7beba10bf7a58d23f40d2dbe30ee681bcfc55fc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000370.fa @@ -0,0 +1,61 @@ +>PROKKA_00306 +MSEPLVADRRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR +TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY +GRYLRHLYKDVVAGLRARPEVAEVVEHRAEATALHPRPDGGARLELRDPDGSVSVLDADA +VVLCLGHQPAELSPGQMRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA +FDLLAQLTQGRGGVYRRTGDGPGRALRYEPTGDEPRLHLMSRRGIPYLPKAEVDAFVPRG +VTLSYLSDAAVDALTARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF +LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV +ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWIAEGRIAEASRIRDVQGWFEPLVE +GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLEPAVVEGA +WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD +GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAAAAVLAG +>PROKKA_00021 +MSEPLVAERRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR +TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY +GRYLRHLYKDVVAGLRARPEVVEVVEHRAEATALHPRPDGGARLELRDADGAVSALDADA +VVLCLGHQPAELSPGQNRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA +FDLLAQLTQGRGGVYRRTGDGPGRALRYEPSGDEPRLHLMSRRGIPYLPKAEVDAFVPRG +VTLSYLSDAAVDALAARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF +LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV +AELMEQTCVEAALGEESPFMMAVGALHAGRLRIKAWVAEGRITEASRIRDVQGWFEPLVE +GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLGPAVVEGA +WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD +GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAATAVLAG +>PROKKA_00031 +MPDAQEAVRRLAVVGAGPRGVMLLERLLARLEGSAPGAHPARLRIDVVDPYPPGPGRVWR +TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVQRHQYPARAVY +GRYLRHLYQDVVAGLRARPEVADVVEHRAEVTALHPTPAGGARLELRDADGAASELAADA +VVLCLGHQPAELSPGQARMAAAARGRDDLHYQGPQIPSDVDWDTVEPGARVLVRGMGLNA +FDLLAQLTQGRGGVYRRTGDGPGRALAYEPSGREPRLHLMSRRGVPYLPKAEVDAFVPRG +VTLSYLSDAAVDALSARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF +LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYTAPFEDAVFASHEDYQRAV +ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWVAEGRIAEDSRIRDVQGWFEPLVE +GLASGPPLWRVEQMLAVHRAGLLTWAGPVPVVDAEERAFSVRSPQVGAADSLGPAVVEGE +WLVEAMMPPNRVQAASSPLIRGMLDDGVAAAGTWEDEEGVRVPAPGFDVTGRPHRLRAAD +GAVHEDVYVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAVAQAVLAG +>PROKKA_00027 +MSPPSISEPTRAIAVVGAGPRGVMVLDRLLARLEAASEPRPTGSLAVHVVDPFPPGPGRV +WRPDQDPLLLMNTPAFFPTACAADNPGLAPSSVSLSFDQWRLARPDRAAGLERTDYPPRA +VYGRYLEDVVAAVLDALRARPEVVAVTVHAAQAVALRAAYEGGPVAAPESPSAWRLTLRP +VDGTPPRELQADVVVLCLGHQDAEPSAAQRRLGEAADASPALHYRGPHLPAELDVDGIAP +GATVLVRGMGLNAFDLQARLSEGRGGRFEPTGGEPGRALRYVPSGREPVLHLLSRRGLPY +LPKAAVDAFVPRGVRMSYLTDTEAEALVARHGQLDLAEHLWPLLHRDVVRAYYATLARVH +PERLGGPADAGRFVRELVGMFESAGRGAPVTARHGQELLHAFAPGMRFLDIRSWAAPFQG +AVFDDAAAYQEAVAGVLEQACGEAAAGEDSPFMQAVGTLHAGRLRIKAWIAQGLLTDASR +IRDVQGWFEPLVEGLASGPPLVRVEQMLALHRAGLLSWAGPGPQVEADAEAGVFRARSPQ +VGADDAVAPAVTEAAWLVEAMMPPSRVEAAATPLVRQMLADGVAAVGRWEDEDGALRSSS +GFDVTARPHRLRGADGTVREGVLVLGLQLSGVQWGTAIAAEAGADVRDRALFLADADAAA +RVALGG +>PROKKA_00313 +MSEPLVAERRLAVVGAGPRGVMLLERILARLEGAAPDAHPRRLRIDVVDPYPPGPGRVWR +TDQSELYLMNTPAFFPTACAADNPGLRPSTAAQTFDQWRRVHPEASLGVRRHQYPARAVY +GRYLRHLYKDVVAGLRARPEVVEVVEHRAEATALHPRPDGGARLELRDADGAVSALDADA +VVLCLGHQPAELSPGQNRMAAAARGRDELHYQGPQIPSDVDWETVEAGADVLVRGMGLNA +FDLLAQLTQGRGGVYRRTGDGPGRALRYEPSGDEPRLHLMSRRGIPYLPKAEVDAFVPRG +VTLSYLSDAAVDALAARHGALDLAEHLWPLLHRDVVRHYYATLVRAQPEILGGPVEARRF +LGELVGQLEEAGRGAPVTSAHAEELLQRYAPGRRFLDILAYGSPFEDAVFASHEDYQRAV +ADLMEQACVEAALGEESPFMMAVGALHAGRLRIKAWIAEGRIAEASRIRDVQGWFEPLVE +GLASGPPLWRVEQMLAVHRAGLLTWAGPAPVVEAEEHAFTAHSPQVGAQDSLGPAVVEGA +WLVEAMMPPNRVQAAASPLVRQMLADGVAAAGTWEDEEGVRVPATGFDVTARPYRLRAAD +GTVHADVFVLGLQLSGVQWGTAIAAEAGADPAGRALFLADADAAATAVLAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000372.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000372.fa new file mode 100644 index 0000000000000000000000000000000000000000..ca60ea0191868c5ccde17412053b998e21e50ff3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000372.fa @@ -0,0 +1,72 @@ +>PROKKA_00308 +MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT +QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA +GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN +ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR +AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG +EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY +QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF +TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG +WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG +YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV +GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG +ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKDADHPGKGRVK +GEDHPGKGRGVQRGAATHPVFSAQAWLTAAGLPR +>PROKKA_00023 +MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT +QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA +GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN +ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR +AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG +EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY +QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF +TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG +WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG +YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV +GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG +ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK +GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR +>PROKKA_00029 +MSSLFRRHAVATAACTVLVLAPASAAPALAVETVAADETTISLLSFNDFHGALSSDFSGT +QFADTVEDYRTAFEAQHGERSVLLTSAGDLIGGSASVSNVQQDDPTIDVMNALGLSALAA +GNHEFDRGLDDLQDRVIPRAEFPVLAANFVDPDTLEPILASHAIFDVNGVSVAVIGAVPN +ELYATTTGAGLQGNTVLDMVEAVNGVAAELEASGAADVIVASYHEGAAGAGDLAAELGKR +EVFRSMVEDTHPAVDVIFNGHTHQLYQYETAGDGVARPVLQAGASGSNLAAVELTVDAAG +EVTAVASRLLDRSTQDPAEAAAESAVTAEVYAIEQEAVAVFEDMQSQVVADLDGSLTTDY +QKRLDEGGTWRAGGTRSAETTLGNWVADATKQTALNADPEVDLGVVNPGGLRSEILVDAF +TGGGTFSPKPADLIGKLTLGELLDVAPFGNSISYFDIPGSSIELALEQNWRDDVRTFTLG +WSENLTWTYDESRPQGEKVTGVWIDGEPLEQDAIYTVATQSFLADDTWVALGDPTAAPDG +YTAFATGREDFVDLGVLDTQAISDYARLQASAEGAVGPDFAKKGVPVSGAPETVAAGEEI +VLTLGDLVIDSDDAPAAAEVAVAFEAADGTVTELGSVTVPAGSEEVTLSGIAAPAEAGAG +ELRMTVRYADGTETIVRHALEVTASEAPVEPTEPTDPTVPADPSEPADPADPTVPADPSE +PADPADPSDPTDPAAPVEGDDDGDDRDEEHTVPSTVETGDASAWWLAGFGALLGAALLRG +RRALGLTASSTPAGR +>PROKKA_00025 +MSSIFSRRTAATLACTTLVLAPAAAPALAADASGERTISVLSFNDFHGALSEDFKGTQFA +DTVEDYRTAFEAQHGEGSTLLTSAGDLIGGSASVSNVQQDNPTIDVMNALGLASLTAGNH +EFDRGLDDLQGRVADRADFPVLSANFVDPNTKAPVLTSHKVFDVDGVRVAVIGASPNELY +ATTTGAGLQGNLVVDMVDAVNAVATGIEAADEADVIIASYHDGAAGAAADLSAELGNRAT +FDAMVERTVPAVDVIFNGHTHQLYQYQTDNGGVPRPIMQAAASGADLAAVELTVDAAGEV +TAVTPRMLPRSTQDPAEAAAESPVTARVYEIEQQAVDVFTDMQSQVIADLSGSITTDYAT +RIAAGMGWKAGGTRTAETTLGNWVADSLKHSVSAAEPGVDLGVVNPGGIRSELLVDQTNA +GGVFSPKPEQLVGKLTMGEVMDVAPFGNTLTYFDLPGSSIKEALEQNWRDGERTFTLGWS +SNLTWTYDDARAQGDKVTGVWIDGEPLQADRMYTVAAQSFLADDTWVKLGDPSKAPDGYT +AFATGRQGFVDLGVLDTTAVLSWARAQDAADGAAHPDYAKKGVPVTGAPASVEGGQDVVL +TLGDLVIDSDGAPAATAVDVAFQGADGAVTELGTVEVPAGQESVTLSGITAPQTAGAGEL +VMTVRYADGTTAVVRHALEVTASAAPVDPSTPAEPTQPGEPSDPAEPTTPGEPTPSAQPT +APVEPTAPVEPSAPAEPTAPVEPTAPAESPEPTPTAQPSTPAEPTAPTPSAPAEDGGEHA +VPGKVQTGDQAIWLVAALGALGAGALVAVRRRAAAR +>PROKKA_00315 +MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSGDYIGT +QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA +GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN +ELYATTTGAGLKGNEVLDEVAAVNAVADELAAQDAADVIVASYHDGAAGAGELAAERAAR +AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG +EVTGLTPRLLTRSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY +QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF +TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG +WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG +YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV +GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG +ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK +GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000376.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000376.fa new file mode 100644 index 0000000000000000000000000000000000000000..ee65e307f79c292d5fafebb34603fbbf88f90fd7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000376.fa @@ -0,0 +1,26 @@ +>PROKKA_00315 +MSTQTEHRGLFVAVEGPDGSGKSTQARALTEVLRAAGHEVVLTREPGGSDLGETLRELLL +DPEHAPVDPRTEALLFAAARSAHAVRTLRPALARGALVVTDRYVDSSVAYQGAARGLGEA +RIAALNEWATDGLVPDLTVLIDVDAATAADRRERRAAGGEGAPDRMERETADRHEALRAA +FLARAAAAPERYLVLDGALPPQELTARALARVTAEAADR +>PROKKA_00030 +MSTQTEHRGLFVAVEGPDGSGKSTQARALTEALRAAGHEVVLTREPGGSDLGETLRELLL +DPGHAPVDPRTEALLFAAARSAHAVRTLRPALARGAVVVTDRYVDSSVAYQGAARGLGEA +RIAALNEWATDGLVPDLTVLIDVDAATAADRRDRRAAEGEGTPDRMERETADRHEALRAA +FLARAAAAPERYLVLDGALPPQELTARALARVTAQAADR +>PROKKA_00022 +MSTETEHRGLFVAVEGPDGSGKSTQARALVAALRAAGREAVLTREPGGSDLGETLRGLLL +DPAHAPVDPRTEALLFAAARAAHAVRTLRPALARGAVVVTDRYVDSSVAYQGAVRGLGEE +WIARLNDWATDSLVPDLTVLIDVDAATAAARRTGRDGDGADRMEQETADQHEALRAAFLA +RAAAAPERYLVLDGALDPEELTARALARVTAEADAR +>PROKKA_00018 +MSTPSPRPAPHPAPTPAADPADSPAAAAQGMPGRGLFVAFEGADGTGKSTQARAVAQALR +DAGREVVLTREPGGSDLGEAVRALLLDPAHAPVDARTEALLFAAARAAHVARTVRPALAA +GTVVLTDRYVDSSVAYQGEVRGLGAERVAELNDWATEGLVPDLTVLLDADAATAEARRAA +RHAGGGDAPDRMEQETAQAHGTLRAAFRARAAAAPHRYLVLDAAGAPEELTAAIAARVLT +AAADAARDGTGA +>PROKKA_00322 +MSTQTEHRGLFVAVEGPDGSGKSTQARALTEALRAAGHEVVLTREPGGSDLGETLRELLL +DPGHAPVDPRTEALLFAAARSAHAVRTLRPALARGAVVVTDRYVDSSVAYQGAARGLGEA +RIAALNEWATDGLVPDLTVLIDVDAATAADRRDRRAAGGEGSPDRMERETADRHEALRAA +FLARAAAAPERYLVLDGALPPQELTARALARVTAQAADR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000378.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000378.fa new file mode 100644 index 0000000000000000000000000000000000000000..e3794c62c06a7315fd38e11bbe7cf3010d4b62c5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000378.fa @@ -0,0 +1,30 @@ +>PROKKA_00317 +MVEKARRLRARTTPGSVPARGPQGHITRGTTAAQRMRRVDRWLTDVHGPLLRRTPRPLAV +DLGFGGEPVTAVEMAERLRVQNPALELVGLEIDPARVARARERAGGLPGVTWAVGGFELP +VPRPPTVVRAFNVLRQYREEDVPAIWSLLCAGLADDGVLVEGTCSEDGRWAAWVDLRRDG +PASLTVALRLGSFARPSDVAARLPKVLIHRHVPGEPVHRLLAEADAAWAAHAPLAAYGTR +QRWLATVGTLRSGGWPVLGGPHQWRRGELSVRWAAVAPSS +>PROKKA_00032 +MVEKARRLRARTTPGPGPARGPQGHITRGTTAAQRMRRVDRWLTDVHGPLLRRTPRPLAV +DLGFGAEPVTAVEMAQRLRVQNPALELVGLEIDPARVARARERAGDLPGVTWAVGGFELP +VPRPPTVVRAFNVLRQYREEDVPAIWSLLCAGLADDGVLVEGTCSEDGRRAAWVDLRRDG +PASLTVALRLGSFARPSDVAARLPKVLIHRHVPGEPVHRLLAEADAAWAAHAPLAAYGTR +QRWLATVGTLRAAGWPVLGGPHQWRRGELSVRWAAVAPSS +>PROKKA_00020 +MVEKARRLSASTTPGRVRGPQGHITRGTTAAQRMRRVDRWLTDVHGALLRRTDRPLAVDL +GFGAEPVTAVEMFTRLRAVNPALELTGLEIDPARVARARERAGGVPGLSWAVGGFELPVP +RPPTVVRAFNVLRQYREEDVPAVWALLCAGLAEDGVLVEGTCSEDGRRATWVDLRRDGPA +SLTLALRLGSFERPSDVAARLPKALIHRHVPGEPVHRFLAEADAAWAAHAPLAAYGTRQR +WLASVAALREAGWPVLGGPRQWRRGEMSVRWEAVAPSS +>PROKKA_00016 +MVQKARRLTLPDGGRARPGARGGPQGHVTRGTTAPQRMRRVDRWVADVHGPLLRRTAAPL +LVDLGYGAQPWTAVEMLTRLRAVQPSAELVGLEIEPERVAHARATAPALPGLSWERGGFE +LATSRPPTVVRAFNVLRQYREEDVPAIWDLMASRMAPGGVVVEGTCSEDGRRAAWVDLRA +DGPASLTLAMRLGAFERPSDVAERLPKALIHRHVPGEPVHRLLADADAAWALHAPLGAYG +TRQRWIAMVRTLKDAGWPVLGRESRWRRGELTVRWDAVAPGVG +>PROKKA_00324 +MVEKARRLRARTTPGPVPARGPQGHITRGTTAAQRMRRVDRWLTDVHGPLLRRTPRPLAV +DLGFGAEPVTAVEMAQRLRVQNPALELVGLEIDPARVARARERAGGLPGVTWAVGGFELP +VPRPPTVVRAFNVLRQYREEDVPAIWSLLCAGLADDGVLVEGTCSEDGRRAAWVDLRRDG +PASLTVALRLGSFARPSDVAARLPKVLIHRHVPGEPVHRLLAEADAAWAAHAPLAAYGTR +QRWLATVGTLRAAGWPVLGGPHQWRRGELSVRWAAVAPSS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000379.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000379.fa new file mode 100644 index 0000000000000000000000000000000000000000..a1bd6680bf2fa3fce3784570ccdee86b8e0364d8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000379.fa @@ -0,0 +1,25 @@ +>PROKKA_00319 +MRELYRADLERLGRDLTEIARLVHRAVMDAQAALEAADVHGAERVISEDARIDQLQESLD +EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEPVRTV +FTAMCDAAVEVAQEVVLLLETQDLAHGDRIDALNEDVNALHVSVFRAIAAPDWSATPATT +TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS +>PROKKA_00034 +MRELYRADLERLGRDLTEIARLVHRAMMDAQAALEAADVHGAERVISEDARIDQLQESLD +EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEQVRTV +ITAMCDAAVEVAEEVLLLLETQDLAHGDRIDALNEDVNALHLSVFRAIAAPDWSATPATT +TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS +>PROKKA_00018 +MRELYRADLERLGRDLTEIARLVHRAMIDAQEALESADVHGAERVISEDARIDRLQESLD +EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPAPVRPV +FTAMCDAAVDVAEETVLLLETQDLAHADRIHAVNEDVNALHASVFRFIAASDWTATPATT +TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWAYHRGSETSGP +>PROKKA_00014 +MRELYRADLERLERDLVGTARLVHRAVLDARAALDAADVHLAEQVISEDARIDLMQEGLD +EQAVRLLSLQAPVASDLRTVLATLRMSASLERMGDLARHIAQLTRLRYPEHVIPCDMRPL +FGSMTDAAVEVAQEVVLLLETQDLAHADRIHALNQVVNDHHVSVFRAIAAPSWGSPPATT +TDVTLASRYLERFTDHGLAVAAKARYLVTGESTRREGSAPA +>PROKKA_00326 +MRELYRADLERLGRDLTEIARLVHRAMMDAQAALEAADVHGAERVISEDARIDQLQESLD +EQAVRILALQAPVATDLRTVVATLRMSSSLERMGDLARHVAQLTRLRYPEHVIPEQVRTV +ITAMCDAAVEVAEEVVLLLETQDLAHGDRIDALNEDVNALHLSVFRAIAAPDWSATPATT +TDVTLASRYLERFTDHGLSVAAKVRYLVTGEWATHRPDATGS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000380.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000380.fa new file mode 100644 index 0000000000000000000000000000000000000000..6076ed805012619967619f5ee39491d5292f9ebc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000380.fa @@ -0,0 +1,40 @@ +>PROKKA_00320 +MDPVIIGLLCGAVGLFTGVASMLAFRASERSRTVDLTVGEPTLAPGAAEVLSVVGRAYAV +VDDVDGVVRANPAAYALGLVRGHSLVQDQLRELTRTVRADGVIVERRMELPRGPLGQSSL +VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLSEAIGDAA +EDEEAVRRFAARLGVESRRLSALVQDIIEFSRLQAKDVVQDGGPVDLNAVVADAVDRLRL +TAEDRGIALRVGGRVDAVVHGDQDQLMTAVRNLVDNAVRYSPEGTTVGIGLSSVDGLAQV +TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG +RGSTFTIRLPEWGDGVAVDGAPGAAHVTERRGHRVTASAAPPTRKETSA +>PROKKA_00035 +MDPVIIGLLCGAVGLFTGVASMLAFRASERSRTVDLTVGEPTLAPGAAEVLSVVGRAYAV +VDDVDGVVRANPAAYALGLVRGHSLVQDQLRELTRTVRADGVIVERRMELPRGPLGQSSL +VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLSEAIGDAA +EDEEAVRRFAARLGVESRRLSALVQDIIEFSRLQAKDVVQDGGPVDLNAVVADAVDRLRL +TAEDRGIALRVGGRVDAVVHGDQDQLMTAVRNLVDNAVRYSPEGTTVGIGLSSVDGLAQV +TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG +RGSTFTIRLPEWGDGVAVDGAPGAAHVTERRGHRVTASAAPPTRKETSA +>PROKKA_00017 +MDPVIIGLLCGAVGLFIGVASMLAFRASERSRTVDLAVGEPTLAPGAAEVLAVVGRAYAV +VDDVDGVVRANPSAYALGLVRGHSLVQQQVKDLTRSVRAEGVIVERRLELPRGPLGQSSL +VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLAEAIGDAA +EDEEAVRRFASRLGIESRRLTALVQDIIEFSRLQAKDVVQDGRAVDLNAVVADAVDRLRL +TAEDRGITLRVGGRVDAVVHGDADQLMTAVRNLVDNAVRYSPEGTTVGIGLSSADGLAQV +TVTDQGIGISPEEQERVFERFYRVDSARSRQTGGTGLGLSIVKHVVINHGGEVSLWSQPG +RGSTFTIRLPEWEDDGAAVDGPPAASHVTERRGHRVTASAASPPRKESSA +>PROKKA_00013 +MDPVIIGLLCGAVGLLIGVASMLAFRASERSRTVDLSVEEPTLSPGAAEVLSVIGRSYIV +VDAVDGVVRANPSAYAMGLVRGHTLVPDALRELTGAVRADGVVRERQVDLPRDPRHQSSL +VVELRVAPLDDEYILVLAEDRTGAMRTEAMRHDFVVNVSHELKTPVGAISLLSEAIADAA +DDDDAVRRFARRLGVESTRLTALVQDIIEFSRLQAKDVVREGRSVDLNLVVAEAVDRVRL +TAEARGISIRAGGHVDTVVHGDPDQLMTAVRNLVDNAVRYSPDGTTVGVGLTSKDGLAQI +TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG +RGSTFTIRLPEWAQAPQTPDAGAPATVATLPERRGHRVAAAAAPARKEHSA +>PROKKA_00327 +MDPVIIGLLCGAVGLFTGVASMLAFRASERSRTVDLTVGEPTLAPGAAEVLSVVGRAYAV +VDDVDGVVRANPAAYALGLVRGHSLVQDQLRELTRTVRADGVIVERRMELPRGPLGQSSL +VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLSEAIGDAA +EDEEAVRRFAARLGVESRRLSALVQDIIEFSRLQAKDVVQDGGPVDLNAVVADAVDRLRL +TAEDRGIALRVGGRVDAVVHGDQDQLMTAVRNLVDNAVRYSPEGTTVGIGLSSVDGLAQV +TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG +RGSTFTIRLPEWGDSVAVDGAPGAAHVTERRGHRVTASAAPPTRKETSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000381.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000381.fa new file mode 100644 index 0000000000000000000000000000000000000000..62e80cc0a8eef4bedcac96bb095c82b7c7cede40 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000381.fa @@ -0,0 +1,25 @@ +>PROKKA_00321 +MSRILIVEDEESFSDPLSYLLEKEGFEVTVAADGNEALSVFERDSADLILLDLMLPGMSG +TEVCRQVRQRSNVPVIMLTAKDSEIDKVVGLELGADDYVTKPYSSRELVARVRAVLRRQG +EQEEPMSATISAGPVRMDVERHVVSVDGEQVSLPLKEFELLEMLLRNAGRVLTRGQLIDR +VWGSDYVGDTKTLDVHVKRLRSKIEPDPSSPRYLVTVRGLGYKFEA +>PROKKA_00036 +MSRILIVEDEESFSDPLSYLLEKEGFEVTVAADGNEALSVFERDSADLILLDLMLPGMSG +TEVCRQVRQRSNVPVIMLTAKDSEIDKVVGLELGADDYVTKPYSSRELVARVRAVLRRQG +EQEEPMSATISAGPVRMDVERHVVSVDGEQVSLPLKEFELLEMLLRNAGRVLTRGQLIDR +VWGSDYVGDTKTLDVHVKRLRSKIEPDPSSPRYLVTVRGLGYKFEA +>PROKKA_00016 +MSRILIVEDEESFSDPLSYLLEKEGFEVAVAADGNEALGVFERDGADLILLDLMLPGMSG +TEVCRQVRQRSNVPVIMLTAKDSEIDKVVGLELGADDYVTKPYSSRELVARVRAVLRRQG +EPEELVSATLGAGPVRMDVERHVVSVDGEQVSLPLKEFELLEMLLRNAGRVLTRGQLIDR +VWGSDYVGDTKTLDVHVKRLRSKIEPDPSSPRHLVTVRGLGYKFEA +>PROKKA_00012 +MSRILIVEDEESFSDPLSYLLNKEGFEVAVAADGNDALEEFERGGADLILLDLMLPGMSG +TEVCRQIRQRSHVPIIMLTAKDSEIDKVVGLELGADDYITKPYSSRELVARVRAVLRRGG +EPEELVTSTVSAGPVRMDVERHVVAVDGEPVNLPLKEFELLEMLLRNAGRVLTRGQLIDR +VWGSDYVGDTKTLDVHVKRLRAKIEPDPSSPRHLVTVRGLGYKFES +>PROKKA_00328 +MSRILIVEDEESFSDPLSYLLEKEGFEVTVAADGNEALSVFERDSADLILLDLMLPGMSG +TEVCRQVRQRSNVPVIMLTAKDSEIDKVVGLELGADDYVTKPYSSRELVARVRAVLRRQG +EQEEPMSATISAGPVRMDVERHVVSVDGEQVSLPLKEFELLEMLLRNAGRVLTRGQLIDR +VWGSDYVGDTKTLDVHVKRLRSKIEPDPSSPRYLVTVRGLGYKFEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000382.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000382.fa new file mode 100644 index 0000000000000000000000000000000000000000..e7cbcf34bd48c27bdb2b426c16bc70a9a2fad013 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000382.fa @@ -0,0 +1,25 @@ +>PROKKA_00322 +MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA +LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE +GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG +EEH +>PROKKA_00037 +MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA +LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE +GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG +EEH +>PROKKA_00015 +MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIEYDASDGINGEEKDFLSYRNLA +LVGDGDSGPARLIGTLENLSDQAQTYTFQAEGGGSATVQVPAGETFKLEDDANQTVLERQ +DAWVGELLPVTVSGNGGQTELEVPLLGATQDHYRDLLPEGVSPSDEELGSHLDEETHDYG +GEH +>PROKKA_00011 +MKSVASRPARRRLAAGALALTAVLGATGCSAVSPVATGIQYSASDGVNATQTGFVEVRNL +GMVGEGASGPARLIGSLKNDSGADKTYTIAVQDGGQITVPVKAGETVKLEEQQLEVERSV +WPGQNAQATVSADGTQLQLGVPVLSATQEQYKEYLPAGQSADTEHLDEQTATYGEGEGEQ +H +>PROKKA_00329 +MKNASRPARRHLAAGALAAVALLGATGCSAVSPIATAIQYSPSDGINGQEQDFLSYRNLA +LVGDGESGPARLIGTVENTSGQDQTYTFQAEGGGSATLKVPAGESRKLEDEANTTVLERE +GVWVGENLPVTVSGNGGTADLAVPLLSATQEQYRDLLPEGVEPSEEDLVGHLHEETHHYG +EEH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000383.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000383.fa new file mode 100644 index 0000000000000000000000000000000000000000..ccbda0ce9e6c22bc715960744a9b82e5e128996d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000383.fa @@ -0,0 +1,21 @@ +>PROKKA_00323 +MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD +VVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQDRGL +SAGEKRMLAKARQVLVSELALAKKVTEEEAEGRLDKVLEG +>PROKKA_00038 +MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD +VVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQDRGL +SAGEKRMLAKARQVLVSELALAKKVTEEEAEGRLDKVLEG +>PROKKA_00014 +MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD +VVDSEGLEEVVEVLQAEQVEEPTNWSRRYKANLEKLASGDVKKVAEVVRDLWRRDQDRGL +SAGEKRMLSKARQVLVSELALAKKVTEEEAEGMLDQVLEG +>PROKKA_00010 +MPDTRGVFRVSVVESTDRKGAFHMVFEVGETVVYPHHGAARIEEIKTRTIKGEEKMYLKL +KVAQGDLTIEVPAENVDLVGVRDVVDDKGLEHVVEVLQAEHVEEPTNWSRRYKANLEKLA +SGDVNKVSEVVRDLWRRDHDRGLSAGEKRMLSKARQVLVSELALAKKVSEEEAEGMLDKV +LEG +>PROKKA_00330 +MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD +VVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQDRGL +SAGEKRMLSKARQVLVSELALAKKVTEEEAEGRLDKVLEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000388.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000388.fa new file mode 100644 index 0000000000000000000000000000000000000000..925e94f1d3de0f72a8ebffeb22b5a11dc6649782 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000388.fa @@ -0,0 +1,69 @@ +>PROKKA_00331 +MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT +VVRAGDGQRVELTHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY +RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSADEAVGTAFAVWAPNARAVRVVGDHN +GWDGRTHAMRSLGSSGVWELLAPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA +SRVLESDYAFGDRTWMERRRVTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG +FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHQAGIGVIVDWVPAH +FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID +GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNMTVYRLHPGVHMIAEES +TAFSGVTAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHGQWTFSMVYAYSENYV +LPLSHDEVVHGKGSLLSRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE +GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFAWVDGGDADGNTLVFL +RMPAAQVVPEPRIDDDGDAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT +DSTDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPHPDSTVTP +>PROKKA_00047 +MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT +VVRAGDGQRVELTHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY +RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSAGEAVGTAFAVWAPNARAVRVVGDHN +GWDGRTHAMRSLGSSGVWELLVPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA +SRVLESDYAFGDRTWMERRRLTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG +FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHRAGIGVIVDWVPAH +FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID +GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNATVYRLHPGVHMIAEES +TAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHEQWTFSLVYAYSENYV +LPLSHDEVVHGKGSLLGRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE +GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFAWVDGGDADGNTLVFL +RMPAAQVVPETRIDDDGAAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT +DATDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPTLDTTATP +>PROKKA_00004 +MLGAHPHPDGAAVTYRVLRPLARTVTVVRTGDGERVELAHEHDGVFAGVARMPRVAGAAA +GDYRLEVAYETADGQTGPAQEQDDAYRHLPTLGELDLHLIGEGRHERLWEVLGARVVRTP +AGEAVGTAFAVWAPNARAVRVVGEHNGWDGRGHAMRSLGSSGVWELLVPGVGHGHRYKFE +ILGRDGRWRQKADPMARWTEVPPATASRVLESEYEFGDRTWMERRRTVDPHERPLSIYEV +HLGSWRPGLDYRELAEQLVEYVQWLGFTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGS +PDEFKHLVDALHRAGIGVIVDWVPAHFPKDEWALARFDGTPLYEHADPRRGEHPDWGTYV +FDFGRTEVRNFLVANALYWLAEFHIDGLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLE +AIDFLREVNATVYRVHPGVHMIAEESTAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLS +QDPVNRRWHHGQWTFSMVYAYSENYVLPLSHDEVVHGKGSLLTRIPGDRRHQLATLRAYY +GYMWAHPGKQLLFMGGEYGQPSEWSEAEGLDWPVSWDESHRGVQLTVRELNALYRSKPAL +WSQDHSPAGFEWVDGGDADGNTLVFLRHPAERVVPEARIDDDGAAVSAAEPGGAPLLCIT +NLSGSPRQGLRVGVPGAGSGPWSWTPTPPTSTGTAGGSRPGSPRC +>PROKKA_00005 +MTSPTLSPQSVDPAVLAAVAEGLHHDPHAVLGAHPHPDGAAVTYRALRPFARAVTVVREG +DAARIELAHEADGVFAGVGALPRKAGVAAGDYRLEVVYPGADGEDVVELHDDAYRHLPTL +GELDLHLIGEGRHERLWEVLGARVRRAADGALVGTSFAVWAPNARAVRVVGDFNGWTGRT +HAMRSLGSSGVWELLVPGVEHGAAYKFEILGADGQWQQNADPMARWTEVPPATASRVMES +EFAFTDRDWMERRRAEDPHERPLSIYEVHLGSWRPGLSYVDLAEQLVEYVQWLGFTHVEF +LPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVNALHEAGIGVIVDWVPAHFPKDAW +ALGRFDGTALYEHPDPRRGEHPDWGTYVFNFGRTEVRNFLVANALYWLGEFHVDGLRVDA +VASMLYLDYSREDGQWTPNALGGNHDLEAISFLQDVNATVYRVHPGILMIAEESTAFSGV +SAPVSAGGLGFGKKWNMGWMHDTLAYLSEDPVNRRWHHDQWTFSMAYAYSENYVLPLSHD +EVVHGKGSLLARIPGDHRQKLATLRAYFAYMWAHPGKQLLFMGGEYGQPSEWSEERGLDW +AASWDESHRGVQLTVRELNALYRAKPALWSADHSPQGFTWVDGGDADGNTLVFLRRPGAG +VEGAPLLCITNLSGGTRQGLRVGVPSSGEWTVVLDTDSTDFHGDGRREQAGQLEVIEAED +GQWQGQPAYLTLNVPPLTTLWLQPDED +>PROKKA_00338 +MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT +VVRAGDGQRVELMHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY +RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSADEAVGTAFAVWAPNARAVRVVGDHN +GWDGRTHAMRSLGSSGVWELLAPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA +SRVLESDYAFGDRTWMERRRVTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG +FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHRAGIGVIVDWVPAH +FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID +GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNATVYRLHPGVHMIAEES +TAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHGQWTFSMAYAYSENYV +LPLSHDEVVHGKGSLLGRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE +GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFSWVDGGDADGNTLVFL +RMPAAQVVPEPRIDDDGAAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT +DATDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPTLDTASTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000392.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000392.fa new file mode 100644 index 0000000000000000000000000000000000000000..8041a44e38150ca1080a53582e679fc701f90794 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000392.fa @@ -0,0 +1,48 @@ +>PROKKA_00339 +MAAAPQAHAVAWDRVELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDD +RASQAFNGRVLERARAEHPDWLSADGQKWADGLVIVALDPDNRLIGVYVGEDRMLSTDQL +RDVREAGHEAARAARWTDTVVEVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAVL +ASRRRRRRRTADLLTEARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRGFRRQAL +DASAELDRLEALPERSLHRTEHARAAEDVRDRARELDRLDDAVAAANTFLNRHPGWPSAW +DQQTAPLRADLDAVGTLASSVGSAGPVRSAVAALESFRAEAQGRLEALGADLQDERLTPA +AALDELDALRRRLTGLVSALADAEVAAFGKDEAERELLRDELRTHRGPARSARGSILDSA +LPTDAYWTVVAFTTGHQAGERSVQDHRQAQSSSSGTGYGSSAGSFSGAGSSGRF +>PROKKA_00055 +MTRPTHRTARRTLAAVALSAAALTGPAAAATVVALPVTAGVTGAVVATAPQAHAVAWDQV +ELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDDRASQAFNGRVLERAR +AEHPDWISADGQKWADGLVIVALDPDNRLIGVYVGEDRTLSTDRLREVREAGHEAARAAR +WTDTVVDVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAALASRRRRRRRTADLLA +EARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRTFRRQALDASAELDRLEALPER +SLHRTEHARAAEDVRDRARELDRLDDAVAAANTFFNRHPGWPAAWDQQTAPLRADLDAVG +TLASSVGSAGAVRSAVAALESFRTEAQDRLEALGADLQDERLTPAAALDELDALRRRLTG +LVSALADAEVAAFGKDEAERELLRDELRTHRGPVRSARGSILDSALPADAYWTVVAFTTG +RQAGERSVQDHRQAQSSSSGTGYGSSGGSFSGAGSSGRF +>PROKKA_02673 +MDEAGVVDPERLRRGLAEVEFREPTRVAVVTERGPDLSGLDDDRAAQAFNGRVLERARAE +HPDWLSADGQTWADGLVIVALDPDNRMLGLYVGEDRSLSTDQLQDVREDGYEAARAAKWT +DALVDVTDSAAELIGRPWWQHPGLWVGAGAVGLVGAGTGAAVMADRRKKQARTQADLESA +RGHLTAVTLELDATEVNASTVPTDSPHAATLLERFRGFRERTLDATAEQQRLEAVPEKDL +HRRKHREAAAALRAQTAELDGLDDAIGAANALLNRHPGWPAAWDLQTAPLREDLDAVAEL +RDAVTDTPSVQAAVAALESFRAEASGRLDALGGDLEAERVTPAAALDELDGLRGRLTSLV +GSVAEAEITAFSDDDEERRILREKLRSRRGTHRAARGSILDCTLPSDAYWTVVAFNAGHR +AGERSVQERREAASSPSSSGTGYGSSGGSFSGTGSSGRF +>PROKKA_02485 +MPEPTAPRPSRLARAPRARLLARAARPLAAAAVAGAALAGAAAPAGVAATAAAVPVAAGA +VVAAPAAHALEWSRVDLADQAGIIDPAQLERDLAGIEFRAPTRVAVFTERGPDIRGLDEE +RKAQAFNGRVLEFARAQRPGWISADGQKWADGLVIVAVDPDNRMLGVYQGEDRKLESGGQ +SAVREAGTDAARDARWTDAVVDMVDEAATRIGRPWNEDPVVWLGLGGGALGVLGAGAGIT +AAVVGPRRSRARRSAEHLEEARHHLTSVTLDWETTELNASTVPLGSRHGARLMERYRGFH +RSALDATARLEELEAAPVKDRSAQSFVDRAGGVRDDVAALDALDDAIADANALLNRLPGW +EDAWDRQVAPLREDLHRVPALHDRLGDVDGTAVPLAALDSFRDEARTELERLGTGLTAQT +VAPDDAIDALERLRRRLTVRIEELARAVAQAQDGRKKQRLMQESLDGQRAVPRDRRGSIL +DAGDGWRTYWTVTAFDAGVDAGDSAVASYESSSSGTGYGSSGGSFSGSGSSGSF +>PROKKA_00346 +MTRPTHRIARRTLTAVALSAAALTGPAASATVVALPVTAGVTGAVVAAAPQAHAVAWDQV +ELVDDAGVIDPAQLRRDLAGIEFREPTRVAVVTERGPDLSALDDDRASQAFNGRVLERAR +AEHPDWLSADGQKWADGLVIVALDPDNRLIGVYVGEDRMLSTDRLREVREAGHEAARAAR +WTDTVVDVTDAAAELIGRPWWQAPELWFGAGIVGVAGGGAAAAALASRRRRRRRTADLLA +EARTHLTSVTLEMDATEVNASTVPEDSPHAAALMERFRNFRRQTLDASAELDRLEALPER +SLHRTEHARAAEDVRDRARELDRLDDAVAAANTFLNRHPGWPAAWDQQTAPLRADLDAVG +TLASSVGSAGPVRSAVAALESFRTEAQDRLEALGADLQDERLTPAAALDELDALRRRLTG +LVSALADAEVAAFGEDEAERELLRDELRSHRGPARSARGSILDSALPADAYWTVVAFTTG +HQAGERSVQDHRQAQSSSSGTGYGSSGGSFSGAGSSGRF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000393.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000393.fa new file mode 100644 index 0000000000000000000000000000000000000000..e6686df1ea8082f56d0a3cc659b9bf7d9deadfc5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000393.fa @@ -0,0 +1,30 @@ +>PROKKA_00340 +MSSSEAAAPAHALPRVVGILGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQ +RHLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLALAGPATRAVVDLTNTWGDE +PVPAWLDDDAAPGTTRIAERWAAAGLRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTE +PADATADPAAVAAARDTVIALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAAL +LADAPTG +>PROKKA_00056 +MSSSEAAAPADALPRVVGVLGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQ +RHLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLTLAGPATRAVVDMTNTWGDE +PVPAWLDDDGAPGTTRIAERWAAAGLRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTE +PADATADSAAVAAARDTVIALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAAL +LADAPIG +>PROKKA_02629 +MSSSEPAAPAALPRAVGILGAGRAGTGVARAIARIPRLSPGLPEVRALVAGTRRPSAVQR +HLTVYAPAAQAVAAEELAARAEVIVVAVPREDLDDVDPLALAGPGVRAVVDMTNTWGEEL +LPAWLEAGPDDAPGTARIAARWAAAGLEVPVVRALSEVSHHDLDVHGRAAAPRRALAVGT +VPAADASDPGAVVAARDAVAALVTAMGFDAVPYEGLERAAVLEPGGAGFGVAHDARELAA +LLGAGPRG +>PROKKA_02484 +MPHDAAPRPDQPAAFESLPASVGILGAGRAGTALARAIARIRVLHPGTAAPRVVLAATRS +PAAVRRHLAIHAPGAEAAHPGDLATDTELTVVAVPREELDEVDPAWLAGPRTLAVVDMTN +TWGDELVPDWLAAAAAPGLPTMPGSAAIAAHWAEAGLTAPVVRAFSEVSHHELDRDGRAQ +PPLRALGVGADSPGPARAAVAALVTAMGFEPVEYAPLARAAALEPGTRAFTRPLPADELA +RELA +>PROKKA_00347 +MSSSEAAPADALPRVVGILGAGRAGTALARAIARIPRLSPGTAAPRVMVAGTRRPAAVQR +HLTIYAPEAVAVSAEDLAAEAELVVVAVPREALDDVDPLALAGPATRAVVDLTNTWGDEP +VPDWLDGDGSPGTARIAARWAAAGVRVPVVRAFSEISHHDLGDAGRATAPRRALAVGTEP +ADTAADPAAVAAARDTVVALVTAMGFDAVPYTGLDRAGVLEPGAAGFGTAHDAGRLAALL +ADAPTG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000394.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000394.fa new file mode 100644 index 0000000000000000000000000000000000000000..2cbc9b8d6f8e5b43ef75f9b5e1e6331042ac8e85 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000394.fa @@ -0,0 +1,30 @@ +>PROKKA_00341 +MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE +MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA +KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR +GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE +LVSYASQLITLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV +>PROKKA_00057 +MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEERRE +MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA +KFAQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR +GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFSADARVLTHVNGELRQEDRVADVVFSPAE +LVSYASQLVTLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV +>PROKKA_02628 +MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPECRDVGEYLTAEPQEQRE +MVESALRAAQEDRSLLLDTSTLVYDTLIPFPTKVFCVGLNYTNHIEETGQNQPEHPTLFA +KFTQSLTGALDPVEVPEEDHLVDYEGELCIVIGEPGRRIAVEDAKEHIAGYAVANDVSMR +GWQGRTSEWLQGKVWEASTPVGPWLVTPDELTADARIITRVNGVERQDDRIADVVFSPEE +LVAYVSQMITLNPGDLIMTGTPAGVAVARKGADGRRPWLQAGDVVEVEITGLGRQRNELV +>PROKKA_02480 +MKLATFRQPDSDASYPGATFAAVLTSFHPQDPQVAVRAVALPECRDVGEFLTAEPQEQKD +MVREALEAAKEDHGLLLDVSTLVYDTLVPFPTKVFCVGLNYADHIRETGQEKPEHPTLFA +KFAQSLTGALDPIEVPEEDHRVDYEGELCVVIGEPGRRIAVEDAKDHIAGYAVANDVSMR +GFQGRTPEWLQGKVWEASTPVGPWLVTADEFPKDARIVTRVNGEVRQDGKVKDVVFSPAE +LVSYVSQLVTLNPGDLIMTGTPAGVAVARRDGDGRRPWLRADDVVEVEITGLGRQRNELV +>PROKKA_00348 +MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE +MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA +KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVADAPEHIAGYAVANDISMR +GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE +LVSYASQLITLNPGDLILTGTPAGVALACRDAEGRRPWLRPDDVVEVEITGLGRQRNELV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000395.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000395.fa new file mode 100644 index 0000000000000000000000000000000000000000..61774c7d0383303647bf016291087afe08aca822 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000395.fa @@ -0,0 +1,35 @@ +>PROKKA_00342 +MSTAPTHPPLDLDPTPATPIVLGTMAWGSVLPPPPDADPGVGPEGPAGEAQAEAAVERAR +RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHETDPA +GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV +GKLGVSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLMEAVVLANHPDAPADA +DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGAVGEVAAELGGSREAVVLAWLLRL +PWDVRPVIGTQDPERVAACAEAAAAAEAMDSAQWHRLWTAARGAGLP +>PROKKA_00058 +MSTAPTHPPLDLDPTPATPIVLGTMAWGSVLPPPPDADPGVGPEGPAGEAQAEAAVERAR +RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHEADPA +GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV +GKLGVSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLVEAVVLANHPDAPADA +DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGVVGEVAAELGVSREAVVLAWLLRL +PWGVRPVIGTQDPERVAACAEAASVAEAMDSAQWHRLWTAVRGAGLP +>PROKKA_02627 +MAWGAAPAPAPAPGEGPALLASAGPEHAEAARERARGALRAGIDAGVDLLDTADIYGAGV +SEETVGALLHELPYEERSALKVQTKCGIVLDEVDADGRPMVRYDSSPEYVRARLEGSLAR +LGELRVDTLVIHRPDVLTPVADTVRAFLDAREEGLVGKLGVSNLGVGRTLEFQRELAAQS +ADGTGLACVQVELGLHHRTLVESVILANHPGAAADADVADLGRVCAAEGIELQAWGSLGQ +GRFSSGDDGAAGVVGEIARELDTSREAVVLAWLLRLPWGVRPVIGSQDPGRIAACADAAA +AAEAMDSAQWHRLWTAARGAPLP +>PROKKA_02479 +MTAQDTAPQTPAASPLILGTMGWGDVERARGALRAGLEAGIGLLDTADIYGAGASEETVG +ALLAELDPAERTRLRVQTKSGIVLHEPGPDGTPAVRYDNSPAYLHERLALSLERLGLDRV +DTLVVHRPDVLTPVSDTVRAFLDAREAGRVDALGVSNMGTRRVLEYQHALREVSADGTGL +ACVQVELGLHHRMLVESVVLANHPAAAPDGGAGDLGEVCAGEGIEIQAWGPLGQGRFTRG +SDGTVPADPAEQAALAAAGGAPAVVARVARELEVSREAVVLAWLLRLPWGVRPVVGTQDP +ARIASCAQAADAAARMDGAQWHRLWTAARGETLP +>PROKKA_00349 +MSTAPTHPPLDLDPTPATPIVLGTMAWGSVPPPPPDADPGAGPEGPAGEAQAEAAVERAR +RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHETDPA +GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV +GKLGLSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLVEAVVLANHPDAPADA +DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGVVGEVAAELGVSREAVVLAWLLRL +PWGVRPVIGTQDPERVAACAEAASVAEAMDSAQWHRLWTAARGRPLP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000396.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000396.fa new file mode 100644 index 0000000000000000000000000000000000000000..b12f19aa40ad40dad2a05963a971ff0a65a326fb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000396.fa @@ -0,0 +1,20 @@ +>PROKKA_00343 +MTFEPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADAHGRNTEVDVLDNTRL +QRRVGAVMLAVAAVLAGVGVWTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP +DGTVLRDEMVLVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP +>PROKKA_00059 +MTFAPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADEHGRNTEVDVLDNTRL +QRRVGAVMLAVAAVLAGVGVGTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP +DGTVLRDEMVLVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP +>PROKKA_02626 +MAFERVDLTTPWLAYWAALLALVIGAALLAAGIWRERRHRRHAAAHGRNTEVDVLDNTRL +QRRVGVVGLVAAVVLAGVGVWTHLAGLDALRQNLTAKYGYTDVERIRQSGTGFIIDLTQP +DGTVLKDEMVLVDPSGEPFIGDDIFIDVIGGA +>PROKKA_02478 +MTFAPVDLQTPWLLYWAAAVAAVVGVSLALAGRWRERDHRRRQAAAGSHVVMRVLENTRL +QRRVGYGALVLALALAVWGAVAHVQGIDALRGNVRQKYGAEVEDVRQSGSGVTVDLVHPD +GTREEDQYMAVEQDGEPVYGAELVESPPIGG +>PROKKA_00350 +MTFEPVNLFTPWLAYWAAALALVVGGILLAAGIWRERRHRRHADEHGRNTEVDVLDNTRL +QRRVGAVVLAVAAVLAGVGVWTHLAGLDTLRQNLTAKYGYTSIERIRQSGTGFIIDLTQP +DGTVLRDEMVVVDPSGEPFVGEDIFHNPPEKYEDLPLRPAP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000398.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000398.fa new file mode 100644 index 0000000000000000000000000000000000000000..72cdee7eee829f4b8561ce12c2c84fcb0004c671 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000398.fa @@ -0,0 +1,45 @@ +>PROKKA_00346 +MDTVETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV +RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV +TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG +FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV +ASYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH +AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV +PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT +TTMLRAVPPADAD +>PROKKA_00062 +MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV +RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV +TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG +FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV +ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH +AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV +PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT +TTMLRAVPPADAD +>PROKKA_02623 +MSERIVTVDTVETPSPDDRLTVTGAPSGDASEDPATALLALPWSTALEDWPEDVLAALPR +GISRHVVRFARVGGGVVAVKETTEDLAFREYRLLRRLEGSPAPSVVPVAVVTGRTDGRGE +PLPAALVTRYLHFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVL +FRRDAGGFAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPA +ATPELFVDAYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMML +AAPVEVHAGYHRRRLTRLTGLQVQENQARRLLVDIEAARRAWDPFLDLEGAAHRWVVEVF +DPVVRSVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRVRRDED +AVALHPTTTMLRTVPPADED +>PROKKA_02475 +MDEHEQPRTDPADRLTVTAAPSGDASEDPATSLLALPWERPLEDWPAEVLAALPRGISRH +VVRFARMGAGVVAVKETTEELAFREYRLLRELEDRPSPSVVPVAVVTGRTREDGTALPAA +LVTRHLRFSLPYRAVFSERMERRTLVRLMDALALLLVELHLEGFFWGDVSLSNVLFRRDA +GGFAAHLVDAETGELRERLSTGQREHDLDVARVNIGGELLDLHASGLADPDVDAIATPDL +FVESYRQLWQQLTEPTVFPRGEPWRMDRRFRRLTELGFEVEEYSLRAADAPGMMVAQPTD +VNSGYHRRRLERLTGLHVQENQARRLLVDIEAARRSWDPFMDMDHAAHRWVIEVFDPVVR +SVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLDEAVDSYVETVLRARRDEDALALH +PTTTMLRAVPAPEADPEG +>PROKKA_00353 +MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV +RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV +TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG +FAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV +ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH +AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV +PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT +TTMLRAVPPADAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000399.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000399.fa new file mode 100644 index 0000000000000000000000000000000000000000..983debf6a3ba2272fa94b29ffc7ab52ccc6f0cf1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000399.fa @@ -0,0 +1,30 @@ +>PROKKA_00347 +MARNTSGSHTSATDARARARQIQEEQRRKDRRRRTGVIWGSVLAAVLVIGLVVAFALTRN +GDDAAAAGPIPAAANEQGGIELTSATGLAEGAGEREVDPSEIEVPKQAASSQPETLPNTE +ARGDGEPTRIVLYADFNCVHCADFESSNAEQIEQWLEQGEVTVEYRMVDFLSAPNNQNYS +ARAANAAYCVADQKPEAYNGFVAALFAAYDEHQGKGLDNAALTQLAQEQGVDISSCVEDG +TFRSAVEHTTRQARVAGVAGTPTVFVDGKNWALDGEDKTFTDWAGAKIAD +>PROKKA_00063 +MARNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNRN +GDDAAAAGPIPAVANEQGGIELTSATDLAEGAGEREVDPSKIEVPKQAASSQPETLPNTE +ARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNNQNYS +ARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASCVEDG +TFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG +>PROKKA_02622 +MARNTSGSHTSATDARARARQIQEQQRKKDGRRRTAVIWGSVLAAILVIGLIVAFALNRG +GDEPAAAGPIPAAANEQGGIELTSATTLAEGAGAREVDASTVEVPEQGAAQQPETIPAAE +APAEGEPSEIVLYADFNCVYCADFETSNAAQIEQWLEAGEVTVEYRMVDFRSAPNNQNYS +ARAANAAYCVADQKPEAYNGFVTALFGTYQEHGGKGIDNAALTQLAQDNGADIASCVEDG +TFRSAVEHTTRQAQAAGVGGTPTVFMDGENWAIGGPDQSFQEWAQSKISG +>PROKKA_02474 +MASRNPAPSEVDARARARQMQVDQQKKARRRRTATIWGAVLAAVLVIGLIVGFVVKGNQG +TEISATGPVPGVVNEEGGVEMTSATALADSGKSERQVDSSSVAVPETATAPEELTTIPAA +GEPADGEPAQIVVYADFNCVHCAEFESQNSEQLQSWLRDGKATVEYRMVNFLSAPNNKNY +SARSANAAYCVAAAKPEAYNEFTTGLFMAWEGHGGKGLSDDELIQRADALGVDIEGCLKD +NTYRPAVEWATNKAKAASVAGTPTVFVNGKNWSTDGGDKSFVDWAKPMVEG +>PROKKA_00354 +MARNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNRN +GDDAATAGPIPAVANEQGGIELTSATDLAEGAGEREVDPSKIEVPKQAASSQPETLPNTE +ARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNNQNYS +ARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASCVEDG +TFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000401.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000401.fa new file mode 100644 index 0000000000000000000000000000000000000000..bfce0934278c1a81f1f9e9f11038f0bf55a06cc5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000401.fa @@ -0,0 +1,59 @@ +>PROKKA_00351 +MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES +AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL +SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL +PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV +ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH +RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG +MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL +PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT +LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAV +AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN +AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG +>PROKKA_00067 +MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES +AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL +SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL +PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV +ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH +RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG +MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL +PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT +LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGVGFGAYLAAQQVGVSDRLVPAV +AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN +AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRR +>PROKKA_02610 +MLAPADADGALPAPDVLPEPDVTVPDPVVPVGPPEKRGRRRGRKAREVFVENLPTQALVL +ADRLHSSPYGRRMRSTLQQRREAETHALEARTTLDFALKLGETMFSFGAASLDVETSIIV +VTQAYGILETEVDLTNQSISLNYAPDSSRGESPYTLQRVVRSSSVNFEGLVAVHRLVEEI +ADGRLDRAEAQRRLVEIRHQPKPFPPVFEILFAGVFVACFIPFIGGNWTGSLLGMISTWL +VFWLKIQADRARFPEIFSTMFGAIVATVIALAAFALELPVNPAVVIAGGIMMLLPTARFV +TAVQDAINGFPVTAAGRFLSALLVFTGVMAGIMVAVALGDLAGLEHLDLAEAGTLQHPPL +LLLALVTAAGMSDAVVEQSRWPQILACGLVSGAGYGVFLAAQQLGIGDRLVPAAAATAVG +FLGRLVAQRIAAPALVIVLPSMLFLLPGLMMFRSVYGFTVETGSTLLGLAGLFNAAVIVV +AIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG +>PROKKA_02469 +MGAEPRRGPAQGTGPLGPDRNPRKDPVRSVDPLAPQDGSPEDGGVPQGARRAGTRPDAAG +SAPAEPAVHVALLPVLRPADARTPAGASDGDAPAGDGVDLAAAPAREPGPEDVLPPVLAP +VAAPTVPVETLPTPEPAPAPEEEPTPAADAPLTAPPLSEPVPTSVLAPAEGDAPTAQEAA +AAVPDVVVPDPLKQHGPEEPRGRRRRRRTREDHRAVFEEVLPTQAIVLVDRLQASPYGKR +MRSTLRQRRDTEAAALEARTTLDFALKLGETMFGFGATSLDVETSIIVVTQAYGIHETEV +DLTNQAISLNYAPDSSRGEVPYTLQRVVRTYSTNFEGLVAVHRLVEEISDGTLERAEAQR +RLVEIRRRPKPYPPAVEILLAGVFVACFIPFIGGTWQGSLLGMVSTWFVFWLHTRTSVFL +PEIYSVMIGAFLATLIALGAYALHVPVNPAIVVAGGIMMLLPTSRFVTAVQDAINGFPVT +AAGRFISAMLVFIGIMAGIMVAVGLTDMLGIARLDLAATQSTAYPTTLLLALVVAATACD +AVVERSGWRTLLASCAVTAAAFAAHTVVAGLGVSAQLLPAAAAAMVGFAGRIVALRVGAP +PIVVVVPAILFLLPGFAVFRGLYEFTVESASTMAGLAGIVNALVIIVGIGAGAVFGDTLA +RPVTERLSPARSTPGPEGHTR +>PROKKA_00358 +MEQEGTQEPARFDPRIAEPPAVPTLIPVLRPAGAEDAAAVGDLAIDPEDPGLLDLDPAES +AHPAAAAVAVEPTEPLPPVVRPAAADPEPEPEEPAEPEAETLPEPAADAPLTEPPLSEQV +PTSVLAPADADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENLPTQA +LVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDVETSI +IVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVHRLVE +EIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALGMVST +WLVFWLKVQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLLPTAR +FVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLLGFEQLDLAEAGTLSYP +PLLLLGLVMAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAVAAAA +VGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFNAAVI +VVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000403.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000403.fa new file mode 100644 index 0000000000000000000000000000000000000000..aecb7d5cc683135e517d6df2702c9dedb930c7a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000403.fa @@ -0,0 +1,15 @@ +>PROKKA_00353 +MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLSPT +AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN +>PROKKA_00069 +MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLPPT +AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN +>PROKKA_02608 +MPTSAPEPRRDALTPQERAVLDLEAATWRHGGAKDHAVRERLGLSPTAYYQVLNGLLDRE +AALAYRPLLVARLLRKRGTRSRARRAPADPAPSTPASRQEN +>PROKKA_02467 +MPDADPRPAAPADGPEPTPQDELTELEEAVLALEAQTWRHGGAKDHAIRERLQITPTAYY +QVLNGLLERRAALARQPLLVSRLARSRGTRSRARRRPAPENSAPPASPQER +>PROKKA_00360 +MSHPTPVSPDPAPDEGARARARRDELTDLERAVLDLEAATWRYGGAKDHAVRERLGLPPT +AYYQVLNGLLDREAALAYRPLLVTRLLRKRGTRSRARRGPADPAPSTPASRQEN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000405.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000405.fa new file mode 100644 index 0000000000000000000000000000000000000000..e3a419e7c15bce74ac8b19d32ed31484b322affe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000405.fa @@ -0,0 +1,35 @@ +>PROKKA_00356 +MTVLIDPPAWPAHGTVFSHLVSDASLEELHAFARAAGLSERAFDRDHYDVPAHRRAELVA +RGAVPVTGRELVRRLAASGLRVPARSRAEKRDVVLARRWARLFEGTAASPDAVTTAGRDL +LARWAEPHRHYHDPAHLLAVLESVDLLERAGAKAGPDPRAVRLAAWFHDAVYAGDPTAPA +GQDEADSAALARDVLTDPRLAVPADVVDEVARLVLLTAAHDPAPHDAAGAVLSDADLEVL +GRSPEAYARYVAAVRQDYAHVCDADWARGRGAVLDALLDAERLYRTAPGRTRWEAAARRN +LAAERAALSA +>PROKKA_00072 +MTVLIDPPAWPAHGTVFSHLVSDASLEELHAFARAAGLSERAFDRDHYDVPAHRRAELVA +RGAVPVTGRELVRRLAASGLRVPARSRAEKRDVVLARRWARLFEGTAASPDAVTTAGRDL +LARWTEPHRHYHDPAHLLAVLESVDLLERAGAKAGPDPRAVRLAAWFHDAVYVGDPAAPA +GQDEADSAALARDVLTDPRLAVPADVVDEVARLVLLTAAHDPAPHDAAGAVLSDADLEVL +GRSPEAYARYVAAVRQDYAHVSDADWARGRGAVLDALLDAERLYRTAPGRTRWEAAARRN +LAAERAALSA +>PROKKA_02605 +MTVLIDPPAWPAHGTVFAHLVSDASLEELHAFARAAGLPERAFDRDHYDVPAHRCEELVA +RGAVPVSGRELVRRLVASGLRVPARGRAEKRDAVLARRWAALFEGTGARAEAVDAAGRDL +RERWAQPHRHYHDRSHLLAVLEAVDLLERAGADPGPEPRAVRLAAWFHDAVYAGDPAAPA +GQDEADSAALAARMLAAPALAVPAAVVGEVRRLVMLTASHDPAPQDAAGALLCDADLEVL +GRSPEAYRRYVQAVRRDFAHVPDADWARGRAAVLESLLGAERLYRTAPGRARWEAAARRN +LEAELADLRP +>PROKKA_02464 +MAVLIDPPRWPAHGTVFSHLVSDASLEELHGFAAAHGLSPRAFDLDHYDVPAHRHAELVA +AGALAVDGGELVRRLIRSGLRVPARRRDGRAEPVLRRRWARLFAGTDASPDAVTAAGAEL +LGRWSEPHRRYHAPAHLLAVLQAVDLLSAAGEDLGPHPLAVPLAAWLHDAVYTADPARGP +GADEEDSARLAERLLAAPGLALGDDVVAETARLVRLTAEHRPAPDDAAGAVLCDADLEVL +GRAPHDYEAYVDLVRADFAHVPDEAWRTGRAAVLEGLLGADRLYATAAGRARWEDPARAN +LERELAAHRPALS +>PROKKA_00363 +MTVLIDPPAWPAHGTVFSHLVSDASLEELHAFARAAGLSERAFDRDHYDVPAHRRAELVA +RGAVPVTGRELVRRLAASGLRVPARSRAEKRDVVLARRWARLFEGTAASPDAVTTAGRDL +LARWAEPHRHYHDPAHLLAVLESVDLLERAGAKAGPDPRAVRLAAWFHDAVYVGDPAAPA +GQDEADSAALARDVLTDPRLAVPADVVDEVARLVLLTAAHDPAPHDAAGAVLSDADLEVL +GRSPEAYARYVAAVRQDYAHVSDADWARGRGAVLDALLDAERLYRTAPGRTRWEAAARRN +LAAERAALSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000406.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000406.fa new file mode 100644 index 0000000000000000000000000000000000000000..c7e5abe416ca4ed58fd7880ab73b6f894beaf244 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000406.fa @@ -0,0 +1,15 @@ +>PROKKA_00357 +MSIVQIDVEDLRAKSGAVEGSIGRLQAEVSTMEANLRQLQDTWRGQAAANFQGVLTEWRA +TQQRVEESLAGIRRAMDAAATQYQDAETANAAMFRF +>PROKKA_00073 +MSIVQIDVEDLRAKSGAVEGSIGRLQAEVSTMEANLRQLQDTWRGQAAANFQGVLTEWRA +TQQRVEESLAGIRRAMDAAATQYQDAETANAAMFRF +>PROKKA_02604 +MSIVQIDVEDLRAKSGAVEGSIGRLQAEVGAMEAHLRQLQDTWRGQAAANFQGVLTEWRA +TQQRVEESLAGIRRAMDAAAQQYQDAEAANAAMFRH +>PROKKA_02463 +MTIVQIDVEDLRAKSGAVEGSIARLQTEVNTMEANLRQLEGTWRGQAAANFQGVLTEWRA +TQARVEESLGGIRRAMDLAATQYSDTEAANAAMFRL +>PROKKA_00364 +MSIVQIDVEDLRAKSGAVEGSIGRLQAEVSTMEANLRQLQDTWRGQAAANFQGVLTEWRA +TQQRVEESLAGIRRAMDAAATQYQDAETANAAMFRF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000409.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000409.fa new file mode 100644 index 0000000000000000000000000000000000000000..1a897ab57a48483b49a3d1defe7710a0728c0170 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000409.fa @@ -0,0 +1,20 @@ +>PROKKA_00361 +MPTGRIKFYDSTKGFGFAQTDEGEEVHVPASALPAGVTELRGGTRVEFGVAEGRRGKQAL +SLRVLDAAPSVVRNHRPGATEMAVLMEDLITWLDQASNGLRRGRYPQRAQAQKMAQVLRR +VADDLEA +>PROKKA_00077 +MPTGRIKFYDSTKGFGFAQTDEGEEVHVPASALPAGVTELRGGTRVEFGVAEGRRGKQAL +SLRVLDAAPSVVRNHRPGATEMAVLMEDLITWLDQTSNGLRRGRYPQRAQAQKMAQVLRR +VADDLEA +>PROKKA_02600 +MPRRTAAPAPDPADPRRAHGSPGRRRDAGDTDDEEQVPHMPTGRIKFYDSAKGFGFAQTD +EGEEVHVPSSALPAGVTELRGGARVEFGVAEGRRGKQALSLRVLDAAPSSVRNHRPRPAE +MAVLMEDLIRWLDETSNGLRRGQYPQSGQAKKMAQVLRRVADDLEA +>PROKKA_02459 +MPTGRIKFYDSAKGFGFAQTDDGEEVHVPAAALPAGVSDLRSGTRVELGVAEGRRGKQAL +TVEVLDDAPSVVRNHRPSPEKMAVLMEDLIKVLDQTSNGLRRGRYPQRAQAQKIAAVLRR +VADDLEA +>PROKKA_00368 +MPTGRIKFYDSTKGFGFAQTDEGEEVHVPASALPAGVTELRGGTRVEFGVAEGRRGKQAL +SLRVLDAAPSVVRNHRPGATEMAVLMEDLITWLDQTSNGLRRGRYPQRAQAQKMAQVLRR +VADDLEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000410.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000410.fa new file mode 100644 index 0000000000000000000000000000000000000000..be43902a91eedb9dff1294badbd34066ab390202 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000410.fa @@ -0,0 +1,20 @@ +>PROKKA_00362 +MTTHDDAPRVDHRSPDAEPAEERTAVPPARGRAPRRDELLAADVDTARAGLAGLAAPDEV +GEHVDVLVDDDRLLTHRFACRLPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLVAP +PWVPYAERVNEEERERLKAVAEGRVPGAPAPDAEGDGTPEAAARG +>PROKKA_00078 +MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD +EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLV +APPWVPYAERVNEEERERLKAVAEGRVPGAPAPEAEGDGTLGAAALG +>PROKKA_02599 +MTDREDATPVEQEQAAPAAEEAVVKAPPARRRAPRRDDLLAAAVDEARAGLAGLAAPEEV +GEHVDVLVDDDRLVTHRFESRLPGYAGWLWYATIARAPRSRLVTVCETGLVAGEGALVAP +PWVPYAERVSEEERERLRAVAEGRVPGAAAPAGQPAPEGDGKG +>PROKKA_02458 +MTEHSDTPGQTDTSGQTHTPEQAPAVAPAGPAADAAPAASARAPRRRAPKRDELLAAAVD +EARAALTELAEEGQVGPHLGVTVDDDRLMTHRFAAEVPGYTGWVWYSTIARAPRAKKVTV +CETGLEAGEGAVVAPAWVPYADRVSAEERERLAAVAEGRVPDAG +>PROKKA_00369 +MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD +EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGALV +APPWVPYAERVNEEERERLKAVAEGRVPGAPAPETAPDDRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000411.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000411.fa new file mode 100644 index 0000000000000000000000000000000000000000..f1dc5e7377db0166ee1bc0cec27afef62d864f5a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000411.fa @@ -0,0 +1,40 @@ +>PROKKA_00363 +MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVARVRS +GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA +PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVVAPVVRPAGIDEDALVVVDATSAAG +GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPAFLDLATAVE +NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPYV +ARPEDRSAVICTVDFSDDVDAAAVAQVLRANGVVDVEPYRKLGRNQLRIATFAATEPEDV +AALLRCIDHVVERLG +>PROKKA_00079 +MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVARVRS +GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA +PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVMAPVVRPAGIDEDALVVVDATSAAG +GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVTEIKESGRWIPAFLDLATAVD +NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPFV +ARPEDRSAVICTVDFSDDVDAAAVAQVLRANGVVDVEPYRKLGRNQLRIATFAAIEPEDV +AALLRCIDHVVERLA +>PROKKA_02598 +MAAPAEITLPQDLLPADGRFGAGPSKVRSEQLQALQDAAGLLGTSHRQKPVKDLVASVRA +GVAELFSAPEDYEVILGVGGSTAFWDAAAFGLVRERAQHLSFGEFGSKFAKATDKAPFLG +ASDIRTAEPGSRPEPEAVAGVDVYAWPHNETSTGVMAPVARPEGIDEDALVVIDATSAAG +GLDVDVSQADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPDFLDLSTAVD +NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLAAMAARTADSSSRVYAWAEASSYATPYV +ARPEDRSGVICTVDFSDDVDAAAVAKALRANGVVDVEPYRKLGRNQLRIATFAAIDPEDV +SALLRCIDHVVEQLG +>PROKKA_02457 +MTDPTAITIPPEMLPQDGRFGAGPSKVRPEQLQALQEAAGLLGTSHRQKPVKDLVASVRA +GVAELFSVPEGYEVVLGVGGSTAFWDAAAFSLVRSKAQHLSFGEFGSKFARATDNAPFLE +ASDIRSSEPGTRPQPEAVPGVDVYAWPHNETSTGVSAPVVRPEGIDDDALVVIDATSAAG +GLDVDVSQADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPEFLDLSIAVD +NCLKDQTYNTPALATLVMLDAQLRWMNANGGLGFTTGRTADSASRVYAWAEASEHATPYV +ADPAERSNVICTVDFDDAVDAAAVAQALRANGVVDVEPYRKLGRNQLRIATFAAIDPEDV +TALLACIDHVVARLG +>PROKKA_00370 +MTSPAEITIPQDLLPADGRFGAGPSKVRPEQLSALQDAAGLLGTSHRQKPVKDLVASVRS +GVAELFSAPEGYEVILGVGGSTAFWDAAAFSLVRERAQHLSFGEFGSKFAKATDQAPFLA +PSDIRTSEPGTRPEPEAVAGVDVYAWPHNETSTGVMAPVVRPAGIDEDALVVVDATSAAG +GLPVDVSEADVYYFAPQKNFASDGGLWLALFSPRALARVAEIKESGRWIPAFLDLATAVE +NSLKDQTYNTPALATLVMLDAQLRWMNGQGGLDAMTARTADSSSRVYAWAEASSFATPFV +ARSEDRSAVVCTVDFSDDVDAAAVAQALRANGVVDVEPYRKLGRNQLRIATFAAIEPEDV +AALLRCIDHVVERLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000414.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000414.fa new file mode 100644 index 0000000000000000000000000000000000000000..a3c9fe31504564ab55b79d5651e0394c8a8a9c81 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000414.fa @@ -0,0 +1,26 @@ +>PROKKA_00368 +MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVHVREDLAAAAEREGSPAIPVSALIVTT +LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV +IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA +ALTLTRWVLLALLALAVAVMLWAGRRRRRGPAARED +>PROKKA_00084 +MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVNVREDLAAAAEREGSPAIPVSALIVTT +LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV +IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA +ALTLTRWVLLALLALAVAVMLWAGRRRRGRATRAA +>PROKKA_02593 +MRGRGPALLDPAPGRQTGTGLGGWSAEVPPLSQKPRKPRKSRPSRASQSGARSGSSAARA +AGGAERARPTLRDLNIREDLAAAGRQEGSPAIPVSALIVTTLLVGAYLHLLVLQQMTQLT +GGLAMPDSMLFYGQDHVRALSAVMDDAARGQLNWVHKTAGVIFPIAVALTLAAVGAWRLR +PAAAKWGALGVGVLFAVVDIAENIAIEQAIAAGGPGTGLAAALTLARWVLLALIALAIVV +MLWAGRRRREPAARRR +>PROKKA_02452 +MSKKQKKSRPARTGSSAAPTAEPRRAGLHDVSPRADLADAAQQEGSPAMLITALIGTTLF +IGAYFHLLVLQQMTQLTGGLAMPDSMLFYGQDHVAALSAVMDDAARGQLNWVHKTAGVIF +AVAVALTVAAVGAWRLKPVAAKWGALALGVLFAVVDIWEGLAIEAAIAAGGPGTGLAATL +TAIRWVLLAVITVAVVVMLWAGRRRRPRT +>PROKKA_00375 +MSQKSRKSRPRPSRPAARPVAESPRSRPTLRDVNVREDLAAAAEREGSPAIPVSALIVTT +LLVGAYLHLLVLQQMTQLSGGLAMPDSLLFYGQDHIRALSAVMDEDARGQLNWVHKTAGV +IFPIAVALTVTAVGAWRLRPVGAKWAVFGLGVLFAVVDICENIAIEQAIAAGGPGTGLAA +ALTLTRWVLLALLALAVAVMLWAGRRRRGRATRAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000415.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000415.fa new file mode 100644 index 0000000000000000000000000000000000000000..df439d43e10051118fbf2cca4e7b4bd0d441c633 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000415.fa @@ -0,0 +1,79 @@ +>PROKKA_00370 +MADLFSALGRTHLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGVDARPAAPSHTPE +SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN +KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT +TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL +RQANALDFDDLIGVTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAG +DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILD +AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV +AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI +LNEPKRGIGDRAEGAVAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ +VAESAGPATVLEAVLEQSGMLAALRESEDVQDESRADNLGELVAVVRSFETTHPDGTLSD +FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH +ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPETLID +WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS +AVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR +LLLRYAPLTKVEG +>PROKKA_00086 +MADLFSALGRTPLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGEDARPAAPAHTPE +SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN +KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT +TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL +RQANALDFDDLIGMTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLSGPAD +DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAATIKLEQNYRSTQTILD +AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV +AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI +LNEPKRGIGDRAEGAVAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ +VAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRSFETTHPDGTLSD +FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH +ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPEALID +WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS +AVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR +LLLRYAPLTKVEG +>PROKKA_02592 +MPTAVTRAAADPEAWGGDPESWGRDAAPAHTPDSLVAGLNPQQSAAVTHTGAPLLIVAGA +GSGKTRVLTHRIAWLLATGRARPHEILAITFTNKAAAEMRERVSGLIGPTAQRMWISTFH +SSAVRLLRNEAANIGLKSTFTIYDSADSLRLVTTIAKLHELDPKRFAPKALLNRISSLKN +ELVEADDYASTVAEGDPWGRAVAAVYRDYTARLRQANALDFDDLIGMTVHMFEAFPRVLD +NYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAGEPEGVDTPGGELTVVGDSDQSIYAFRG +ADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILDAANAVISNNPDRRKKDLWTAEGAGAAI +VGYAAENESAEAEWIASTIDRLQDEDGIRPADVAVFYRTNAQSRALEERLVTRGIPYRVI +GGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRILNEPKRGIGDRAEGAVAAWAERNRTTF +SAALRDAEHAPGMATRSLKAVNGFVQMMDDLAQVAESAGPATVLEAVLEQSGMLAALRES +EDLQDESRADNLGELVAVVRSFEKTTPDGTLSDFLEQVALVADADQLPTAPDVEGESLAE +AQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPHARSMTDEKELAEERRLAYVGLTRARRR +LFLTRAEARSLWGQHQFNPPSQFLGEIPEALIDWEREGAVRSAGSLSLTGAGTSRYAGRF +GSGGGRPAWRSRDDDGGARPQRLTRGDEPTDLTVPSAVVRGRAPSRVQPQKEIVALSPGD +RVSHATFGQGRVDAVAGAGDKTVATVTFEDSGAQKRLLLRYAPLTKVED +>PROKKA_02451 +MADLFSSLGRDPLFAPRTRPADPETALPGLVPTAVTRAADPEAGAWGAGRDAGAPSAGPL +TPEGLVEGLNPQQAAAVQHTGSPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEVLAIT +FTNKAAAEMRERIAGLIGDTARRMWISTFHSSCVRILRNEAANIGLKSTFTIYDSADSLR +LVTQIAKVQDLDPKRFAPKALLSRISALKNELVDPEDHASRVAEGDPWGRAVAAVYTEYT +ARLRQANALDFDDLIGMTVHMFEAFPRVLDGYRRRFRHVLVDEYQDTNHAQYRLIRLLSG +PAGEPEGVDTPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAATIKLEQNYRSTQT +ILDAANAVIAHNPDRRKKDLWTAEGEGPRIIGYAAENESAEAEWIASTIDRLQDEEGIRP +ADVAVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNV +RRILNEPKRGIGDRAEGAVAAWAERNRVPFFTALRDAENAPGMATRSLKAVQGFVQLMDD +LAQVAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRAFEKGTPGGT +LTDFLEQVALVADADQLPAAPDVEGEELAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGV +FPHSRSLTDEKEMAEERRLAYVGITRARRRLHLSRAEARSLWGQHQFNPPSQFLGEIPDE +LIEWERAGTDRSFGGLTSLAGAGTSRYANRFSGGGSGSARRGSMTGAWGDRAAGGVGGGL +ASNRPQRLTRGEEAADLTVPSSVVRGRAPSRVQPQKEVVALSAGDRVEHATFGAGRVDAV +AGTGDKTVATVTFDATGAQKRLLLRYAPLTRVEG +>PROKKA_00377 +MADLFSALGRTPLNLDRTRRPADPETALPGLVPPAVTRAAADPEAWGEDARPAAPAHTPE +SLVAGLNPQQAAAVTHTGAPLLIVAGAGSGKTRVLTHRIAWLLATGRARPHEILAITFTN +KAAAEMRERVAGLIGPTAQRMWISTFHSSAVRLLRNEAANIGLKSTFTIYDSADSLRLVT +TVAKQHELDPKRFAPKALLNRISSLKNELVEADDYAATVAEGDPWGRAVAAVYRDYTARL +RQANALDFDDLIGMTVHMFEAFPRVLDNYRRRFRHVLVDEYQDTNHAQYRLIRLLAGPAG +DPEGVETPGGELTVVGDSDQSIYAFRGADIRNIVEFEQDFTDAVTIKLEQNYRSTQTILD +AANAVIERNPDRRPKRLWTAEGEGPAIVGYAAENESAEAEWIATTIDRLQDEDGIRPADV +AVFYRTNAQSRALEERLVTRGIPYRVIGGTRFYDRKEIKDALAYLRVIVNPDDDVNVRRI +LNEPKRGIGDRAEGAIAAWAERNRSTFSAALRDAENAPGMAARSLKAVRGFVQMMDDLGQ +VAESAGPATVLEAVLEQSGMLAALRESEDLQDESRADNLGELVAVVRSFETSHPDGTLSD +FLEQVALVADADQLPTAPDVEGEALAEQQGQVTLMTLHTAKGLEFPVVFLTGMEHGVFPH +ARSMTDEKELAEERRLAYVGLTRARRRLFLTRAEARSLWGQHQFNPPSQFLGEIPEALID +WEREGTTRSAGSLSLTGAGTSRYAGRFGGGRPAWRSRDDDGARPQRLTRGDEPADLTVPS +GVVRGKAPSRVQPQKEIVALSPGDRVSHATFGEGRVDAVAGAGDKTVATVTFDATGAQKR +LLLRYAPLTKVEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000426.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000426.fa new file mode 100644 index 0000000000000000000000000000000000000000..bab43e81a8b259c2101212d30c263c75144ab48b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000426.fa @@ -0,0 +1,25 @@ +>PROKKA_00384 +MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV +TLCQVLGASPGDVLDAPEVTVVRLADAPAVNLGGEGIRERLITPRGSRDLQILRADIAPR +GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV +VLWTLVGHA +>PROKKA_00108 +MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV +TLCQVLGASPGDVLDAPEVTVVRLADAPAVSLGGEGIRERLITPRGSRDLQILRADIAPR +GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV +VLWTLVGHA +>PROKKA_02571 +MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV +TLCQVLGASPGDVLDAPEVTVVRLSDAPAISLGGEGIRERLITPRGRRDLQILRADIAPH +GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTLPGREPHSWANPDDRPAI +VLWTLVGHA +>PROKKA_01754 +MKSLPLHPTPTTPQVGRRLRALREQARISLADLAQVTGLSKGFLSRVERDLTSPSVASLV +AVCQALGTSPGHVLDAPEVTVVRGGEAPAISLGGQGITESLLSPPGLRPLQVIRAEIAPG +GTGEDELYTVDCEVESVHVVSGRLTLRTVDGAHALAAGDTATFSGQEPHSWQNPDPDSPA +LVLWILAGRT +>PROKKA_00390 +MKALPLETAPGQALIGRRLRALREARRLTVAQLAEAAGVSKGFLSRLERDLTSPSVSTLV +TLCQVLGASPGDVLDAPEVTVVRLADAPAVNLGGEGIRERLITPRGSRDLQILRADIAPR +GRGEAELYTVDCRVEAVHVVTGRLELRTTEAVHLLEEGDTVTFPGREPHSWANPDDRPAV +VLWTLVGHA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000427.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000427.fa new file mode 100644 index 0000000000000000000000000000000000000000..a53cf38072ff77afc75bd0fec1e0e4d08d55149a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000427.fa @@ -0,0 +1,35 @@ +>PROKKA_00385 +MLEIPRVEDNGRLGPVNSALVPRYGGTPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS +YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQAQVVDAGDMAVNPFDIGEAIEAIQQDA +MDLTEDGSSLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAEYTHGTP +FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRQGVDEIVDQLRQ +RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA +YDHAELTGVAASHVAYDLISLMADRRATRAAAGEESAR +>PROKKA_00109 +MLEIPRVEDNGRLGPVNSALVPRYGGTPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS +YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQAQVVDAGDMAVNPFDIGEAIEAIQQDA +MDLTEDGSSLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAEYTHGTP +FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRQGVDEIVDQLRQ +RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA +YDHAELTGVAASHVAYDLISLMADRRATRAAAGEESAR +>PROKKA_02570 +MLEIPRVEDNGRLGPVNSALVPRYGGAPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS +YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQSQVVDAGDMAVNPFNIGEAIEAIQQDA +MDLTEDGASLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFAAEYTHGTP +FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRKGVDEIVDQLRQ +RIGDRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA +YDHAELTGVAASHVAYDLITLMADRRASRAAAGEEQGR +>PROKKA_01755 +MLEIPRVEDNGRLGPVNSALVPRYGGAPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS +YRPGARFGSGHVRQSSRLLRPYNPATETSPFAQAQVVDTGDMAVNPFHIGEALESIQQDA +MDLTEDGASLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAAYTHGTP +FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRKGVDEIVDQLRQ +RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGLTSRELLEILRGLRGLDIVGADLVEVAPA +YDHAELTGVAASHVAYDLISLMADRRATRAAAEGGVDA +>PROKKA_00391 +MLEIPRVEDNGRLGPVNSALVPRYGGAPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS +YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQAQVVDAGDMAVNPFDIGEAIEAIQQDA +MDLTEDGSSLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAEYTHGTP +FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRQGVDEIVDQLRQ +RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA +YDQAELTGVAASHVAYDLISLMADRRATRAAAGEEPGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000428.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000428.fa new file mode 100644 index 0000000000000000000000000000000000000000..37839c6d19ffd83f7cdb04020f22ef38d8c75150 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000428.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000429.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000429.fa new file mode 100644 index 0000000000000000000000000000000000000000..2b8e71baf876f369ecd4d9fc38967354e2cbae81 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000429.fa @@ -0,0 +1,34 @@ +>PROKKA_00389 +MSPALPRPAELRAIALDAARAVVGDLAAAFRSPTAIGPEAKTTHHDLVTVHDRHTEARLV +AALTTAVPGSGVLGEELGAQAGTGEAARLTWIVDPIDGTSNFTHGFAMFSVSLAAEVDGE +VVAGVVLDPVGRLAFSADADGAYLTRGDGPERPLAEVGRPAPAGGERAQNLVTSYPAGEA +IAREGEDALRRFGRLVTAHATVRRTVSGALELAHTAAGWADAALYVDTKPWDVAAGQLIL +RRAGGRWLTPDPAAPSSGRLVDDGPRAHTCPFALAVAPGREAPTTAAVLGDIVASRATDH +V +>PROKKA_00113 +MSPALPRPAELRAIALDAARAVVGDLAAAFRSPTAIGPEAKTTHHDLVTVHDRHTEARLV +AALTTAVPGSGVLGEELGAQAGTGEAARLTWIVDPIDGTSNFTHGFAMFSVSLAAEVDGE +VVAGVVLDPVGRLAFSADEDGAYLTRGDGPERPLAEVARPAPAGGERAQNLVTSYPAGEA +IAREGEDALRRFGRLVTAHATVRRTVSGALELAHTAAGWADAALYVDTKPWDVAAGQLIL +RRAGGRWLTPDPAAPSSGRLVDDGPRAHTCPFALAVAPGREAPTTAAVLGDIVASRATDH +V +>PROKKA_02567 +MSATVPSPAALRRIALDAAGAVSADLAAAFRRPSAAGPGPEAKSTHHDLVTVHDRRTEAR +LVAALTTAVPGSAVLGEELGGRDGAGEAARLTWIVDPIDGTSNFAHGFAMFSVSVAATVD +GEVVAGVVLDPVSGLAFSADDHGAWLARPGEAERPLADVARPAPAGGERAQNLVTSYPAG +EALALEGEDALRRFGRLVSAHATVRRTVSGALELAYTAAGWADAALYVDTKPWDVAAGQL +ILRRAGGRWLTPDPAAPLSGRLVDDGPRAHTCPFALAVAPGREVPTTAAVLGDIVASRAA +DHV +>PROKKA_02438 +MVSSDSGPRSAAGSPLAPSPARLRAIGLEAARAVAPALAAAFRTPDAAAATKRNHHDLVT +AHDRATEEALVATLTAAVPGSAVLGEETGVTAPPADAGVPRVRWIVDPIDGTSNFSHGFD +LFSVSIAAEVDGEVVAGVVLAPAAGLEFSADDAGAWLGEAPLPLRAAPDGGERALNIVTS +YPAAEALAREGEAALRRFAQLVDAHATVRRTVSGALELAFVAAGWADVTLAVDTHPWDVA +AGQLLVARAGGTLVAADDAGPAPALVPHLAPHLLAVGPGRRAPTARAVLAGLVADRAAE +>PROKKA_00395 +MSPALPRPAELRAIALDAARAVAGDLATAFRSPTATGPEAKTTHHDLVTVHDRHTEARLV +AALTTAVPGSGVLGEELGAQAGTGEAARLTWIVDPIDGTSNFTHGFAMFSVSLAAEVDGE +VVAGVVLDPVGRLAFSADADGAYLTRGDGPERPLAEVGRPAPAGGERAQNLVTSYPAGEA +LAREGEDALRRFGRLVTAHATVRRTVSGALELAHTAAGWADAALYVDTKPWDVAAGQLIL +RRAGGSWLTPDPAAPSSGRLVDDGPRAHTCPFALAVAPGREAPTTAAVLGDIVASRATDH +V diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000431.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000431.fa new file mode 100644 index 0000000000000000000000000000000000000000..ee3c9a0a2ac432ff5bb916b7000306d1e9b07fd1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000431.fa @@ -0,0 +1,20 @@ +>PROKKA_00392 +MTASRSVEVRIPLRWADMDAYGHVNNIAVVQLLEEARVAAFGVPANTGAGGGQAPPIDLL +EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVDAVKAASVHVGYALHDGVDDTLCAT +ATSVMVFVDGQTGRPVRISPEQRAALAG +>PROKKA_00116 +MTASRSVEVRIPLRWADMDAYGHVNNIAVVQLLEEARVAAFGVPANTGAGGGQAPPIDLL +EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVDAVKAASVHVGYALHDGVDDTLCAT +ATSVMVFVDGQTGRPVRISPEQRAALAG +>PROKKA_02564 +MTGPRAVEVRIPLRWADMDAYGHINNIAVVQLLEEARVAAFGVPANTGAGGGEAPPIDLL +EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVEAVKAASVHVGYALHDGVDDTLCAT +ASSVMVFVDGETGRPVRVTPEQRAALQG +>PROKKA_02435 +MTETTTSSAARDGAGRWVEVSVPLRWADMDAYGHINNIAVVQLLEEARVAVFGVPANTGA +GGGGAPPVDLLEGVPEGVRTFVSEHTVKYRAQMPYRPVPLRVRVGVAAVKAVSVEVAYEL +YDGVDGTLCVTARSVMVFVDGASGRPVRLTAEQRAALAG +>PROKKA_00398 +MTASRSVEVRIPLRWADMDAYGHVNNIAVVQLLEEARVAAFGVPANTGAGGGQAPPIDLL +EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVDAVKAASVHVGYALHDGVDDTLCAT +ATSVMVFVDGQTGRPVRISPEQRAALAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000433.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000433.fa new file mode 100644 index 0000000000000000000000000000000000000000..229bc5e586a7478c59b839462912871b8779401a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000433.fa @@ -0,0 +1,45 @@ +>PROKKA_00394 +MNESLETLRDEVFARNPGEAEFHQAVSEVFEALGPVVQRHPQYVEAGVMHRLCEPERQII +FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGM +PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGAREIGYMFGQ +YKRLTNRFEAGALTGKGLTWGGSLVRTEATGYGAVMFVDSMLRTRGESMDGQQVLISGSG +NVAIYAAEKAAALGATVLTASDSSGYIVDPDGLDLDLLKQIKEVERARISEYAERRGGRS +RYVTGGSVWDVEGTVALPCATQNELDESAARTLLKNGVKAVAEGANMPCTEAAAHLFVDS +GTLFGPGKAANAGGVATSALEMQQNASRDSWSFDYTHDRLEQIMRDIHDRCVETAEEYGT +PGNYVAGANIAGFIKVADAMIAQGVV +>PROKKA_00118 +MNESLETLRDEVFARNPGEAEFHQAVSEVFEALGPVVQRHPQYVEAGVMHRLCEPERQII +FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGM +PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGAREIGYMFGQ +YKRLTNRFEAGALTGKGLTWGGSLVRTEATGYGAVMFVDSMLRTRGESMDGQQVLISGSG +NVAIYAAEKAAALGATVLTASDSSGYIVDPDGLDLDLLKQIKEVERARISEYAERRGGRS +RYVTGGSVWDVEGTVALPCATQNELDESAARTLLKNGVKAVAEGANMPCTEAAAHLFVDS +GTLFGPGKAANAGGVATSALEMQQNASRDSWSFDYTHDRLEQIMRDIHDRCVETAEEYGT +PGNYVAGANIAGFIKVADAMIAQGVV +>PROKKA_02562 +MNHALETLRDEVFARNPGEAEFHQAVSEVFEALDPVMERHPQYVEAGVLHRLCEPERQII +FRVPWIDDNGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIIKFLGFEQIFKNSLTGM +PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGGREIGYMFGQ +YKRLTNRFEAGVLTGKGLTWGGSLVRTEATGYGAVMFADSMLKTRGESMDGQQVLISGSG +NVAIYAAEKAASLGATVLTASDSAGYIVDPDGLDLDLLKQIKEVERARISEYVERKGGRA +RYVAGGSVWDVEGTVALPCATQNELDESAAKTLLGNGVKAVAEGANMPCTEAATRLFLHA +KTLFGPGKAANAGGVATSALEMQQNASRDSWNFEYTHDRLEAIMRDIHDRCVETAEEYGT +PGNYVAGANIAGFIKVADAMIAQGVV +>PROKKA_02434 +MHQVLQTLRDEVFARNPGEAEFHQAVSEVFEALDPVVERHPHYVDAGVLHRLCEPERQII +FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIIKFLGFEQIFKNSLTGM +PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGGREIGYMFGQ +YKRLTNRFESGVLTGKGLTWGGSLVRTEATGYGAVMFADSMLRTRGESMDGQKVLISGSG +NVAIYAAEKAAQLGATVLTASDSAGYIVDPDGVDVELLKQIKEVERARISEYAERKGGKV +RYVAGGSVWDVEGTVALPCATQNELDESAAKTLLQNGVKAVAEGANMPSTEAATHLFLDA +GTLFGPGKAANAGGVATSALEMQQNASRDSWDFDYTHDRLERIMRDIHDRCVETAEEYGT +PGNYVAGANIAGFIKVADAMIAQGVV +>PROKKA_00400 +MNESLETLRDEVFARNPGEAEFHQAVSEVFEALGPVVQRHPQYVEAGVMHRLCEPERQII +FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGM +PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGAREIGYMFGQ +YKRLTNRFEAGALTGKGLTWGGSLVRTEATGYGAVMFVDSMLRTRGESMDGQQVLISGSG +NVAIYAAEKAAALGATVLTASDSSGYIVDPDGLDLDLLKQIKEVERARISEYAERRGGRS +RYVTGGSVWDVEGTVALPCATQNELDESAARTLLKNGVKAVAEGANMPCTEAAAHLFVDS +GTLFGPGKAANAGGVATSALEMQQNASRDSWSFDYTHDRLEQIMRDIHDRCVETAEEYGT +PGNYVAGANIAGFIKVADAMIAQGVV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000437.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000437.fa new file mode 100644 index 0000000000000000000000000000000000000000..929318e1d2ccb005edb388b7f6ef66eb2e7c2643 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000437.fa @@ -0,0 +1,25 @@ +>PROKKA_00399 +MRIVALVSGSGTNLQAVLDAVASGALDMEIAAVGADVADAGGLERARAHGIETFVVSPKD +HADRRAWDEALADAVAAYAPDWVVCSGFMRILGAPLLERFDGRILNTHPALLPSFPGAHG +VRDALAHGVKVTGCTVHVVDAGVDTGPILAQAAVPVLDTDTEAELHERIKVQERALLLRV +LGELSRR +>PROKKA_00123 +MRIVALVSGSGTNLQAVLDAVASGALDMEIAAVGADVADAGGLERARAHGIETFVVSPKD +HADRRAWDEALADAVAAYAPDWVVCSGFMRILGAPLLERFDGRILNTHPALLPSFPGAHG +VRDALAHGVKVTGCTVHVVDAGVDTGPILAQAAVPVLDTDTEAELHERIKVQERALLLRV +LGELSRR +>PROKKA_02558 +MRIVALVSGSGTNLQAVLDAVASGALDVEIAAVGADVADAGGLERARAHGIETFVVSPRD +HADRHAWDVALADAVAAHEPDWVLCSGFMRILGAPLLERFEGRILNTHPALLPSFPGAHG +VRDALAHGVKVSGCTVHVVDAGVDTGPILAQAAVPVLDTDTESELHERIKVQERALLLRV +LGELSRR +>PROKKA_02429 +MRILALVSGSGTNLQAVLDAVASGALPLEVAAVGSDVPGVQGLARAEAAGIPTFTVAPAD +HPDRAAWNVALAEAVAAYEPDWVVCSGFMRILGAPLLEAFPGRIVNTHPALLPSFPGAHG +VRDALAYGVKVTGCTVHLVDAGVDTGPILAQAAVPVLDTDTEEVLHERIKVQERVLLLRV +LGELAAGRSPRQA +>PROKKA_00405 +MRIVALVSGSGTNLQAVLDAVASGALDVEIAAVGADVADAGGLERARAHGIETFVVSPKD +HADRRAWDEALADAVAAYAPDWVVCSGFMRILGAPLLERFEGRILNTHPALLPSFPGAHG +VRDALAHGVKVTGCTVHVVDAGVDTGPILAQAAVPVLDTDTEAELHERIKVQERALLLRV +LGELSRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000439.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000439.fa new file mode 100644 index 0000000000000000000000000000000000000000..a454bf48e7f24b3a2e3e8f1115fd904e7fb04124 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000439.fa @@ -0,0 +1,55 @@ +>PROKKA_00401 +MLEDTRTPSKERPLVTSAQPTTTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVST +GSTAQRIAAAGVPVTEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEV +EPFDLVVVNLYPFVDTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEV +VQAAQSGGFDLRARRRLAALAFAHTAAYDNAVAAWTAAHFGEDTHADEIPVFPPYAGFSL +ERAQILRYGENPHQPAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVP +AVAIVKHANPCGVAVTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQAKDVF +TEVVVAPSFEPEALEILTAKKNLRLLSLPEGFVRDAVEAKQVSGGMLLQITDAVDADGDD +PATWTLAAGPAADEATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLA +VERANTLGAAQTGGQDVSTAGGAENVSGDGAPERARGAVAASDAFFPFADGLQILLDAGV +RAVVQPGGSVRDEEVVAAAEAAGVTLYLTGARHFFHG +>PROKKA_00125 +MTSAQPIPTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV +TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEVEPFDLVVVNLYPFV +DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR +RRLAALAFAHTAGYDNAVAAWTAAHFGEDTDADEIPVFPPYAGFSLERAQILRYGENPHQ +PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVPAVAIVKHANPCGVA +VTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQVKDVFTEVVVAPAFEPEAL +EILSAKKNLRLLSLPEGFLRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGPAADE +AVLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG +QDVSSAGGAENVSGEGAPERARGSVAASDAFFPFADGLQILIDAGVKAVVQPGGSVRDEE +VVAAAEAAGVTLYLTGARHFFHG +>PROKKA_02556 +MTSAQPTTTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV +TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVAQLRDLEVEPFDLVVVNLYPFV +DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR +RRLAALAFAHTAGYDNAVAAWTAAHFAEDTEQDDVPIFPPYAGFSLERAEILRYGENPHQ +PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPAPAVAIVKHANPCGVA +VTDEGADVAQAHAKAHACDPVSAFGGVIAANRPVTAVMAAQVKDVFTEVVVAPSFEPEAL +QILTAKKNLRLLALPEGFVRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGAAADE +ATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG +QDVTTSEVTTAGGAENVSGEGAPERARGAVAASDAFFPFADGLQILIDAGVRAVVQPGGS +VRDEEVVAAAEAAGVTLYLTGARHFFHG +>PROKKA_02425 +MSSAPSVTTVLDEVPLKRALISVYDKTGLEELATGLHAAGVQLVSTGSTAQRIAAAGVPV +TEVSEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVAQLADLDVEPFDLVVVNLYPFV +ETVRSGADEDAVVEQIDIGGPSMVRAAAKNHASVAVVVDPARYVDVVAAAQAGGFDLRTR +RRLASLAFAHTAAYDNAVAAWTAAHFGEDAEDEDAPVFPPYAGFSLERAATLRYGENPHQ +PAALYVDHEAAPGIAQAELLHGKAMSYNNYVDADAAVRAAFDHAVPAVAIVKHANPCGVA +VAGEGEDVAVAHAKAHACDPVSAFGGVIAANRPVTRAMAEQVAPIFTEVVVAPSFDEDAL +EVLTAKKNLRLLALPEGFARDAVEAKQVSGGMLMQIADAVDADGDDPRTWTLAAGEAADE +ATLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG +QDVSSAGGAENVSGEGAPERARGAVAASDAFFPFADGLQILVDAGVKAVVQPGGSVRDQE +VVDAANAAGITMYLTGARHFFHG +>PROKKA_00407 +MTSAQSIPTVLDTVPLKRALISVYDKTGLEELATGLHAAGVQIVSTGSTAQRIAAAGVPV +TEVAEVTGFQECLDGRVKTLHPRVHAGILADRRREDHVTQLRELEVEPFDLVVVNLYPFV +DTVNSGAAEDAVVEQIDIGGPSMVRAAAKNHASVAIVVDPARYGEVVQAAQSGGFDLRAR +RRLAALAFAHTAGYDNAVAAWTAAHFGEDTDADEIPVFPPYAGFSLERAQILRYGENPHQ +PAALYLDSSAAPGIAQAELLHGKPMSYNNYVDADAAVRAAFDHPVPAVAIVKHANPCGLA +VTDEGTDIAQAHAKAHACDPVSAFGGVIAANRPVTAAMAAQVKDVFTEVVVAPAFEPEAL +EILSAKKNLRLLSLPEGFLRDAVEAKQVSGGMLLQIADAVDADGDDPATWTLAAGPAADE +AVLADLAFAWRAVRAAKSNAVLLAHDGATVGVGMGQVNRLDSCRLAVERANTLGAAQTGG +QDVSSAGGAENVSGEGAPERARGSVAASDAFFPFADGLQILIDAGVKAVVQPGGSVRDEE +VVAAAEAAGVSLYLTGARHFFHG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000440.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000440.fa new file mode 100644 index 0000000000000000000000000000000000000000..002bdafa2676639b110e85edc6d8b6e6205335a9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000440.fa @@ -0,0 +1,70 @@ +>PROKKA_00403 +MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFKDVLPEDQRT +ADALAELGELVKSPEANVIKLPNISASVPQLRAAIKELQADGYALPEYPDEPKTDEEKDA +KARYDSVKGSAVNPVLREGNSDRRAPKAVKAYAKRFPHSMGEWTPDSKTAVATMGADDFR +ANEQSVTLPAADVLTIEFTGEDGKTTVLKEGLKVLKGEVVDGTFMSAKALDAFLAEQVKR +AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLAAAGLSANNGLAAIEG +GLDKLDAETAEGVRAAIAAAYENGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRTSGR +MWNKDDQTQDTLAVIPDSSYAGVYQAVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS +HDKTFIMDAAGTVAVKNSAGETLLSHDVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT +PAVFWLDETRAHDRELIKKVEEYLKEHDTEDLDIRILSPVEAAKLSVERIRRGEDTISVT +GNVLRDYNTDLFPILELGTSAKMLSVVPLLNGGGLFETGAGGSAPKHVQQLVEENHLRWD +SLGEFLALAVSFEHEAVANENHRARVLADTLDAATGTLLIEGKSPKRKVGELDNRGSHFY +LALYWARELAKQTEDAELAAAAKPVAEELEAQEETILGELNGVQGSPVDLGGYYWPELEK +VTSVMRPSATLNAIVDKLSV +>PROKKA_00126 +MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFKDVLPEEQRT +ADALAELGELVKTPEANVIKLPNISASVPQLRAAIKELQAHGYALPEYPDEPKTDAEKDA +KARYDSVKGSAVNPVLREGNSDRRAPKAVKAYAKRFPHSMGEWTPDSKTAVATMGADDFR +ANEQSVTLPAADVLTIEFTGEDGKTTVLKEGLKVLKGEVVDGTFMSAKALDAFLAEQVKR +AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLAAAGLSANNGLAAIEG +GLDKLDAETAEGVRAAIAAAYENGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRTSGR +MWNKDDQTQDTLAVIPDSSYAGVYQAVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS +HDKTFIMDAAGTVAVKNSAGETLLSHEVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT +PAVFWLDETRAHDRELIKKVEEYLKEHDTEGLDLRILSPVEATKLSVERIRRGEDTISVT +GNVLRDYNTDLFPILELGTSAKMLSIVPLLNGGGLFETGAGGSAPKHVQQLLEENHLRWD +SLGEFLALAVSFEHEAVANENHRAQVLADTLDAATGTLLIEGKSPKRKVGELDNRGSHFY +LALYWARELAKQTEDAELAAAAKPIAEELEAQEETILAELNGVQGSPVDLGGYYAPEMEK +VTSVMRPSATLNAIVDKLSV +>PROKKA_02553 +MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFRDVLPEDQRT +ADALAELGELVKSPEANVIKLPNISASVPQLRAAIKELQEDGYALPEYPDEPKTDEEKDA +KARYDSVKGSAVNPVLREGNSDRRAPKAVKNYAKMFPHSMGEWTPDSKTAVATMGADDFR +SNEKSVTMPADDTLTIEFTGEDGKTTVLKEGLKVLAGEVVDGTFMSAKALDAFLAEQVKR +AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLEAAGLNPNNGLAAIEG +GLDKLDAETAEGVKKAIAAAYEEGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRTSGR +MWNKDDQTQDTLAVIPDSSYAGIYQAVIEDCKKHGAYDPTTMGTVPNVGLMAQKAEEYGS +HDKTFILESAGTVAVKNAAGETLISHDVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT +PAVFWLDETRAHDRELIAKVEEYLKEHDTEGLDLRILSPVEAAKLSVERIRRGEDTISVT +GNVLRDYNTDLFPILELGTSAKMLSVVPLLNGGGLFETGAGGSAPKHVQQLVEENHLRWD +SLGEFLALAVSFEHEAVANENHRAQVLADTLDAATGTLLIEGKSPQRKVGELDNRGSHFY +LALYWARELAKQTEDAELVAAAKPVAEELEAQEETILAELNGVQGSPVDLGGYYWPELEK +VTSVMRPSATLNAIVDKLSV +>PROKKA_02422 +MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFNDLLPEEQRV +NDALAELGELVKTPEANVIKLPNISASVPQLRAAIKELQADGYALPEYVDDPQTDKEKDA +RKRYDSVKGSAVNPVLREGNSDRRAPKAVKNYAKKFPHSMGAWTADSKTAVATMGQDDFR +SNEKSVTMPKDDVLSIEFTGQDGTTKILKEGLKVLEGEVVDGTFMSAKALDAFLAEQVTR +AKEEGVLFSAHLKATMMKVSDPVIFGHVVKAYFADLFAQYGEQLAAAGLDPNNGLAAIEA +GLDKLDAETAEGVRKAIADAYQNGPDVAMVNSDKGITNLHVPSDVIVDASMPAMIRTSGH +MWDKDGAERDTLAVIPDSSYAGIYQVVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS +HDKTFVMEADGTVEVKDSAGEVLFSHEVEAEDIWRACQTKDVPVQDWVKLAVTRARASQT +PAVFWLDETRAHDRELIKKVEQYLQGHDTEGLDLRIMSPVEATKFTVERMRRGEDTITVT +GNVLRDYNTDLFPILELGTSAKMLSIVPLINGGGLFETGAGGSAPKHVQQLVGENHLRWD +SLGEFLALAVSFEHEAAHNGNHRAQVLADTLDAATGILLIEGKSPERKAGQLDNRGSHFY +LALYWAQELAKQTADAELAAAAKPVAEELEAQEETILAELNGVQGSPVDLGGYYAPSMDK +VSEVMRPSATLNGIIATLGA +>PROKKA_00409 +MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFKDVLPEEQRT +ADALAELGELVKSPEANVIKLPNISASVPQLRAAIKELQADGYALPEYPDEPKTDEEKDA +KARYDSVKGSAVNPVLREGNSDRRAPKAVKAYAKRFPHSMGEWTPDSKTAVATMGADDFR +ANEQSVTLPAADVLTIEFTDEDGETTVLKEGLKVLKGEVVDGTFMSAKALDAFLAEQVKR +AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLAAAGLSANNGLAAIEG +GLDKLDAETAEGVRAAIAAAYENGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRNSGR +MWNKHDQTQDTLAVIPDSSYAGVFQAVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS +HDKTFIMDAAGTVAVKNSAGETLLSHDVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT +PAVFWLDETRAHDRELIKKVEEYLKEHDTEDLDIRILSPVEAAKLSVERIRRGEDTISVT +GNVLRDYNTDLFPILELGTSAKMLSVVPLLNGGGLFETGAGGSAPKHVQQLVEENHLRWD +SLGEFLALAVSFEHEAVANENHRARVLADTLDAATGTLLIEGKSPKRKVGELDNRGSHFY +LALYWARELAKQTEDAELAAAAKPIAEELGAQEETILAELNGVQGSPVDLGGYYWPELEK +VTSVMRPSATLNAIVDKLSV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000441.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000441.fa new file mode 100644 index 0000000000000000000000000000000000000000..71b2748115f2871a4b855b60dac76bb7679032e4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000441.fa @@ -0,0 +1,25 @@ +>PROKKA_00404 +MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEDSEPPAAAIGRLLETLMDR +LVALDPETADREMNPRPVEPRPGASQPVADALAAYAAGDVAALDALDVTQPGTAFRQRAW +RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY +GTAAKQALLAHEAAHAG +>PROKKA_00127 +MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPGDSEPPAAAIGRLLETLMDR +LVALDPETADREMNPRPVEPRPGVSQPVADALAAYTAGDVAALDALDVAQPGTAFRQRAW +RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY +GTAAKQALLAHEAAHAG +>PROKKA_02552 +MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEGAEPHAAAIGRLLEALMDR +LEALDPATADREMNPRPVEPHPGVSQPVADALAAYAAGDVAALDALEVAQPGTAFRQRAW +RELRGIAPGSPATYGGLAERCGTPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY +GTAAKRALLAHEAAHAG +>PROKKA_02420 +MTHPPAFLPELRWTAATLPGTSLALVAVYSPEDDAVRASGVAVPEGAEPPAAAIGRLLLE +LMDRLEELAPETAAREMDPRPVEPREGLDQTVADALAAYAAGDVDALDGLAVVQPGTAFR +QASWEALRSITPGSPVAYGELATRAGAPKAVRAAGGACAANLAAVVVPCHRVVPASGGVG +SYLYGSAAKAALLAHEAAHAPA +>PROKKA_00410 +MDLLPELRWTAAALPATELTLVAVFSPEDQTVRASGVAVPEDSEPPAAAIGRLLETLMDR +LVALDPETADREMNPRPVEPRPGVSQPVADALAAYAAGDVAALDALDVTQPGTAFRQRAW +RELRGIAPGSPATYGGLAERCGAPRAVRAAGGACAANLVAVVVPCHRVVRADGAAGHYLY +GTDAKQALLAHEAAHAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000442.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000442.fa new file mode 100644 index 0000000000000000000000000000000000000000..68dd4eb1784cfd4549ac62ec4f060111e0fb5652 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000442.fa @@ -0,0 +1,50 @@ +>PROKKA_00405 +MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ +APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL +ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF +EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR +VIRLVRSPKRAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFTDAHKEAVHDS +RVRGTRTLVDALARIAAREGDDARVRALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF +LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGLGGPVATSGGES +HDGSPWLSWIGADDIAGAFAHAVIDDGVTGPVNAVAPEPVTAREFATVLGRVLHRPAVIP +VPDAGPRLLLGEEGRVETVAADQKVVADRLVASGYDMRDPELEGALRHVLGR +>PROKKA_00128 +MTEITVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ +APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL +ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF +EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR +VIRLVRSPKKAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFSDAHKEAVHDS +RVRGTRTLVDALARIAAREGDDARARALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF +LAEVVADWEAEARRAETSGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGVGGPVATSGGES +HDGSPWLSWIGADDIAGAFAHAVLDDGVTGPVNAVAPEPVTAREFATVLGRVLRRPAVIP +VPEAGPRLLLGEEGRVETVAADQKVLADRLVASGYEMRDPELEGALRHVLGR +>PROKKA_02551 +MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPSDGLRVGSESRLRIQ +APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL +ASWRHTHLLDDAAPGEADTADGRRGTVVTDHIEYALPGEDLLGRVPGVGAAASRRAHEAF +EAELSRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR +VVRLVRSPKKAGALDAALWDPGRETVDEDALAGADVVVNLAGEPIAGRFTDEHKEAVHDS +RVRGTRTLVDALARITAREGDDARARALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF +LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGVGGPIASSGGES +HDGSPWLSWIGADDIAGAFAHAVLDDGVTGPVNAVAPEPVTAKEFATVLGRVLRRPAVIP +VPEAGPRLLLGEEGRVETVAADQKVVADRLVASGYDMRDPELEGALRHVLGR +>PROKKA_02419 +MTETRVFEHRTLLRHPRRTVFDWLAAPGALQRMNPPFASELAAGPSDGLREGSQTRLRIG +APGSLGLFAGAVDGALRAALPAAVSRRIPAALSPRLPWRARHTAYEEGRMFRDEMASGPL +SAWRHTHSVEDAAPGEADTAEGEPGAVVVDRVEYALPGVGTAGRLPVVGRPAADAAHRVF +EAELRRQFEFRGRVMAEDLDFHAGHPGPLVGGPARTVLVTGAGGLVGTQLCALLTGGGHR +VIRLVRSPAQAEAEDAVLWDPAGGTVDTAALRAADVVVNLAGEPLAGRFTEKHRRAVHDS +RVDGTRTLVDAIARLPEAERPTVLVNGSAVGWYGADAGAGPDGRGLTEDLPAGDDFLAGV +VADWEAQARRAEELGLRVVRVRTGIVLSPTGGMLAQLLPLFLAGAGGPVATRGGRSHDGS +PWISWIGVDDIAGVFAHAALAEGVVGAVNGTAPEPVTAKEFARVLGTVLHRPAAVPVPEF +GPRLLLGEQGAAELVRADQKASAELVLDSGYAFRDAALEGALRRLLGR +>PROKKA_00411 +MTEIRVFEHRTLLRHPREVVFRWLENPGALERLTPPFAGEVVQGPTDGLRVGSESRLRIQ +APGAAGLFAGAAHGMLTGLLPDAVASRLPGGAAPAVPWRARHTAYEEGRMFRDEMVSGPL +ASWRHTHLLDDAAPGEADMADGRRGTVVTDHIEYALPGESLVSRVPGLGAAASRRTHEAF +EAELGRQFAYRARVMADDLDFHAAHPGPLVGGPARTVAVTGSGGLIGRQLCALLTTGGHR +VIRLVRSPKKAGALDAALWDPGRETVDEDALAEADVVVNLAGEPIAGRFSDAHKEAVHDS +RVRGTRTLVDALARIAAREGDDARVRALVNGSAIGYYGADAGTGPFGSGLVEDLEPGDDF +LAEVVADWEAEARRAEAAGIRVAMLRTGVVLSPAGGMLQQVLPLFLAGLGGPVATSGGES +HDGSPWLSWIGADDIAEAFAHAVLDDGVTGPVNAVAPEPVTAKEFATVLGRVLRRPALIP +VPEAGPRLLLGEEGRVETVAADQKVLADRLVASGYQMRDPELEGALRHVLGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000443.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000443.fa new file mode 100644 index 0000000000000000000000000000000000000000..926909f3afcbc26421ede6b9db445a5e5f106b7c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000443.fa @@ -0,0 +1,60 @@ +>PROKKA_00406 +MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA +LEDLGAVRVGERVGAVPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA +RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA +AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP +GWASTRGGTVLVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA +ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL +ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL +PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ +HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL +TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF +TALSQLIRETGALQD +>PROKKA_00129 +MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLMVDGHRYVSGSMTPVPLATLASPLFHAQA +LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA +RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA +AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP +GWASTRGGTVFVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA +ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL +ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMAAVEESVEVDL +PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ +HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL +TPGMTFGEMALGQPGRQPSTVRARGPVTTRVLTAQVMVALQEGFPQLALALWEALARDAF +TALGQLIRETGALQD +>PROKKA_02550 +MTTPVQKHLDRLTSAHTGEGDVPDGLGVAMLMVDGHRYVSGSMTSVPLATLASPLFHAQA +LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA +RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA +AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP +GWASTRGGTVLVVVPGHLGLALQSDTTDENALGAAAMAALRTIVEDFELHPSVVTGSPRA +ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVLELGGHLGFSQVDAIARVSRGLPEAL +ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEIRELMAAVEESVEVDL +PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSQHAPHLLPRDAQEAAVAPLLQ +HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL +TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF +TALSQLIRETGALQD +>PROKKA_02418 +MKSPVQDRLDRLTAAHTPGTAADADATSDAGTGLALSVATVGGDHYSAGELVAVPLAGLA +GPVVHALALEDLGVERVGEAVGTVPRPDLRTRLELEPGTGRPLTPLQDAGTMALAALVKG +RGGRDRAARLLQQLAGLIGRETAPTDAAVRAADRAQHRARAAAWLLRSVGVLEADPDGLL +ADVATLRAAPVTVADLALLAGTLAAHGVHPVSGERVLAEETVRAVLSALDACGMDTVDGA +WALDVGQPGWSSARAGTVIAVVPGHMGIAVQGPADPDDADAPSPAALAALRTLVRDFELH +PSQAAGSPRAAFRTHYRVDQAPSGSVRSAEVLELLSAHGDTAHVLELGGHVGFSQVDALA +HVARNLPAALETIIVDVRSVSSTSHAAAVLAAQWFAYALHHGLDVVVVDRDTAAVDQVMA +TAEASGVTLPDPLHDADDADPGHQDLGPAFRFFDSRSRAVQWAEQRLLARHAPHLLPASE +EEAAMAPLLQHLSSEDARLLESMMDERVYEDGQIIRRAGQPFGGIYVITSGRVELTGQGT +GGRRVRRTVLTPGMTFGEMALGQPGRQPSTVRARGRVTTRVLTAQVMYALQEGFPSLALT +LWEALARDAYTALGQLIRETGALQD +>PROKKA_00412 +MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA +LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA +RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA +AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSAMDSCGMDTRDSRWAYDVGQP +GWASTRGGTVLVVVPGHLGLALQSNTTDENGLGAAAMTALRTIVEDFELHPSVVTGSPRA +ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL +ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL +PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAALAPLLQ +HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL +TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF +TALGQLIRETGALQD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000446.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000446.fa new file mode 100644 index 0000000000000000000000000000000000000000..dc087c81ab50ca1d2a1a3d54e06e35b04d26bc22 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000446.fa @@ -0,0 +1,32 @@ +>PROKKA_00413 +MSTAASAPAPEGRAPEGRAPHRRGTGKATALWWILTVVIGVWCLFPLFSIFATSFKTPAD +LANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAYAIARL +DFPGKRLVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWVGLIIPYLSLTLPISIWTLA +AFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFGISLTS +TETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTNGAVKG +>PROKKA_00133 +MSTAASAPAPEGRAPEGRAPHRRGTGKATALWWILTVVIGVWCLFPLFSIFATSFKTPAD +LANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAYAIARL +DFPGKRIVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWVGLIIPYLSLTLPISIWTLA +AFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFGISLTS +TETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTNGAVKG +>PROKKA_02546 +MSTAVSAPAPEGRAPEGRGPEGRAPRRRGTGKATALWWILTVVIGVWCLFPLFSIFATSF +KTPADLANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAY +AIARLDFPGKRLVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWIGLIIPYLSLTLPIS +IWTLAAFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFG +ISLTSTETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTN +GAVKG +>PROKKA_02414 +MSTGNPIPAPQEPVTTRPDGAAERTEAGTAVGDRGVAPTTTRRTRKGSSSWIWWLLAVLI +GVWCLFPLFSIFATSFKTPADLSNGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGIT +VIATLIAVVLATLCAYAIARLDFPGKRIVLTVSLMVSMFPVISLVTPLFNVWRTLGLYDT +WLGLIIPYLSLTLPISIWTLAAFFRQIPWELDQAAQVDGATPLQAFRKVIVPLAAPGVFT +TAIIAFFIAWNDFVFGISLTSTEAARTVPAALAFFTGASQFESPTGAISAAAIVVTIPIV +ILVLLFQRQIVAGLTNGAVKG +>PROKKA_00416 +MSTAASAPAPEGRAPEGRAPHRRGTGKATALWWILTVVIGVWCLFPLFSIFATSFKTPAD +LANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAYAIARL +DFPGKRIVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWVGLIIPYLSLTLPISIWTLA +AFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFGISLTS +TETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTNGAVKG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000447.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000447.fa new file mode 100644 index 0000000000000000000000000000000000000000..90985e0de1ad8b17d0a8b97f26aa155cc15f1404 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000447.fa @@ -0,0 +1,45 @@ +>PROKKA_00414 +MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE +MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD +AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI +SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS +PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS +RRDRGSTFDATLTHLEWLGHEQYGYIEFDPDPAVAEMLSSLAKDLDADELRPVVVATLSG +ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAAEERRRQIEMAAERDA +AEHEADAPRR +>PROKKA_00134 +MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE +MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD +AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI +SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS +PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS +RRDRGSTFDATLTHLEWLGHEQYGYIEFEPDPAVAEMLSALAKDLDADELRPVVVATLSG +ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAGEERRRQIEMAAERDA +AEHEADAPRR +>PROKKA_02545 +MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDISDGE +MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPAEEEIDRKVRN +AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI +SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGVLQQVASPRELYEQPLNLFVAGFIGS +PSMNFLPASLKEKDGVHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS +RRDQGSTFDATLTHLEWLGHEQYGYIEFDPDPAVAEMLSSLAKDLDADELRPVVVATLSG +ESRARPGTPTRLWVDTTRVHLFDPKTGENLTRDPEVGAELTRRAAEERRRQIEVAAERDA +AADREAADTRR +>PROKKA_02413 +MASITLNHIEKTYDDGYHAISDVNLDIEDGEFVILVGPSGSGKSTLLRMIVGLEDISGGD +LLIDGRRVNEAAPKDRNLAMVFQNYALYPHLSVYENIAFPLRLAKDGKLSEEELDRKVRD +AARVLELQDHLDRKPANLSGGQRQRVAMGRAIVRDADAFLFDEPLSNLDAKLRGQMRAEI +SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGVLQQVASPRELYEQPLNLFVAGFIGS +PSMNFLPATVKEQGGQYVLSSPIGDIPVPAEKAQRAAGRDIVFMGLRPEFFEDAELVEDA +KRPHGSEFDATLTHLEWLGHEQYGYIEFEPDPEVAELLSSLAKDLDADELRPVVVTTLSA +ESAARPGVPTRLWVDTTRVHLFDPKTGENLTRDAEAGAELTRRTAEARRRQIEAAQARDA +EGR +>PROKKA_00417 +MASITLNHIDKTYDDGFHAIKDVNLEIEDGEFVILVGPSGSGKSTLLRMIVGLEDITDGE +MLIDGRRVNEAAPKDRNLAMVFQNYALYPHLTVYENIAFPLRLIKDNKPSEEEIDRKVRD +AARVLELEDHLERKPGNLSGGQRQRVAMGRAIVREADAFLFDEPLSNLDAKLRGQMRAEI +SQLQRRLATTSVYVTHDQTEAMTLGDRVAVLKKGELQQVASPRELYEQPLNLFVAGFIGS +PSMNFLPASLKQKEGGHVLSSPIGDIPVPPEKARAAEGRDIVFLGLRPEFFEDAELVEDS +RRDRGSTFDATLTHLEWLGHEQYGYIEFEPDPAVAEMLSALAKDLDADELRPVVVATLSG +ESRARPGTPTRLWVDTTRVHLFDPTTGENLTRDPEVGAELTRRAGEERRRQIEMAAERDA +AEHEADAPRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000449.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000449.fa new file mode 100644 index 0000000000000000000000000000000000000000..6642d51c6980b265528002dfd36e456381e9fd36 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000449.fa @@ -0,0 +1,34 @@ +>PROKKA_00417 +MDTAALSPSPSPASGAEHAHVLTLACTNRKGIVHAVTGALLGVEADITESQQYGSPDTGD +FFMRVEFMTPAVREDIEQALAPVREEFGMRMGLWDAAHRMRTLVMCSKDGHTLNDLLFQQ +RAGTLPIEIPVVVSNHLDLQPLASFYGVPFIHVPVSKDPSSRDSKEAAEDRLRDLIAQFD +IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV +TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLAQAVRWHAQHRVLTDGRRTVVF +S +>PROKKA_00138 +MDTAALSPSPSPASGAEHARVLTLACTNRKGIVHAVTGALLGVEADITESQQYDSPDTGD +FFMRVEFVTPATREDIEQALAPVREEFGMRMGLWDAAQRMRTLVMCSKDGHTLNDLLFQQ +RAGTLPIEIPVVVSNHLDLQPLASFYGVPFIHVPVSKDPSSRDSKEAAEDRLRDLIAQFD +IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV +TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLAQAVRWHAQHRVLADGRRTVVF +S +>PROKKA_02543 +MDTATLSPSPTPASGAEHAHVLTLACTNRMGIVHAVSGALLQVGADITESQQYDSPESGD +FFMRVEFVTPARREEVAAALEPVREEFGMRMGLWDAGHRMRTLVMCSKDGHTLNDLLFQQ +RAGTLPIEIPVVVSNHLELQSLASFYGVPFIHVPVSADPESRDSKAAAEDRLRGLIAEYD +IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV +TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLVQAVRWHAQHRVLADGRRTVVF +S +>PROKKA_02411 +MDSTPAAPSEASARHRIVLTLSCPDRPGIVHAVTGALLEADANITESQQYDSPDTGTFFM +RVAVDAAATREEVEAAVRPVADRFGMHLQVWDADTPLRALVMCSKDGRTLNDLLFQQRTG +SLPVQIPVVVSNHLDLQPLASFYGVPFIHVPLSTDPASRNSKAAAEDRLRELIREYEIDV +VVLARYMQILSDELCRDLEGMAINIHHSFLPSFKGARPYHQAHERGVKIIGATAHYVTAD +LDEGPIIAQSVHPVTHAQTAEDFVERGRDVEGATLVQAVRWHAEHRVLLDGHRTVVFS +>PROKKA_00420 +MDTAALSLSPSPASGAEHAHVLTLACTNRKGIVHAVTGALLGVEADITESQQYGSPDTGD +FFMRVEFMTPAVREDIEQALAPVREEFGMRMGLWDAAHRMRTLVMCSKDGHTLNDLLFQQ +RAGTLPIEIPVVVSNHLDLQPLASFYGVPFIHVPVSKDPSSRDSKEAAEDRLRDLIAQFD +IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV +TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLAQAVRWHAQHRVLTDGRRTVVF +S diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000451.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000451.fa new file mode 100644 index 0000000000000000000000000000000000000000..abda4d79d0d04a48b17f6c8da979a6cfea0cfab2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000451.fa @@ -0,0 +1,45 @@ +>PROKKA_00420 +MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA +EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM +MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS +AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR +SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL +AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP +RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY +DGLEGW +>PROKKA_00141 +MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA +EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM +MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS +AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR +SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL +AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP +RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY +DGLEGW +>PROKKA_02539 +MTQTPDINTQPLSEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA +EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTALMDHGDTL +MGLSLAHGGHLTHGMKINFSGKNYKIAAYEVEPDTYRIDMDKVREKALEAQPKVIVAGWS +AYPRQLDFAAFRSIADEVGAKLWVDMAHFAGLVAAGLHPNPVPHADVVTSTVHKTLAGPR +SGFILSTEEFKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLQGAQIL +AERLTAPDMTELGISVLTGGTDVHLVLVDLRESQLDGKQGEDILHEVGITVNRNSVPWDP +RPPMTTSGLRIGTPALASRGFGEAEFREVAEIVAAALKPSPDVQALRARVVKLTEDFPLY +DGLEGW +>PROKKA_02408 +MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA +EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM +MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS +AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR +SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL +AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP +RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY +DGLEQW +>PROKKA_00423 +MTQTPDINTQPLAEVDPEIAAALADELGRQRGTLEMIASENFVPRAILETQGSVLTNKYA +EGYPGRRYYGGCEFVDVAENLAIQRAKDLFGAEHANVQPHAGAQANVAVMTSLLDHGDTM +MGLSLAHGGHLTHGMKLNFSGKNYSIAAYEVEPDTHRIDMDKVREKALEARPKVIVAGWS +AYPRQLDFAAFRSIADEVGARLWVDMAHFAGLVAAGLHPNPVPHADVVSSTVHKTLAGPR +SGFILSTEELKKKIDSAVFPGQQGGPLMHAIAGKAVAFKIAGSADFKEKQERTLAGAQIL +AERLTAPDMAEHGISVLTGGTDVHLVLVDLRESQLDGRQGEDILHEVGITVNRNSVPWDP +RPPMTTSGLRIGTPALASRGFGEAEFREVSDVIAEALKPSPDVEALRARVVKLTEDFPLY +DGLEGW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000452.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000452.fa new file mode 100644 index 0000000000000000000000000000000000000000..6dc1c6c704ddc6507b7a4ff4acb6b14f32988d0b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000452.fa @@ -0,0 +1,35 @@ +>PROKKA_00421 +MTAKVLDGKATAAAIKEELRGRVAALAERGHTPGLGTLLVGEDAGSQKYVAGKHRDCAEV +GIESIQRELPADATEEQILDVVRELNEDPACTGYIVQLPLPKHVDTQKVLEAIDPDKDAD +GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVELAGKHVLVIGRGVTIGRPAGL +VLTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVTPEQVKEGVIVLDVGVSRV +TGEDGTSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAADGEDWAGER +AGA +>PROKKA_00142 +MTAKVLDGKATAAAIKEELRGRVAALAERGHTPGLGTLLVGEDAGSQKYVAGKHRDCAEV +GIESIQRELPADATEEQILDVVRELNEDPACTGYIVQLPLPKHVDIQKVLEAIDPDKDAD +GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVGLAGKHVLVIGRGVTIGRPAGL +VFTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVKPEQVKEGVIVLDVGVSRV +TGEDGTSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAADGEDWAGER +AGA +>PROKKA_02538 +MTAKVLDGKATAAALKEELRERVSALTERGHTPGLGTVLVGEDAGSQKYVAGKHRDCAEV +GIESIQRELPADATEEEILAVVRELNEDPACTGYIVQLPLPKHVDTQKVLEAIDPDKDAD +GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRRHGVELAGKHVLVIGRGVTIGRPAGL +VLTRREVNATVTLAHTGTQNLDELLGQADVVIAAAGSAHMVRPEQVKDGVIVLDVGVSCV +TGEDGTSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLSNVVEAAERAADAEDWAGER +AEA +>PROKKA_02407 +MTAKVLDGKATAAAIKEELRGRVAALAERGHTLGLGTLLVGEDAGSQKYVAGKHRDCAEV +GIRSIQKELPGDATEEQILDVVRELNEDPECTGYIVQLPLPKHVDTQKVLEAIDPDKDAD +GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVELAGKHVLVIGRGVTIGRPAGL +VLTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVKPEQVKEGVIVLDVGVSRV +TGEDGKSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAADGEDWAGER +AGA +>PROKKA_00424 +MTAKVLDGKATAAAIKEELRGRVAALAERGHTPGLGTLLVGEDAGSQKYVAGKHRDCAEV +GIESIQRELPADATEEQILDVVRELNEDPACTGYIVQLPLPKHVDTQKVLEAIDPDKDAD +GLHPMNLGRLVASVGGELDSPLPCTPAGCVELLRHHGVELAGKHVLVIGRGVTIGRPAGL +VLTRREVNATVTLAHTGTTNLDELLASADVVIAAAGSAHMVKPEQVKEGVIVLDVGVSRV +TGEDGKSRVLGDVDPAVKEKAAWMAPNPGGVGPMTRVMLLANVVEAAERAAEDDGRAGER +AGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000453.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000453.fa new file mode 100644 index 0000000000000000000000000000000000000000..f65e0d090b4cc6db316abeb3532f6263bd6a5c03 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000453.fa @@ -0,0 +1,35 @@ +>PROKKA_00422 +MSHTTLHASPGDASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM +LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY +SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ +ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR +EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA +LPAPVTTLTRRASLEDVFLILTGRTLVD +>PROKKA_00143 +MSHTTLHASPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM +LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY +SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ +ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR +EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA +LPAPATTLTRRASLEDVFLILTGRTLVD +>PROKKA_02536 +MSHATPASPSPSQSPADAPDAGPAPVIRARGLRKQYGDFHAVKGIDLDVRPGECFGLLGP +NGAGKSTTMRMLAGTSQRTAGELSILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENI +LIYGRYFGLPYSYLRPKADELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFL +LDEPTTGLDPQARHILWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDGGQIMAAGT +PAALIREHAAREVLEARFGADRNEAAARTVQARAGDGVVHRVEVLPDRVLVYAAHADDLH +AVVQGLVDDGALPAPVTTLTRRASLEDVFLILTGRTLVD +>PROKKA_02406 +MTRTTSSPSPAAPAGGGAAPVILARGLRKQYGDFHAVQGIDLDVRPGECFGLLGPNGAGK +STTMRMLAGTSQRTGGELRILGIDPEEDGPAVRARLGVVPQQDNLDEDLTARENILIYGR +YFGLPYSYLRPKAEELLAFAQLTDKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPT +TGLDPQARHTLWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDAGRIMAAGTPASLI +REHASREVLEARFGTDRNATAARLLRESLPGLHRLEVLPDRVLLYTEHADTLQQDLDRLV +AEGHVTAPVTQLTRRASLEDVFLILTGRTLVD +>PROKKA_00425 +MRLCCRLVSPTTLHAPPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAG +KSTTMRMLAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYG +RYFGLPYSYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEP +TTGLDPQARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAEL +IREHASREVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQ +RLVDEGALPAPATTLTRRASLEDVFLILTGRTLVD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000455.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000455.fa new file mode 100644 index 0000000000000000000000000000000000000000..183897dc20a910ae5581261f352902a0d3fd9214 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000455.fa @@ -0,0 +1,25 @@ +>PROKKA_00425 +MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL +VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT +KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP +VSGTVIG +>PROKKA_00146 +MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL +VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT +KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP +VSGTVIG +>PROKKA_02532 +MSQPLTTGSGETRRGPRAGLRVGSVGFAAMIVILIVAIMFAANQNDVIGWLVVAVAAGWL +VFALVVFLQMRRGVQAAGRKVDAAMENARADVAALRGQGAAAAPQAAAHAPAGDPMRDTK +LDHSFKIAQVQVKVVREQLAAGGAMDREMVDRALETIDITAANARDMIKESRGQGGSEGP +VSGTVIG +>PROKKA_02402 +MPQSIPSGSAGTRPARAGLTVGSTGFAVMVAVLLVAIVFAANANDLIGWLVVAIAAGWLV +FAVVVFLQMRKGVREAGRKVDTAMQNARADVAALRAPQQPAPAAAVPAAAGDPMRDTKLE +HSFKICQVQARVITQQLDAEGPLDREMVDRALETITITAQNARDMIKESARDAEGPVSGT +VVS +>PROKKA_00428 +MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL +VFAVVVYLQMRRGVQAAGRKVDTAMQNARADVAALRGRDADAAAPAVAPSAPAADPLRDT +KLDHSFKIAQVQVRVVREQLAAGESMDREMVDRALETIDITASNARDMIKESRAGGAEGP +VIG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000456.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000456.fa new file mode 100644 index 0000000000000000000000000000000000000000..6a5543856bf25920721ab2a528573513e8dfa285 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000456.fa @@ -0,0 +1,35 @@ +>PROKKA_00426 +MTALPEKDPVTGKYPEPAEGEPVVHANAGAPKADGAVRVATVNVNGIRASHRKGMREWFA +GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV +RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQVDKYRFLDEMVRR +LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR +ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA +PLVVDYQF +>PROKKA_00147 +MTALPEKDPVTGKYPEPAEGEPVVHANAGAPKADGAVRVATVNVNGIRASHRKGMREWFA +GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV +RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQEDKYRFLDEMVRR +LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR +ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA +PLVVDYQF +>PROKKA_02531 +MTVLPEKDPVTGKYPEPAEGEPVVHANAGAPKEDGALRVATVNVNGIRASHRKGMREWFA +GRGVDVLTLQEVRAPADITAKLVREVVGEDWDEVHLADAEAAAKGRAGVAIASRFPIEAV +RTGISDADAYFDDAGRWIEADLRLPDGSALTVVSAYVHSGEADTPKQVDKYRFLDEMVRR +LGELSAGPDHALVTGDLNVGHTELDIKNWKGNQKKAGFLPEERAYFDRFFGELGFTDVHR +SLAGQVPGPYTWWSMRGKAFDNDAGWRIDYQMATAALAEKASSAVVDRAPSWGTRFSDHA +PLVVDYRF +>PROKKA_02401 +MTVPQKDPVTGKHPGPAAGEPVVHANAGAPKPEGALRVATVNVNGIRASHRKGMGGWFAG +RGVDVLTLQEVRAPQEIAHALVRDVVGDAWDEVHVADVEAASKGRAGVAVASRFPFEDVR +TGIGGAEDHAADAGRWIEADVRLPDGSLLTVVSAYVHTGGVDTPKQVDKYRLLDEMVRRL +PELAADGRHVLVTGDLNVGHTERDIKNWRGNVKKAGFLPEERAYFDRFFGELGYVDVHRT +LAGDVPGPYTWWSMRGQAFDNDAGWRIDYQMATPELAARATSAVVDRAPSWGTRFSDHAP +LVVDYQF +>PROKKA_00429 +MTALPEKDPVTGKYPEPAEGEPVVHAHAGAPKADGAVRVATVNVNGIRASHRKGMREWFA +GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV +RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQVDKYRFLDEMVRR +LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR +ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA +PLVVDYQF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000461.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000461.fa new file mode 100644 index 0000000000000000000000000000000000000000..7be982f77c1a2734aaa1df26530e125e1638ec64 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000461.fa @@ -0,0 +1,20 @@ +>PROKKA_00432 +MHPLDDDPHAATDRDPAPDRAALRPLRLFQTVTAVTGALSAAGVAGVLALQSTPGYARAV +LEARSWGASEVTDADVAAFVTPAGAWPVAAAAVVLLAVVLLAGITRRIRAVRPVGSVLVV +LGMLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAMWLRVAHRRETRDGFDG +>PROKKA_00153 +MMGGMHPLHDDPHETTERDPGPDRAALRPLRLFQTVTAVTGALSAAGVGGVLALQATPGY +ARAVLEARSWGASEVTDADVAAFLTPAGAGPVAAAAVVVLTLVLLAGITRRIRAVRPVGS +VLVVLGMLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAVWLRVAHRRETRDAFDV +>PROKKA_02525 +MHTPDDAAADADDAAARAALHDRVVRRPLRRLLTLTAVTGALSALGTAGVLALQGAPGYA +RAVLEARSWGRAAVTDADVASFLTPPWGVPAAVLGVLAVAALLMLGVARRVRAVRPVGTV +AVGLGLLSAAFWMVDGGRMVAAGGAGPLVLAAVVAMFLACAVWLLTAHLRATRDAFDG +>PROKKA_02396 +MRSDDVAPASARPSGLDDPAVRGPIRRYQAMTAGTGLVSAAAVAGVLGLQSDPGYAREVL +QSRTWGQYEVSAQQVQDFLTPPGGAVLGAVGVLLTAALLVWGAQRLWGATRWLGTALAGV +GLLSAVFWAVDGGRMAARGASGMAVLVAVGAMAVFCAVWLVTAHSKAVREAFLG +>PROKKA_00435 +MHPLDDDPHETTDPAPDLASLRPLRLFQTVTAVTGALSAAGVGGVLALQSTPGYARAVLE +ARSWGASEVTDADVAAFLTPAGAWPVAAAAVVVLTLVLLAGITRRIRAVRPVGSVLVVLG +MLTAAFWMVDGGRMVQAGGGGPVVLGAVVGMLVSSAVWLRVAHRRETRAAFDV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000462.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000462.fa new file mode 100644 index 0000000000000000000000000000000000000000..ff079f596fad6929fd1b471438103df6e6e6c4c3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000462.fa @@ -0,0 +1,30 @@ +>PROKKA_00433 +MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD +RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP +IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA +CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA +CPRGIQVTKAISEVKRAILARQF +>PROKKA_00154 +MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD +RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP +IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA +CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA +CPRGIQVTKAISEVKQAILARQF +>PROKKA_02524 +MSHAATETEAPVAQDQTQAAGGGMGAIESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD +RVLDALHKVKWDHDGTLSFRRSCAHGICGSDAMRINGRNRLACKTLLKDLDLSKPILVEP +IKGLPVEKDLIVDMDPFFQSYREVMPFLVAEGHEPSKERYQSQADRARYDDTTKCILCAA +CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTDA +CPRGIQVTKAIAEVKQAILARQF +>PROKKA_02395 +MSHAATETQAPAAPAQQTQGQDGGMGEIESFDITLRVRRFLPESSEESYWDEWRLTMFGT +DRVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSQPITVE +PIKGLPVEKDLIVDMEPFFQSYREVMPFLVAKGHEPSKERYQSQADRAIYDDTTKCILCA +ACTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTE +ACPRGIQVTKAIAEVKQAILARSF +>PROKKA_00436 +MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD +RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP +IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA +CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA +CPRGIQVTKAISEVKQAILARQF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000463.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000463.fa new file mode 100644 index 0000000000000000000000000000000000000000..6cd8d67d2fb69ce4dab05d5d91b69927e00ed81a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000463.fa @@ -0,0 +1,55 @@ +>PROKKA_00434 +MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED +NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT +RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA +YKQKRTAGVVSYELATGEIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL +PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR +SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT +CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG +IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE +DSIRRALAKIEELRGRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR +GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY +>PROKKA_00155 +MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED +NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT +RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA +YKQKRTAGVVSYELATGGIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL +PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR +SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT +CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG +IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE +DSIRRALAKIEELRGRYENVSVQDKGRRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR +GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY +>PROKKA_02523 +MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED +NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT +RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFYNEFYVLDLLLVEEDAVREDGTP +YKQKRAAGVVSYELATGEIHVFQAKSVVFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL +PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNSDGERFMERYAPTIKDLAPRDIVAR +SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT +CHYFMGGVPTNIKAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG +IYAAEYAQTADFVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE +DSIRRALAKIEELRGRYENVSVQDKGKRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR +GGHYREDYPDRDDANFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY +>PROKKA_02394 +MQVHKYDVVIVGAGGAGMRAAIESGQRARTAVLTKIYPTRSHTGAAQGGMCAALANVEED +NWEWHTFDTVKGGDYLVDQDAAEIMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT +RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHDVEFYNEFYVLDLLLVDEDATREDGTP +YTQKRVAGVVSYELATGEIHVFQAKAVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL +PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNAEGERFMERYAPTIKDLAPRDIVAR +SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT +CHYFMGGMPTNVKAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG +IHAAEYAAQADWVELPEGGELPTVQHIENLRSATGSERVADIRAELQESMDADMQVFRDE +DSIRRALAKIEELRHRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR +GGHYREDYPNRDDANFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY +>PROKKA_00437 +MQVHKYDVVIVGAGGAGMRAAIEAGQRAHTAVLTKIYPTRSHTGAAQGGMCAALANVEED +NWEWHTFDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHT +RDHGKAPVRRACYAADRTGHMILQTLYQNCVKHNVEFFNEFYVLDLLLVEEDAVREDGTA +YKQKRTAGVVSYELATGEIHVFQAKSVIFATGGAGKVYKTTSNAHTLTGDGMAIAYRAGL +PLEDMEFVQFHPTGLAGLGILLSEAARGEGGILRNADGERFMERYAPTIKDLAPRDIVAR +SMAEEVRQGRGAGPNKDYVLLDLTHLEPSHIDEKLPDITEFARTYLGVEPYTEPVPVFPT +CHYFMGGIPTNIQAEVLQDNDTVVPGLYAAGEVACVSVHGSNRLGTNSLLDINVFGRRAG +IYAAEYAAQADWVELPEGGELPTVEHIENLRSATGSERVADIRAELQESMDADMQVFRDE +DSIRRALAKIEELRGRYENVSVQDKGHRFNLDLLEGMELGYLLDIAEAMTLAALGRKESR +GGHYREDYPDRDDENFMAHTMIYRDETAEMEGVKGIRFETKPVVVTRYQPMERKY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000464.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000464.fa new file mode 100644 index 0000000000000000000000000000000000000000..ade8fe9f6a0ae2657d32ee5f9d296464e907900d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000464.fa @@ -0,0 +1,20 @@ +>PROKKA_00435 +MSTTAETTIAAPRSRRLDPKYTRDGGGRGNFEMLAWLFMRISGVFLVVLIAVHLTTNLLV +GDGIHAIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTRRGSARFWLTMI +LYIATAVIIILGTLVIFTFDPCMVDASGALLEGSPAFCG +>PROKKA_00156 +MSTTAETTIAAPRSRRLDPKYTRDGGGRGNFEMLAWLFMRISGVFLVVLIAVHLTTNLLV +GDGIHAIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTRRGSARFWLTMI +LYIATAVIIILGTLVIFTFDPCMVDASGALLEGSPAFCG +>PROKKA_02522 +MSTTAETTIAAPRTGRIDPKYTRDKGGRGNFEMLAWLFMRVSGVILVLLIAVHLTSNLLM +GDGIQGIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTERGTARFWLTMI +LYIATAVIITLGTLVIFTFDPCMVDASGALLEGSPAFCG +>PROKKA_02393 +MSTTAETPLAAPRTGRLDSKYVRGESGKGNFEMLAWLFMRVSGVFLVVLVFAHIFANLMV +GDGISGLDFGFVAGKWANPLWQLWDLALLWLAMLHGANGVRTIINDYAERDGVRFWLSMI +LYVATAVIIVLGSLVIFTFDPCMVDASGALLEGSPAICR +>PROKKA_00438 +MSTTAETTIAAPRSRRLDPKYTRDGGGRGNFEMLAWLFMRISGVFLVVLIAVHLTTNLLV +GDGIHAIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTRRGSARFWLTMI +LYIATAVIIILGTLVIFTFDPCMVDASGALLEGSPAFCG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000465.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000465.fa new file mode 100644 index 0000000000000000000000000000000000000000..e04b3d532a84666ed1aa38a5135239909e76fe78 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000465.fa @@ -0,0 +1,20 @@ +>PROKKA_00436 +MSSATAQAPAKNGRGTLYRGHGGMWSWVGHRVTGVVIFFYLLVHVLDTALVRVSPEAYNA +VIGSYKTWYFALGEAGLVAAIIFHALNGLRIILVDFWKGGTQHHKTLLWIVLGLWVVLTL +GFAIRHFSLALGGH +>PROKKA_00157 +MSSATAQAPAKNGRGTLYRGHGGMWSWVGHRVTGVVIFFYLLVHVLDTALVRVSPEAYNA +VIGSYKTWYFALGEAGLVAAIIFHALNGLRIILVDFWKGGTQHHKTLLWIVLGLWVVLTL +GFAIRHFSLALGGH +>PROKKA_02521 +MSSATAQAPAKNGRGTLYRGHGGMWSWVGHRVTGVVIFFYLLVHVLDTAMVRVSPEAYDA +VIGAYKTWYFALGEAGLVAAIIFHALNGLRIILVDFWKGGTKHHKTLLWIVLALWAVLTV +GFAIRHFSLALGGY +>PROKKA_02392 +MSSATAQAPAKNGRGTLYRGHGGMWSWVGHRVTGVVIFFYLLVHVLDTAMVRVSPEAYDA +VIRSYKTWYFALGETALVAAILFHALNGLRIILVDFWKGGTKHHKTLLWVVLAVWAVLFL +GFAVRHLSIAFGGH +>PROKKA_00439 +MSSATAQAPAKNGRGTLYRGHGGMWSWVGHRVTGVVIFFYLLVHVLDTALVRVSPEAYNA +VIGSYKTWYFALGEAGLVAAIIFHALNGLRIILVDFWKGGTQHHKTLLWIVLGLWVVLTL +GFAIRHFSLALGGH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000466.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000466.fa new file mode 100644 index 0000000000000000000000000000000000000000..b70aa21a897105524d8c638528e5568fb4ad1e47 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000466.fa @@ -0,0 +1,40 @@ +>PROKKA_00437 +MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR +ATWDRLAPLAAGMLVVTGEAHREAVCTQLPALAETDLVLEPSPKDSAAAIGLAAAILSLR +DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL +RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG +LMEIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA +IARLNPVRDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT +TEHAQEVKKAVEALKAEGVDEVL +>PROKKA_00158 +MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR +ATWDRLAPLAAGMLVVTGEAHREAVCMQLPALAETDLVLEPSPKDSAAAIGLAATILSLR +DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL +RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG +LMEIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA +IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT +TEHAQEVKKAVEALKAEGVDEVL +>PROKKA_02520 +MSTDPNLTEAGREDAPGSALSRFHVVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR +ATWDRLAPLAAGMLVVTGAAHRDAVCGQLPDLDTADLVLEPSPKDSAAAIGLAAAILSLR +DPDTIMGSFAADQVIAPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL +AVPGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG +LMEIAHAWETERRDEVMERVWPELTKTAIDYAVAEPAAAVGDVAVIPGAFTWDDVGDFAA +IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTRRVIALIGIEDVVVVDTEDALLVTT +TDHAQEVKKAVEALKAEGVDEVL +>PROKKA_02391 +MSIDPTAAQSAPSQPSASALERFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR +ATWDRLAPLAGGIMVVTGRAHEDAVCRQLPDVGAADLVLEPEPKDSAAAIGLAAAILWLR +DSDTIMGSFAADQVIGPVDVFQDAVRQAVETAATGRIVTIGITPTHAATGFGYIRTGRRL +SVAGAPDAHDVAAFVEKPDQRVAERYVASGRYLWNAGMFVAPVALMLQHLEANEPELHAG +LTEIARAWETPERDAVMARVWPGLKKTAIDYAVAEPAATAGDVAVIPGAFTWDDVGDFAA +IARLNPVKDGSGVTVIGDTPRVYSDSATGVVVTDTSRVIALIGVEDVVVVDTGDALLVTT +TEHAQDVKRTVESLKAQGADDVL +>PROKKA_00440 +MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR +ATWDRLAPLAAGMLVVTGGAHREAVCMQLPDLAETDLVLEPSPKDSAAAIGLAAAILSLR +DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL +RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG +LMQIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA +IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT +TEHAQEVKKAVEALKAEGVDEVL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000467.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000467.fa new file mode 100644 index 0000000000000000000000000000000000000000..f7e07a2f6a169b2ea18e44ce6619003351d3b418 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000467.fa @@ -0,0 +1,40 @@ +>PROKKA_00438 +MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG +YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT +AVMAGVAVALGRILRGATADADLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD +VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA +VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE +VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA +WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH +>PROKKA_00159 +MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG +YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT +AVMAGVAVALGRILRGATADPDLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD +VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA +VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE +VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA +WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH +>PROKKA_02519 +MTTSDSVLSDQRPASLPSVASVVAELEAEVVAFRRDLHRHPELSYEEYRTTDRIMELLTG +YGFSPVRMESTGAYVDIGEGPVVLALRADIDALPLEEETGLPYVSVNDGVTHACGHDMHT +AVMAGAALVIGRILRGATADPALRTAGERARGSVRVIFQPAEERLPGGSLSVLRQGILDG +VPRILAAHCDPAVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA +VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGDLLDE +VVTQVAAPYGVQVQLEHVRGVPPVHNTDAETALIETAARRELGARAIQLTPQSMGGEDFA +WMTQRVPGSMLRLGTRTPGGPVYDLHRGDFTPDERAIGVGMRVFAAAALQALVGEEGH +>PROKKA_02390 +MTTSESVVTGTAPRLAPPSVAPVVQQLEEHVTAFRRDVHRHPELSYEEYRTTDLIVETLA +EYGLNPVRLEGTGAYVDLGEGPVVLGLRADIDALPVEEETGLPYVSVNDGVAHACGHDMH +TAVMLGTALTLGRILRGAAPTAELRAVGERARGRVRVIFQPAEERLPGGSLAVIRQGVLE +GVPRVLAAHCDPHFDVGTIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQI +AVNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDAGVWEEAGALLD +EVVTQVASPYGVQVQLEHIRGVPPVDNAEAETALIEDAARRELGAHAIALTPQSMGGEDF +AWMTQKVPGAMLRLGTRTPGGPTYDLHRGDYAPDERAIGVGMRVFAAAALDVLAGPAR +>PROKKA_00441 +MTTSDSVLTGPRPTSVPSVGPVVAELEDEIVSFRRDLHRHPELSYEEYRTTDRIVELLSG +YGLSPVRMESTGAYVDVGEGPVVLALRADIDALPVEEETGLPYVSVNDGVAHACGHDMHT +AVMAGVAVALGRILRGATADPDLRAVGERVHGTVRVIFQPAEERLPGGSLAVLRQGILDD +VPRILAAHCDPQVDVGSIGTRIGAITSAADTIRITLTGRGGHTSRPHLTEDMVFALSQIA +VNVPAVLSRRIDVRSAVSVVWGQIAAGSAPNAIDNTGYLAGTMRCLDADVWEEAGALLDE +VVRQVAAPYGVHVQLEHVRGVPPVHNTEGETALIETAARRELGSRAIVLTPQSMGGEDFA +WMTQKVPGSMLRLGTRSPGGPIYDLHRGDYAPDERAIGVGMRVFTAAALQVLTGEDHH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000468.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000468.fa new file mode 100644 index 0000000000000000000000000000000000000000..a7f5cab04f95c634c435e9f7554e96eeffeb3133 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000468.fa @@ -0,0 +1,40 @@ +>PROKKA_00439 +MGIATPSAARRRRLLLPAAALGVSGLLLTACGAPPEQSEASDSGAAESEAIATVDGVGSD +NKDYKACIVSDEGGFDDRSFNQSSYEGLKAAEEAYGITTSEAESNEPSEYTPNVTAMVNG +DCDAVIGVGFLLGDAMKPIAAQHSDTHFFGVDVTDGDFTDNFQKLTYDTAQAAFLAGYLA +AGTTETGAVATYGGAEIPTVTIFMDGFARGVEHYNEVKDKDVKVLGWDKDAKTGSFTGDF +ENVANGKTNTANFINEGADIVMPVAGPVGLGTLDAVREANQGGKDVKVIWPDSDGYESTK +DGNLILTSVKKNMGQSVTDVIAADLKDEFSAEPYVGTLENKGVELAPFHDFEDTVPQELK +DELKDLEAKIISGELKVGSEYSPEA +>PROKKA_00160 +MGIATPSAARRRRLLLPAAALGVSGLLLTACGAPPEQSEASGSGAAESEAIATVDGVGSD +NKDYKACIVSDEGGFDDRSFNQSSYEGLKAAEKAYGITTSEAESNEPSEFTPNVTAMVNA +DCDAVIGVGFLLGDAMKPIAAQHSDTHFFGVDVTAEGFSDNVQKLTYDTAQAAFLAGYLA +AGTTETGTVATYGGMEIPTVTIFMDGFARGVEHYNEVKDKDVKVLGWDKDAKTGSFTGDF +KNVANGKTNTANFINEGADIVMPVAGPVGLGTLDAVREANQGGKDVKVIWPDSDGYESTK +DGNLILTSVKKNMGQSVADVIAADLKDEFSAEPYVGTLENKGVELAPFHDFEDTVPQELK +DELKDLEAKIVSGELKVGSEYSPEA +>PROKKA_02518 +MGTATPSAEGRRRLLLPAAVLGASALLLTACGQAPEASNSSEPAGSASATGAAAEVGSDN +SDYTGCIVSDEGGFDDRSFNQSSYEGLKAAEEEFGIEIREAESNSVGEYVPNLNAMLDAD +CNLVVAVGFQLGDTMKPIAEENAETKFVGVDVTAPGFPENVRNIIYDTAQGAFLAGYLAA +GMTETGTVATYGGMEIPTVSIFMDGFARGVEHYNEVKGEDVRVLGWDTENRTGSFIGDFS +NQNAGKTNTANFINEGADIIMPVAGPVGLGTIDAVKEANGGGKDVKVIWVDSDGYETTQD +GEVILTSVMKRMGDAVKQVIAEDINDEFTSEAYVGTLENDGVALAPFHDFEDAVPQELKD +ELEALEAGIVSGEIEVGSEDSPEA +>PROKKA_02389 +MGIVSPLAGRRRLAVPAALLSSGLLLAGCGAPPAENSGSASGSGAAVSADAAAGSDNKDY +KSCIVSDAGGFDDRSFNQSSYEGLKAAEEAYGIETNKAESKDASEFTPNVNAQVNAQCDS +IIGVGYMLGDTIKPIAQKNPDIHFLGVDVTADGFSDNVKKLTYDTAQAAFLAGYVSAGMT +KTGTVATYGGMEIPTVTVFMDGFAAGVEHYNEVKGKDVKVLGWDREAKTGSFTGDFDNQA +NGKTNTANFINQGADIVMPVAGPVGLGTLDAVKEANAGGKSVAVVWPDSDGYESTKDGAL +ILTSVVKNMGQSVSDVIGQDLKGEFSADPYVGTLENKGVELAPFHDFDSKVPQELKDEVQ +TLQEDIISGKVKVDSEYSPKS +>PROKKA_00442 +MGIATPSAARRRRLLLPAAALGVSGLLLTACGAPPEQSEASDSGAAESEAIATVDGVGSD +NNDYKACIVSDEGGFDDRSFNQSSYEGLKAAEEAYGITTSEAESNEPSEYTPNVTAMVNG +DCDAVIGVGFLLGDAMKPIAAQHSDTHFFGVDVTDGDFTDNFQKLTYDTAQAAFLAGYLA +AGTTETGTVATYGGAEIPTVTIFMDGFARGVEHYNEVKDKDVKVLGWDKDAKTGSFTGDF +ENVANGKTNTANFINEGADIVMPVAGPVGLGTLDAVREANQGGKDVKVIWPDSDGYESTK +DGNLILTSVKKNMGQSVTDVIAADLKDEFSAEPYVGTLENKGVELAPFHDFEDTVPQELK +DELKDLEAKIISGELKVGSEYSPEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000469.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000469.fa new file mode 100644 index 0000000000000000000000000000000000000000..96468da6df2a05037b68a09a013198432e2d5af3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000469.fa @@ -0,0 +1,50 @@ +>PROKKA_00440 +MRLELRGISKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL +LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI +REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG +IIRQLREDGTAIVFISHKLREVKAVSDDITVLRRGRVVGTADPSAEAAELAALMVGRSVV +LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA +IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV +APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF +IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV +PGDTSRETLGLMMAGQTPDDAALASGADVAAGTPGTAGEAPAAHPTTEGERP +>PROKKA_00161 +MRLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL +LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI +REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG +IIRQLRADGTAIVFISHKLREVKAVSDDITVLRRGRVVGTAEPSAEAAELAALMVGRNVV +LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA +IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV +APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF +IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV +PGDTSRETLGLMMAGQTPDDAALASGTDVAADTPGTAGAAPAAHPTTEGERP +>PROKKA_02517 +MKLELRGITKRFGTFTANDSVDFVVRSGEVHTLLGENGAGKSTLMNVLFGLYDPTEGEIL +VDDRPVRFAGPGEAMRAGIGMVHQHFMLVPVFTVAENIALGDEHTRAAGVLDLEATRRKI +RAISDEYGFAVDPDAVVEDLPVGVQQRVEIIKALVRDAKVLILDEPTAVLTPQETDELLA +IIDRLRQDGTAIVFISHKLREVKAISEHITVLRRGKVVGTAEPSASAAELAALMVGRQVS +LNRAKTAPTLGEETFKVQDLTVVSPTGQVLVDHVSFAIRQGEILGVAGVQGNGQTELTEA +IMGLHKATGSVTLDGRELVGRSTRQIIRAGVGYVPEDRSTDGLVGSFTVAENMVLNRFDR +EPAGSALQLRPRAVRELAEARVQEFDVRTQGVVSPVSSLSGGNQQKVVMARELVDELRLF +IASQPTRGVDVGSIEFLHERIVRERDNGTPVMIVSTELDEILELSDRIAVMYHGRIVGIV +DGDASRETLGLMMAGQTPESLATETATTEEGPRA +>PROKKA_02388 +MKLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGQIL +LDGEPVAFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRGAGVLDLEATRRKI +REISDAYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLA +IIRQLRADGTAIVFISHKLREVKAISDDITVLRRGRVVGTADPSASAAELASLMVGRDVV +LNRRKTAPQLGEETFRVEHLTVVSPTGQVLVDDVSFGIRQGEVLAVAGVQGNGQTELTEA +IMGLQAKAAGSIRLDGRELLGRSTRQIIHAGVGYVPEDRSTDGLVGSFSVAENMVLNRFD +VAPAGSAVQLRPRAVRELAERRVEEFDVRTQGVDVPVSSLSGGNQQKVVMARELVDGLRL +FIASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVRELADRIAVMYHGRIVDI +VPGDASREHLGLLMAGQTAEDTHQEGARA +>PROKKA_00443 +MRLELRGITKRFGSFAANEDVNLTVESGRVHTLLGENGAGKSTLMNVLFGLYEPTEGEIL +LDGEPVRFSGPGEAMRAGIGMVHQHFMLVPVFTVAENVALGDEHTRALGVLDLEATRRRI +REISAQYGFDVDPDAVVEDLPVGVQQRVEIIKALVRDARILILDEPTAVLTPQETDELLG +IIRQLRADGTAIVFISHKLREVKAVSDDITVLRRGRVVGTAEPSAEAAELAALMVGRNVV +LERRKTAPTLGEETFRVEDLSVVSPTGQVLLDAVSFAVRQGEVLAVAGVQGNGQTELTEA +IMGLVKATGSVTLDGRELIGRSTRQIIRAGVGFVPEDRSTDGLVGPFSVAENMVLNRYDV +APAGNAVQMRPAAVRALAERRVAEFDVRTQGVDLPVSSLSGGNQQKVVMARELVDGLRLF +IASQPTRGVDVGSIEFLHDRIIAERDAGTPVLIVSTELDEVLELADRIAVMYHGRIVGIV +PGDTSRETLGLMMAGQTPDDAALASGADVAADTPGTTGAAPAAHPTTEGERP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000470.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000470.fa new file mode 100644 index 0000000000000000000000000000000000000000..b61c4e76136b06b573c8d76353f8a02c9f2a878d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000470.fa @@ -0,0 +1,45 @@ +>PROKKA_00441 +MSTAAPQRPAPASDPRVRPAPADSALRRILSGNGTVTALAILLSLLISGLLIIAVDEDVR +DAAGYFFARPGDLLSAAWAAFAGAFAALFRGAVFNYRASDATGMLYPLTETLTVATPLII +ISLGIAIAFRAGLFNIGGQGQFIFGAMFATWFGVHLHLPAGVHLLLVVVMGVLGGVLWGS +VVGVLKAWTGAHEVILTIMLNYVAVNLLAYLLNTPVLRAPATTNPVSAPLDRSAMFPRLL +GTDFRLHWGFFVALLAVLFTWWLMQRSTLGFRLRAVGANPDAARTAGISVKGSYVAAMAI +SGGLAGLAGATHVAGTESTLNTSVAGSFGFDAITVALLGRSHPVGVLFAGLLFGALRAGG +VTMQTETGVPVDIVLVVQSVIVLLIAAPPLVRAIFRLPAPGAARARRAADPVTQPAVAGA +ALTGAGGHAAAPSTGVQEAAAAAVADPQAPTTQPTDTAPTHRPHEQKGDAR +>PROKKA_00162 +MSTAAPQRPAPASDPRVRPAPADSALRRILSGNGTVTVLAILLSLLISGLLIIAVDEDVR +DAAGYFFARPGDLLSAAWAAFAGAFAALFRGAVFNYRASDATGMLYPLTETLTVATPLII +ISLGIAIAFRAGLFNIGGQGQFIFGAMFATWFGVHLHLPPGVHLLLVVVMGVLGGVLWGS +VVGVLKAWTGAHEVILTIMLNYVAVHLLAYLLNTPVLRAPGTTNPVSAPLDRSAMFPRLL +GTDFRLHWGFFVALLAVLFTWWLMQRSTLGFRLRAVGANPDAARTAGISVKGSYLAAMAI +SGGLAGLAGATHVAGTESTLNTSVAGSFGFDAITVALLGRSHPVGVLFAGLLFGALRAGG +VTMQTETGVPVDIVLVVQSVIVLLVAAPPLVRAIFRLPAPGAARARRAADPVTQPAVAGA +AVTGAGGHAAAPSTGVQAAAATAVADPQAPTTQPTDTAPTHRPHEQKGDAR +>PROKKA_02516 +MSQNPPQTPASEPVQPPGGAPVPAAGVTGADAPPAPERGSQESVLREILSGNAMVTALAI +VLSLAISAVLIIVTSPDVIDAAGYFFARPMDTLSAAWTVVSDAYLALFRGSIVNYRADSF +ADMIRPLTETLTVATPLIIASLGVAIAFRTGLFNIGGQGQFLIGAAFATVGGVYLDLPLG +VHLLLVIVMGALGGLLWGAVVGLLKAYTGAHEVILTIMLNYVALHLVSYLLNTPFLRRAG +TNNPISEQFPDSAAFPALLGDGFRLHWGFVMALVLTFLAWWMLERSTLGFRLRAVGANPA +AARTAGISVKGGYVAAMAIAGALAGLGGVAHISGTEKVLTSGIAGQFGFDAITVALLGRS +HPVGVLFAGLLFGALRAGGVTMQTQTGVPIDIVLVVQSFIVLLIAAPPLVRAIFRLPAPG +SVRARANADVVTQPALAGAAVPGAAAEAVPAETGSATTSKGEGR +>PROKKA_02387 +MSTAVASRPAGARTQEDGSALRRLASSNGAVTVLAVLLSLVISAVLIVVTDEDVQDAAGY +LFARPQDALTAAWKAVSGAYAALFRGAVFNYEADTFTDMVRPLTETLTVATPLIIISLGV +AVAFRAGLFNIGGQGQFIFGAMVATWTAVHLPLPFGLHLLVVLLAGVVGGVLWGAVVGVL +KAWTGAHEVILTIMLNYVAVNVLAYLLNTPVLRRAGTTNPVSEFLPESGMFPKLLGDGYR +LHWGFVLALLVTAFTWWLMSRSTLGFRLRAVGANPAAARTAGMSVKGTYVAAMAISGGLA +GLAGMTHVSGTENALNTSVAGSYGFDAITVALLGRSNPVGVLFAGLLFGALRAGGVTMQT +ETGVPIDIVLVVQSMIVLFIAAPPLVRGLFRLPAPGAARARRTADVVTQPAVAGAAVPGA +AGLASVPSAQTQDAAATAVAADPADPVAGTGPHREKGQDL +>PROKKA_00444 +MSTAAPQRPAPESDPRARPAPADSALRRVLSGNGTVTALAILLSLLISGLLIIAVDEDVR +DAAGYFFARPGDLLSAAWAAFAGAFAALFRGAVFNYRASDATGMLYPLTETLTVATPLII +ISLGIAIAFRAGLFNIGGQGQFIFGAMFATWFGVHLHLPAGVHLLLVVVMGVLGGVLWGS +VVGVLKAWTGAHEVILTIMLNYVAVNLLAYLLNTPVLRAPGTTNPVSAPLDRSAMFPRLL +GTDFRLHWGFFVALLAVLFTWWLMQRSTLGFRLRAVGANPDAARTAGISVKGSYLAAMAI +SGGLAGLAGATHVAGTESTLNTSVAGSFGFDAITVALLGRSHPVGVLFAGLLFGALRAGG +VTMQTETGVPVDIVLVVQSVIVLLIAAPPLVRAIFRLPAPGAARARRAADPVTQPAVAGA +AVTGAGGHAAAPSTGVQEAAATAVADPQAPTTQPTDTAPTHRPHEQKGDAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000471.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000471.fa new file mode 100644 index 0000000000000000000000000000000000000000..22ab6c47747c245d36adf4e137632fe77d76ce7a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000471.fa @@ -0,0 +1,45 @@ +>PROKKA_00442 +MSATAARPHADVVRPEAAEPARVVVRHWTTPIALTILTLLALAVFALGAPEATATFRLSH +ASDAVVLPDLTADPVLGGWLLVGLMAVLTAVAWLATLRSGRTPGWAAALFAVAFVAAFLI +WVIGSADNTTVFLTGLIAGSFALAVPLIFGSMAGILAERSGVVNIAIEGQLLAGAFTAAV +VGTATGSPWAGLVAAIVAGVLVSWLLAVFSIKYLVNQVIVGVVLNVLVAGLTSFLYSTVL +TDGDTELNAPPHFPNLRIPGLADIPVLGPILFDQTILGYAMYLLVIALWFALFRTRWGLR +VRAVGEHPKAADTVGIDVNRTRYAAVLLGGAVAGMGGAFFTLVSASSFTKEMTAGQGFIA +LAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVTVFAVAGLVG +RSRGPAASGVPYVKE +>PROKKA_00163 +MSATAARPHADVVRPEAAEPARVVVRHWTTPIALTILTLLALAVFALGAPETTATFRLSH +ASDAVVLPDLTADPVLGGWLLVGLMAVLTVVAWLATLRSGRTPGWAAALFAVAFVAAFLI +WVIGSADNTTVFLTGLIAGSFALAVPLIFGSMAGILAERSGVVNIAIEGQLLAGAFTAAV +VGTATGSPWAGLAAAIVAGVLVSWLLAVFSIKYLVNQVIVGVVLNVLVAGLTSFLYSTVL +TGGDTELNAPPHFPNLRIPGLADIPVLGPILFDQTILGYAMYLLVIALWFALFRTRWGLR +VRAVGEHPKAADTVGIDVNRTRYAAVLLGGAVAGMGGAFFTLVSASSFTKEMTAGQGFIA +LAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVTVFAVAGLVG +RSRGPAASGVPYVKE +>PROKKA_02515 +MSTAAQTNPVQPTPAGTGRAPSAEAPREGGTVVVRSWTTPIVFTVFTVLALVVFGLNAPD +AAATFRVSTEADAFRIPDLVADGAGGGWIVTAILVVLTVLAWMRAARGRAVGAVLGISFA +LVFVAGFLIWVVGSAANTSVFLTGLIAGSFALAVPLIFGSMAGILSERAGVVNIAIEGQL +LAGAFTAALVGSMTGSPWAGLAAAVVAGVLVSVILAVFSIKYLVNQVIVGVVLNVLVAGL +TGFLFSTVLSENSSGLNSPPRFETLRIPGLADIPVIGPILFEQTLLGYGMYLIVAVIYIG +LFHTRWGLRVRAVGEHPKAADTLGINVLRTRYVNVLLGGAVAGMGGAFFTLVQSSSFSRE +MTAGMGFIALAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVT +IFAVAGLVGRSRAPAASGVPYVKE +>PROKKA_02386 +MSTAAPARESATPSERAGAASSGVVVRHWSTPVLLSVFTLVSLVVFALGASDSTAVFRIS +EASDAVRLPDLLADPAVTGWALTAVMAAITAAAWVLTLRGRRLPGWAAGLFALAFTAAFL +VWVVGAATNNEVFLTGLIAGSFTLAVPLIFGSMAGILSERSGVVNIAIEGQLLAGAFMAA +VVGSLTGSPWAGLGAAIVAGVLVSWLLAVFSIRYLVNQVIVGVVLNVLVAGLTNFLFSTV +LTADSDLNAPPRFPDLRIPLLADIPVIGPILFDQTILGYLMYAIVALLWFGLFRTRWGLR +VRAVGEHPKAADTVGIDVNRTRYVNVLLGGAVAGMGGAFFTLVSASSFSKEMTAGQGFIA +LAAVIFGRWNPIGAFFAALLFGFATNMQFVFAILGTPVPSPFMAMLPYLVTVFAVAGLVG +RSRGPAAAGEPYVKE +>PROKKA_00445 +MSATAARPHADVVRPEAAEPARVVVRHWTTPIALTILTLLALAVFALGAPEATATFRLSN +ASDAVVLPDLTADPVLGGWLLVGLMAVLTAVAWLATLRSGRTPGWAAALFAVAFVAAFLI +WVIGSADNTTVFLTGLIAGSFALAVPLIFGSMAGILAERSGVVNIAIEGQLLAGAFTAAV +VGTATGSPWAGLAAAIVAGVLVSWLLAVFSIKYLVNQVIVGVVLNVLVAGLTSFLYSTVL +TGGDTELNAPPHFPNLRIPGLADIPVLGPILFDQTILGYAMYLLVIALWFALFRTRWGLR +VRAVGEHPKAADTVGIDVNRTRYAAVLLGGAVAGMGGAFFTLVSASSFTKEMTAGQGFIA +LAAVIFGRWNPIGAFFAALLFGFATNMQYVLAILGTPVPSQFMAMLPYLVTVFAVAGLVG +RSRGPAASGVPYVKE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000473.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000473.fa new file mode 100644 index 0000000000000000000000000000000000000000..9491962fe25441084b015e7ba960d87ddfa162ba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000473.fa @@ -0,0 +1,45 @@ +>PROKKA_00444 +MTAQPQAEPFDAVEVIRTKRDRGTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD +RAEIARWTDAMIASGERMDFGGLTTPDGRPLATADKHSTGGVGDKITLPLAPLVASFGVA +VPQLSGRGLGHTGGTLDKLEAIPGWRADLSNEAMLRQLSEVGAVICAAGSGLAPADKRLY +ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG +RDAGVDTSALLTDMSVPLGRTAGNALEVRESVEVLAGGGPADVVELTVALAAAMLAGAGV +TDVDPAEHLANGRAMDVWNRMIEAQGGDPRAALPTAAHTEDVVAETDGVLTELDAMAVGL +AAWRLGAGRERQGQAVQAAAGVEVHVRPGERVARGQKVLTLHTDTPERFERAKAALAGGW +AVGELDDAAARTLRERSVILDRIG +>PROKKA_00165 +MTAQPQAEPFDAVEVIRTKRDRGTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD +RAEIARWTDAMIASGERMDFGGLTTPDGRPLATADKHSTGGVGDKITLPLAPLVASFGVA +VPQLSGRGLGHTGGTLDKLEAIPGWRADLSNEAMLRQLSEVGAVICAAGSGLAPADKRLY +ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG +RDAGVDTSALLTDMSVPLGRTAGNALEVRESVEVLAGGGPADVVELTVALAAAMLAGAGV +TDVDPAEHLANGRAMDVWNRMIEAQGGDPRAALPTAAHTEDVVAETDGVLTELDAMAVGL +TAWRLGAGRERQGQAVQAAAGVEVHVRPGERVARGQKVLTLHTDTPERFERARAALAGGW +SVGELDDDAARALRERSVILDRIG +>PROKKA_02513 +MTAQQQAEPFDAVEVIRAKRDRQTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD +RAEISRWTDAMIASGERMDFSGLTAPDGRVLPTADKHSTGGVGDKITLPLAPLVASYGVA +VPQLSGRGLGHTGGTLDKLEAIPGWRADLTNEQMMRQLSEVGAVICAAGSGLAPADKRLY +ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG +RDAGVDTVALLTDMSVPLGLTAGNALEVRESVEVLAGGGPADVVELTVELARAMLAGAGV +TDVDPAQNLANGKAMDVWHRMIEAQGGDPRADLPTAAHTEDVVAEADGVLAELDAMAVGL +AAWRLGAGRERQGQPVQAGAGVELHVRPGERVARGQKVMTLHTDTPERFARAKAALEGGW +AVAEKGEAEAAALRDRSVILDRIG +>PROKKA_02384 +MTTTSMPAQPAAPEAFDAIEVIRLKRDGHRLDPERIDWVVDAYTRGVVAPEQMSALAMAI +LLNGMDREEIARWTAAMIASGERMDFSGLSAPDGRRLATADKHSTGGVGDKITLPLAPLV +ASYGVAVPQLSGRGLGHTGGTLDKLESIPGWRADLTNDQMMRQLGEVGAVVCAAGAGLAP +ADKKLYALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELAR +TMVDLGRDAGVDTSALLTDMSVPLGLTAGNALEVRESVEVLAGGGPADVVELTVELARAM +LAGAGVTDVDPAENLANGKAMDVWHRMIQAQGGDSHAELPAARHQETVTADADGVLTELD +AMAVGLAAWRLGAGRERQGEPVQAGAGVELHARPGDAVRAGQPLMTLHTDTPERFDRARA +ALAGGWAVTAADEAEAAALRSRSVILDRIG +>PROKKA_00447 +MTAQPQAEPFDAVEVIRTKRDRGTLSPEQIDWVVDAYTRGVVADEQMSALAMAILLNGMD +RAEIARWTDAMIASGERMDFGGLTTPDGRPLATADKHSTGGVGDKITLPLAPLVASFGVA +VPQLSGRGLGHTGGTLDKLEAIPGWRADLSNEAMLRQLSEVGAVICAAGSGLAPADKRLY +ALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELARTMVDLG +RDAGVDTSALLTDMSVPLGRTAGNALEVRESVEVLAGGGPADVVELTVALAAAMLAGAGV +TDVDPAEHLANGRAMDVWNRMIEAQGGDPRAALPTAAHTEDVVAETDGVLTELDAMAVGL +AAWRLGAGRERQGQAVQAAAGVEVHVRPGERVAQGQKVLTLHTDTPERFERARAALAGGW +AVGELDDVDARTLRERSVILDRIG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000474.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000474.fa new file mode 100644 index 0000000000000000000000000000000000000000..ea51d6cc29a2129c2107cc6eb8892eb1cf0729e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000474.fa @@ -0,0 +1,25 @@ +>PROKKA_00445 +MLAWLEGAILHASAQWWVLPLTLLLCLLDGIVPIFPSESVLVALGAIVRDGHPFSLWALW +GVGFAGAFLGDVAAYAIGRAVGVERFRWMRLRRVRATVEVARHHLHSHGALLLFTARFIP +GGRVALNFTAGATRYPPVRFVALDLLSTASWAAYSIMIARLTAGWLENPVLQIAVSVTGA +ALVGLLLDRLLKALLRRRLGAGVKGLTLAEQEALR +>PROKKA_00166 +MLAWLEGAILHASAQWWVLPLTLLLCLLDGIVPIFPSESVLVALGAIVRDGHPFSLWALW +GVGFAGAFLGDVAAYAIGRAVGVERFRWMRLRRVRATVEVARHHLHSHGALLLFTARFIP +GGRVALNLTAGATRYPPVRFVALDLLSTASWAAYSIMIARLTAGWLENPVLQIAVSVTGA +ALVGLLLDRLLKALLRRRLGAGVKGLTLAEQEALR +>PROKKA_02512 +MLEWIEETVLHAAAQWWMLPLTLALCLLDGIVPVFPSESVIVALAAIVRDGQPFSLWALW +AVGFAGAFLGDILAYAIGRAVGVDRFRWMRTPRVRASVAVARHHLNGHGALLLFTGRFIP +GGRVAINLTAGAIRYPLHRFVVLDLLSTAAWSAYSIMIARLTTGWLDNALLQIAVSVTGA +ALVGVLLDRALKAVLRRRLGTGVKGLRQAEDEALR +>PROKKA_02383 +MVQALEQAILAGASHPWALPLAALLCLLDGLVPVFPSESVLVALASIVEDGRPFPLAALW +AAGFVGAFLGDVAAYGAGRGVGVTRFRWMRHGRVRRTIVMARRNLDSHGALLLFTARFIP +GGRVAVNLAAGAMHYSPWRFVGLDLVSTALWSVYSIAIARLTVGWLDSTVLRMAVAVLGA +ALVGLLLDRAVKALLRRRLARDGHRLGADEQAALR +>PROKKA_00448 +MLAWLEEAILHASAQWWVLPLTLLLCLLDGIVPIFPSESVLVALGAIVRDGHPFSLWALW +GVGFAGAFLGDVAAYAIGRAVGVERFRWMRLRRVRATVEVARHHLHSHGALLLFTARFIP +GGRVALNLTAGATRYPPVRFVALDLLSTASWAAYSIMIARLTAGWLENPVLQIAVSVTGA +ALVGLLLDRLLKALLRRRLGSGVKGLTLAEQEALR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000476.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000476.fa new file mode 100644 index 0000000000000000000000000000000000000000..82964d7495fafe560fd210262dc1de13d064434e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000476.fa @@ -0,0 +1,30 @@ +>PROKKA_00447 +MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA +YPALAAELGDVLFQVVLHAAVSRAPGAPAETAGFRVDDAADALTAKMIRRNPLVLTPEGG +LRPAEELAAVTPEAVELAWERVKAQERAAAGLSPAAPAHDDGGTGPGLDVGDIPARLPAL +AAAANVVDRAARQEPDPLAAHVPAPAAEAGERPAAGWPDEAALGAELFALVRRARAAGLD +PERALRTTVARVRAGDWSALRPSG +>PROKKA_00168 +MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA +YPALAAELGDVLFQVVLHAAVSRAPGAPAETAGFRVDDAADALTAKMIRRNPLVLTPEGG +LRPAEELAAVTPEAVELAWERVKAQERAAAGLSSAAPAHGDGGTGPGLDVGDIPARLPAL +AAAAKVVDRAARQEPDPLAAHVPAPAAEAGERPAAVWPDEAALGAELFALVRRARAAGLD +PERALRTTVARVRAGDWSALRPSG +>PROKKA_02510 +MDRLVAVVEALRDHCPWTAALTHGDLAEYLVEEAYEAVAEIEARDAAAWADVPARRADGA +YPALAAELGDVLFQVVLHAAVSRPPGAPVSSAGFRVADAADALTVKMIRRNPLVLTPEGA +PRSAEELARVTPEAVELAWEEVKAQERAAAGETASGEAEQAGGPASDPGFGGIPARLPAL +AAAAKVVDRAARQPADPLARHAPLSGDPDSGHRAGHAAPDDGDPGWGDEAALGAELFALV +RRARAAGLDPERALRGTVARVRSGDWDALRPPTAG +>PROKKA_02381 +MSDAVDRLVATTEALRTHCPWTRALTHRSLTQYLVEEAYEALAEIEARTDAEWADVPARR +ADGSYPALAGEMGDVLFQVVLHAAVSRAPDAPAPAAGFRLDDAADALTAKLVRRNPLVFT +PDGAVRPPAELEGITPEAVELAWERVKRAERAAAEGGGAPDGPTGAPRPDDVGLGGIPAH +LPALAAASAVVDRAARQDVDPLAGHVPLPERTGEAWEDEAALGAELFETVRRARAAGLDP +ERALRGAIACVRAGDWDALRR +>PROKKA_00450 +MDRLVAVVEALRDHCPWTAALTHADLAEYLVEEAYEAVAEIESRDAAAWADVPARRADGA +YPALAAELGDVLFQVVLHAAVSRAPGAPAESAGFRLDDAADALTAKMIRRNPLVLTPEGG +LRPAEELAAVTAEAVELAWERVKARERAAAGLSPAAPAHDDGGTGPGLDVGDIPARLPAL +AAAAKVVDRAARQEPDPLAAHVPAPAAEAGERPAAGWPDEAALGAELFTLVRRARAAGLD +PERALRATVARVRAGDWAALRPSG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000478.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000478.fa new file mode 100644 index 0000000000000000000000000000000000000000..599d71082797102e06f026ac49b833fb6c815b5f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000478.fa @@ -0,0 +1,51 @@ +>PROKKA_00450 +MTVSPRPAQDRTVTEQDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRFSNGIPFP +TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT +GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA +WDEAAAVPTKDLSRHVRHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAVADP +TAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA +SRDVSNRAAFVDGVRERLGVEPEVVSGDEEAALSFAGAVSAVETADLGPEDLVLVVDLGG +GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVAAARADARRLLDDAAARL +PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERSE +RGFMHPGRVDVIGAGALLWSTVLERVAETAGVTEAWASEHDILDGIVLSLRS +>PROKKA_00171 +MTVSPRPAQDRTVTEKDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLSNGIPFP +TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT +GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA +WDEAAAVPTKDLSRHVRHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAVADP +TAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA +SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAGLSFAGAVSAVETADLGPEDLVLVVDLGG +GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVTAARADALRLLDDAAARL +PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERAE +RGFMHPGRVDVIGAGALLWSTVLERVAEVAGVTEAWASEHDILDGIVLSLRS +>PROKKA_02506 +MTASTRPAHDRAVTEADLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLTNGIPFP +TTFYLTHPALTAAVSRVEADGEMARMNERLEQDAELAAAHRAAHEAYIAERDRVGADAGT +GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDETIALVAPWWTPEVCACEGA +WDEAAAVPTKDLSRHVKHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAGADP +AAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVEEYARLVQRHHAGRVRFVATSA +SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAALSFTGAVSAVETADLGPEDLVLVVDLGG +GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLHSDPPTSDEVAAARADARRLLDDAAARL +PLERVARVVGVAGSVTTVTAEALGLSAYEPAAIHGARLPITEFRAAAQGLVAATRAERSE +RGFMHPGRVDVIGAGALLWSTVLERVAETAGVTEAWASEHDILDGIVLSLRS +>PROKKA_02378 +MTTPASRPASQEDALTETPAPQDPRAVTEQDLDTLSRQLGRPVRDVVEVGARCVCGNPLV +ATTAPRLSNGIPFPTTFYLTHPVLTAAVSRLEAGGLMAEMNDRLAADPELAAAHRAAHEA +YLAERERIRVASGTGEVPEIAHVSAGGLPDRVKCLHALVGHALAAGPGVDPLGDEAIAAV +AEWWTPGVCACAGAWDEAAPVPTRDLSRHVKHLERVERLERVTVAGVDCGTNSIRLLIAR +PAGAEDAAEPAGLPAGAPLEDVVREMRVVRLGEGVDATGAFSEAALERTFAAVDEYAHLV +KRHHAGRVRFVATSASRDVSNREAFVQGVSERLGVEPEVISGEEEARLSFAGAVSAVDVS +ALDDDALVLVVDLGGGSTEFVVGTPAGEVVDAVSMDMGCVRFTERFGLAGSAAADGVAAA +RAAVEQVMDDVAARLPLERVGAAVGVAGTVTTVTAEALGLAEYDPAAIHGAVLPVERLRA +AAEALLTADREERAARGFMHPGRVDVIGAGSLIWSTVLARVAAASGVTEAVTSEHDILDG +IALSLRG +>PROKKA_00453 +MTVSPRPAQDRTVTEKDLDTLSRQLGRPVRDVVEIGARCVCGNPLVATTAPRLSNGIPFP +TTFYLTHPVLTAAVSRVEADGEMARMNDRLAQDPALAAAHRAAHEAYIAERDRVGAEAGT +GPVPEIAGVSAGGMPERVKCLHALVGHALAAGPGVNPLGDEAIALVAPWWTPEVCACEGA +WDEAAAVPTKDLSRHVKHLERVAALKEVTVAGVDCGTNSIRLLISRPAGTDETTGAGADP +AAPLADVVREMRVVRLGEGVDATGAFSDAALERTFAAVDEYARLVQRHHAGRVRFVATSA +SRDVSNRAAFVDGVRERLGVEPEVVSGAEEAGLSFAGAVSAVETADLGPEDLVLVVDLGG +GSTELVVGTPAGEVVGAVSLDMGCVRFTERHLRSDPPTSDEVTAARADALRLLDDAAARL +PLERVARVVGVAGSVTTVTAEALGLSTYEPEAIHGARLPIAEFRAAAEGLVAATRAERAE +RGFMHPGRVDVIGAGALLWSTVLERVAEVAGVTEAWASEHDILDGIVLSLRS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000480.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000480.fa new file mode 100644 index 0000000000000000000000000000000000000000..87687b04c8c67fdafc87a1e6046b184c64896bad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000480.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000481.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000481.fa new file mode 100644 index 0000000000000000000000000000000000000000..0c42a7babe16ba86e63bac790ac88fc0349e5343 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000481.fa @@ -0,0 +1,35 @@ +>PROKKA_00457 +MTETSDLPAFGAPDATGTQHRLHRGSAEAVVVGLAGALRRYRVAGVDLTEPYGPDVVPPA +ANGIQMSPWPNRVAGARWILDGVEQRLDVTEPARGHASHGLLRNTHFVTETFSAHAVTLR +GEIHPQHGWPFRLTHRVTYELEADGGLTVTAEVQNHTDATVPVAVGAHPFLRIGDVPTAE +LSLRVPADAWIRTGEDLIPVETLPVDGTDLDFRRGRAVGEAALDVCLTGLTPDADGRHRQ +TLLAADGRAVTLWSDHAFAYTHVFVTDRLPGRDTALAVEPLTAPADALNSGEGLHRLAPH +ARWSVQWGLTPHVPDHPHEEDRA +>PROKKA_00175 +MTETSDLPAFGAPDATGTQHRLHRGSAEAVVVGLAGALRRYRVGGVDLTEPYGQDVVPPA +ANGIQMSPWPNRVAGARWILDGVEQRLDVTEPARGHASHGLLRNTHFVTETFSAHAVTLR +GEIHPQHGWPFRLTHRVTYELEADGGLTVTAEVQNHTDATVPVAVGSHPFLRIGDVPTAE +LSLRVPADAWIRTGEDLIPVETLPVDGTELDFRRGRAVGEAALDVCLTGLTPDADGRHRQ +TLLAADGRAVTLWTDHAFAYTHVFVTDRLPGRDTALAVEPLTAPADALNSGEGLHRLAPH +ARWSVQWGLTPHVPDHPHEEDRA +>PROKKA_02490 +MSETSAAEAFGAPHATGTQHRLRRAGAEAVAVGLAGALRTYRVHGVDLTEPYGPESIPPA +GNGIQMSPWPNRVAGARWELGGAEQGLDVTEPARGHAIHGLLRNTHFVAEASSEHAVTLR +GEIHPQHGWPFRLTHRVTYELDADGGLTVTQELENHADAPAPVAFGAHPFLRIGDVPVPE +LSLRVPADAWIRTGEDLIPVETLPVEGTDRDFRRGRPVGEDALDVCLTGLAPDADGRHRQ +TLLAGDGRAVTLWSDHAFAYTHVFVTDRLPGRDVAVAVEPLTAPADALNSGEGLHRLAPR +TRWSAQWGLTPHVPPHADEENRS +>PROKKA_02374 +MTVPPAPDADAVFGAPRASGAQYRIARGGAEAVVAALAGALRTYRLDGVDLTEPYGPDMV +PPAGNGIQMSPWPNRVAGGRWELDGAAQQLDVTEPSRGHASHGLLRNTHFTAESVAEDAV +TLRGEIHPQHGWPFRLTHRVAYALDDAGALTVTMSLENHADAEAPVAFGAHPFLRIGDVP +SAELTLQVPAREWIRTGEDLIPVETLPVDGGPQDFRSGRPVGAQGLDVGLTGLEADADGL +HRARLLAPDGRSVTLWSDPAFTVTHVFVTDRLPGRDVAVAVEPLTAPADALNSGTGLHRL +APGATLTARWGLVPDLAPAAPAAAPKEDAA +>PROKKA_00457 +MTETSDLPAFGAPDATGTQHRLHRGSAEAVVVGLASALRRYRVGGVDLTEPYGQDVVPPA +ANGIQMSPWPNRVAGARWILDGVEQRLDVTEPARGHASHGLLRNTHFVTETFSAHAVTLR +GEIHPQHGWPFRLTHRVTYELEADGGLTVTAEVQNHTDATVPVAVGSHPFLRIGDVPTAE +LSLRVPADAWIRTGEDLIPVETLPVDGTDLDFRRGRAVGEAALDVCLTGLTPDADGRHRQ +TLLAADGRAVTLWTDHAFAYTHVFVTDRLPGRDTALAVEPLTAPADALNSGEGLHRLAPH +ARWSVQWGLTPHVPDHPHEEDRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000483.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000483.fa new file mode 100644 index 0000000000000000000000000000000000000000..e93a98f2a21206a36885a3bc935377a425904ded --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000483.fa @@ -0,0 +1,45 @@ +>PROKKA_00459 +MGAAQATDTPDRTVPTPSPRWVRPAGGPPAPTALPVTLEEIERARETLRGIAELSPLQHS +RALSRAVGTDVHLKCENLQRAGSFKVRGAYVRMAQLSEEERGRGVVAASAGNHAQGVALA +AAKLGIRARIFMPHGVALPKLQATRDHGAEVVLHGSTVDESLAEAQRWATETGAVFIPPF +DDPAVIAGQGTVGLEILDVLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTVRVIGVQ +AATAAAFPGSLEEGRVQVLESVSTIADGIAVGRPGALPLRIAAELVDAVVTVTDDEIAAA +LVHLLERSKLVVEPAGAVGVAALLAGRTADLGFELGTTAVILSGGNIDPMLMLKSIQAGL +SAAGRYMTVRIPLRDRPGELATISRIIADTDANVVRVDHTRVGPDLSMGGVHITIDMETR +GTEHSAQVLEALRAAGYSPAPLP +>PROKKA_00177 +MGAAQATDTPDRTVPTPSPRWVRPAGGPPAPAELPVTLEEIERARATLRGIAELSPLQHS +RALSRAVGTDVHLKCENLQRAGSFKVRGAYVRMAQLSEEERGRGVVAASAGNHAQGVALA +AAKLGIRARIFMPHGVALPKLQATRDHGAEVVLHGSTVDESLAEAQRWATETGAVFIPPF +DDPAVIAGQGTVGLEILDVLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTVRVIGVQ +AATAAAFPGSLEEGRVQVLESVSTIADGIAVGRPGALPLRIAAELVDAVVTVTDDEIAAA +LVHLLERSKLVVEPAGAVGVAALLAGRTADLGFELGTTAVILSGGNIDPMLMLKSIQAGL +SAAGRYMTVRIPLRDRPGELATISRIIADTDANVVRVDHTRVGPELSMGGVHITIDMETR +GAEHSAQVLEALRAAGYSPAPLP +>PROKKA_02488 +MTAGEVAQEQESVQTAADAAPVAGPRWVRPADAEPAWEGLPVSYEDVEAARETLRGVSEV +SPLQLSRSLSRAVGTDVHLKCENLQRAGSFKIRGAYVRMAGLSEAERVRGVVAASAGNHA +QGVALAAAKLGISARIYMPRGVALPKLQATKDHGAEVVLHGSTVDESLAEAQRWAAETGA +VFIPPFDDPAIIAGQGTVGLEILDTLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTV +RVIGVQAATAAAFPGSLEEGRVQVLESVSTIADGIAVGKPGNLPLQITAELVDAVVTVTD +DEIAAALVHLLERAKLVVEPAGAVGVAALLAGRTADLGFELGSTVAVLSGGNIDPMLLLK +SVQSGLSAAGRYMTVRIPLRDRPGELATISRIIADSDANVVRVDHTRVGPELSMGGVHIT +IDMETRGPEHSAAVLEALREAGYSPVPIH +>PROKKA_02372 +MTAGGAAPAPWLRPADAQEPTGDRLPVRLEDVEAARGVLEDVAEHTPVMLSRALTDQLGT +PVHLKCENLQRAGSFKVRGAYVRMARLSAEERAAGVVAASAGNHAQGVALAAAKLGIHAR +IVMPRGVALPKLQATQDHGAEVQLYGSTVDEALAEAQRYAAATGAVFIPPFDDPAIVAGQ +GTVGLEIMDDLPRVDTVLVGIGGGGLIAGLAIAVKERARREGRTVRVVGVQAATAAAYPV +SLREGRVQVLESVSTIADGIAVGRPGALPFDIVSGLVDAVVTVTDDEIAGAMVHLVERSK +LVVEPAGAVGVAALLSGRARDLGFDLGTTAVVLSGGNIDPMLMLKSIQSGLSAAGRYMTV +RIPLRDRPGELATISRVIAETEANVVRVDHTRVGPELSMGSVHITLDMETKGWDHCEAVL +TALRESGYSPLRLT +>PROKKA_00459 +MGAAQATDTPDRTVPTPSPRWVRPAGGPPAPTALPVTLEEIERARETLRGIAELSPLQHS +RALSRAVGTDVHLKCENLQRAGSFKVRGAYVRMAQLSEEERGRGVVAASAGNHAQGVALA +AAKLGIRARIFMPHGVALPKLQATRDHGAEVVLHGSTVDESLAEAQRWATETGAVFIPPF +DDPAVIAGQGTVGLEILDVLPDVDTVIMGIGGGGLIAGTAVALKEAARRRGRTVRVIGVQ +AATAAAFPGSLEEGRVQVLESVSTIADGIAVGRPGALPLRIAAELVDAVVTVTDDEIAAA +LVHLLERSKLVVEPAGAVGVAALLAGRTADLGFELGTTAVILSGGNIDPMLMLKSIQAGL +SAAGRYMTVRIPLRDRPGELATISRIIADTDANVVRVDHTRVGPELSMGGVHITIDMETR +GAEHSAQVLEALRAAGYSPAPLP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000484.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000484.fa new file mode 100644 index 0000000000000000000000000000000000000000..180e999fb475d9729b07225a665c4dfe757ef159 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000484.fa @@ -0,0 +1,25 @@ +>PROKKA_00460 +MLTVEKAHLLLTREDGRSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG +TTGDPVLDSSLGQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGRLTERKAFLATRHVP +RGTERTELLAHLTAVVLDEAEPCDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE +TLTREDLLVQAVRRAVGGTCGTVTAAAAGSVA +>PROKKA_00178 +MLTVEKAHLLLTREDGLSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG +TTGDPVLDSSLAQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGCLTERKAFLATRHVP +RGTERTELLAHLTAVVLDEAEPSDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE +ALTREDLLVQAVRRAVGGTCGTVTAAAAGSAA +>PROKKA_02487 +MLTAEKTHLLLTREDGRSESPSHHGVALAAAALADYRAAGIVTVEDAPVDRARVLVTAAG +VTGHPVLDARLGKVDALAGTPVTAAVAAGRPNLRKAVIARLTETGDLAEHKAFMATRHLP +RGGTRAELLDRLTAVVLDEREATDEDVLLLGVLQHLNLAWRLLPGTHERYGRRELVRRVE +SLTRSDLLVQAVRRAVGGTAAAVTAAAAGSLA +>PROKKA_02371 +MLTSEKLHLLLTREDGRSLSPSHHGVALAAAVLADLRDAGIVSLEDAPVSRARVLVTGAG +STDHPVLDALLPELDGLRGKKVAAVVGKGRPKARKPVVAHLVETGELVEHKALLNTRHTP +VGPGRPALVAGLTSALDGDSPSDEDRLLLGVLHQLNVLRRVLPEAGAEGESRREQSRRLE +RLTHDDLLVQAVGRTVSTAAAAAAAAG +>PROKKA_00460 +MLTVEKAHLLLTREDGLSESPSHHRVALAAAALADHRSAGIVTLEDVPVDRARVLVTAAG +TTGDPVLDSSLGQVDALAGRPLVSTVAAGKPDLRKAVVAHLTETGRLTERKAFLATRHVP +RGTERTELLAHLTAVVLDEAEPSDEDVLLLGVLQHLNLARRLLPGAHERYDRREMVRRIE +ALTREDLLVQAVRRAVGGTSGTVTAAAAGSAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000486.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000486.fa new file mode 100644 index 0000000000000000000000000000000000000000..f3bd5e2ac8c8a89c2160dcd3e73f277b25747a85 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000486.fa @@ -0,0 +1,20 @@ +>PROKKA_00462 +MSHHAPAVRAQDPTLANRYGTDHTRPGRRRLWAGLGGLGLVVAVLLSVWIGLNMSVGAIE +YKDVGFTIEDDGHATVTFQASVPEGVQAECDVLVTDSHAAPVGFRTVRLETLPADRRDSP +SDAQQRYTVDVRTVVRGDSGVVETCRKV +>PROKKA_00180 +MSHHAPAVRAQDPTLANRYGTDHTRPGRRRLWAGLGGLGLVVAVLLSVWIGLNMSVGAIE +YKDVGFTIEDDGHATVTFQASVPEGVQAECDVLVTDSHAAPVGFRTVRLETLPADRRDSP +SDAQQRYTVDVRTVVRGDSGVVETCRKV +>PROKKA_02485 +MSHHAHAVHAQDPTLANRYGTDQDRPSRRRLWVGLGVLGLLGAVLLAVWLGLNLSVGNIE +YKDVGYTIEDDGNATVTFQVLVPEGVQAECDVLVMDSHAAPVGFRTVRLVSVPQDQRDTP +SDAQQVYTVDVRTVVRGDSGVVEACRKL +>PROKKA_02369 +MSSTPAPAASAPETTLATRYGVGQRRDRRRLWTVLGAVALVLAVATAVAVALGNSVGRVE +AEDVGYRIDDAAHAAVTFQVTLPRGVEAAACDLKVMDARYAPVGFHTVRVSAGPDHPAGE +TVTYTADVRTVGRGVTGVVEGCRPA +>PROKKA_00462 +MSHHAPAVRAQDPTLANRYGTNHTRPGRRRLWAGLGGLGLVVAVLLSVWIGLNMSVGAIE +YKDVGFTIEDDGHATVTFQASVPEGVQAECDVLVTDSHAAPVGFRTVRLETLPADRRDSP +SDAQQRYTVDVRTVVRGDSGIVETCRKV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000489.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000489.fa new file mode 100644 index 0000000000000000000000000000000000000000..c84a25ffdadffaa9a93c82e9db3a2163a7c1d645 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000489.fa @@ -0,0 +1,30 @@ +>PROKKA_00466 +MGRPEAFYRLYERRLTRGLDPERLPRHIGVLVDGNRRWARAFGASTQQGHQAGAERILDF +IGWCDEAGIPVVTLYMLSTENLRRPAEELAPLLEIIQTTAERLAQPAEGRAPVCVQPVGA +VDLLPEPMARRLAEVAEQTKGHDGVHVNVAVGYGGRQEILDAVRELLRDEHALGHSAAEV +AESVTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD +FLRALRDYGSRQRRFGT +>PROKKA_00184 +MGRPEAFYRLYERRLTRGLDPERLPRHIGVLVDGNRRWARAFGASTQQGHQAGAERILDF +IGWCDEAGIPVVTLYMLSTENLRRPAEELAPLLEIIQTTAERLAQPAEGRAPVCVQPVGA +VDLLPEPMARRLAEVAEQTKGHDGVHVNVAVGYGGRQEILDAVRELLRDEHALGHSAAEV +AESVTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD +FLRALRDYGSRQRRFGT +>PROKKA_02481 +MQRPEAFYRLYERRLARGLDPERLPRHVGVLVDGNRRWARAFGATTQEGHQAGAERILEF +IDWCDETGIPVVTLYMLSTENLGRPPEELEALLGIILATAERLAEPREGRRPVRVQTVGA +VDMLPEEMARRLRAVEERTRDNDGVHVNVAVGYGGRQEILDAVRELLRDEHGRGRTAAEI +ADAMTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD +FLRALRDYGSRQRRFGA +>PROKKA_02365 +MRRPEVFYRLYERRLAGELDPERLPHHVGVLVDGNRRWARAFGATTQEGHQAGADRIIDF +IGWCDEVGVPVVTLYMLSTENLARPAAELTPLLEIITTTTQRLAEPREDRAPVRVQPVGA +VDLLPPRMAQQLRDVAERTRDNTGVHVNVAVGYGGRLEIVDAVRELLEEAAAEGRSAADV +AAELTVDAISDRLYTRGQPDPDLVIRTSGEQRLSGFMTWQSAYSEFYFCEAMWPAFRRTD +FLRALRDYGRRQRRFGS +>PROKKA_00466 +MGRPEAFYRLYERRLTRGLDPERLPRHIGVLVDGNRRWARAFGASTQQGHQAGAERILDF +IGWCDEAGIPVVTLYMLSTENLRRPAEELAPLLEIIQTTAERLAQPAEGRAPVCVQPVGA +VDLLPEPMARRLAEVAEQTKGHDGVHVNVAVGYGGRQEILDAVRELLRDEHALGHSAAEV +AESVTVEQIADRLYTRGQPDPDLVIRTSGEQRLSGFLLWQSAYSEFYFCEAMWPAFRKVD +FLRALRDYGSRQRRFGT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000490.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000490.fa new file mode 100644 index 0000000000000000000000000000000000000000..cbf1b24f51feb7b4631ba79d55a2e11f28ead70a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000490.fa @@ -0,0 +1,25 @@ +>PROKKA_00467 +MHRPSPGLPDLPGGPAPAPTLAERAGGRLLGAVAPTAVLIAAMWVAQFVLIFLGRVIIPG +VGLIPRRLDGLDGVLFSPVLHAGWAHLIGNTTALLVLGPLAALVSRRPVALLVCAWLGSG +LLTWVIGTPGVHIGASGIVYALIAFLIVYGVAVRRIGAVVVSVLVALTHLGSSLIGLLPA +PGISWTGHLAGAVVGVLLGLWWGRADRQVPNRR +>PROKKA_00185 +MSMHRPSPGLPDLPGGPAPAPTLAERAGGRLLGAVAPTAVLIAAMWVAQVVLIFLGRVII +PGVGLIPRRLGGLDGVLFSPVLHAGWAHLIGNTTALLVLGPLAALVSRRPVALLVCAWLG +SGLLTWVIGTPGVHIGASGIVYALIAFLIVYGIAVRRIGAVVVSVLVALTHLGSSLIGLL +PAPGISWTGHLAGAVVGVLLGLWWGRADRQVPNRR +>PROKKA_02480 +MSMHRPTPRLPERGAVPAARPAPSLAERVSGRLVAVIAPTLLLVAALWVVQIALVFFGRL +VIPSLGLIPRSVTGLDGILFSPLLHAGWGHLIGNASALILLGPLAALISGRPLALLAAAW +LGSGVLTWVIGSPGVHIGASGIVYALVAFLVVYGIAVRRVVPVVVSVLVALTHLGSSLIG +LLPAPGVSWTGHLAGAVVGVLLGLWWGRGDRRPRHADI +>PROKKA_02364 +MPLPDRRPADDAVPAPRPSLTQAAAQGLVRTVAPTAVLVAAMWVMFLVSIVGGSTLIGGL +GLIPRRAAGLDGILFSPLLHGGWRHLVGNTTALLVLGPVAAAVSRRPLALLAAAWLGSGA +LTWVIGTPGVHVGASGIVYALIAFLLVYGVVARRVLAVVVAVAVAAAHLGSSLLGLLPQP +GVSWTGHLAGAVVGVGLALLWGRADRPARAPLGP +>PROKKA_00467 +MHRPSPGLPDLPGGPAPAPTLAERAGGRLLGAVAPTAVLIAAMWVAQFVLIFLGRVIIPG +VGLIPRRLDGLDGVLFSPVLHAGWAHLIGNTTALLVLGPLAALVSRRPVALLVCAWLGSG +LLTWVIGTPGVHIGASGIVYALIAFLIVYGVAVRRIGAVVVSVLVALTHLGSSLIGLLPA +PGISWTGHLAGAVVGVLLGLWWGRADRQVPNRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000491.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000491.fa new file mode 100644 index 0000000000000000000000000000000000000000..fd6c17485b915bde06121f95f0f6493fc5d5ac3a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000491.fa @@ -0,0 +1,49 @@ +>PROKKA_00468 +MVAELVEHAQTRQEPSSRPGQARAEAGAAEATGLRTYVVDTSVLLSDPRALLHFAEHEVV +LPLVVVSELEAKRADPDLGYDARTALRLLDDLRGRHGALDQPVPITPEGGTLRIELNHVS +VDVLPLGIRGTDNDSRILAVAKALADEGAMVTVVSKDLPMRVKAAAMGLAADEYRHELVR +DSGWRGTVSLSVAQERLDALYDDGEVDLAGVPLGTLTGTGVETGPEEAPAEADRLPVNTG +LVLTAPRGSALARVGEGGRACLVRGDRDVFGLHGRSAEQRLAIELLTDPSVGIVSLGGRA +GTGKSALALCAGLDAVMERREHRRVVVFRPLYAVGGQDLGYLPGSEGDKMGPWAQAVFDT +LGALVSPSVVDEVVDRGMLEILPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRN +SKVVLTHDVAQRDNLRVGRHDGIAAVVERLKGHPLFGHVTLTRSERSPIAALVTDLLEEG +RA +>PROKKA_00186 +MVAELVEHAQTRQEPSSRPGQARAEAGAAEATGLRTYVVDTSVLLSDPRALLHFAEHEVV +LPLVVVSELEAKRADPDLGYYARTALRLLDDLRGRHGALDQPVPITPEGGTLRIELNHVS +VDVLPLGIRGTDNDSRILAVAKALADEGATVTVVSKDLPMRVKAAAMGLAADEYRHELVR +DSGWRGTVSLSVAQERLDALYDDGEVDLAGVPLGTLTGTGVETGPGEAPAEADRLPVNTG +LVLTAPRGSALARVGEGGRACLVRGDRDVFGLHGRSAEQRLAIELLTDPSVGIVSLGGRA +GTGKSALALCAGLDAVMERREHRRVVVFRPLYAVGGQDLGYLPGSEGDKMGPWAQAVFDT +LGALVSPSVVDEVVDRGMLEILPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRN +SKVVLTHDVAQRDNLRVGRHDGIAAVVERLKGHPLFGHVTLTRSERSPIAALVTDLLEEG +RA +>PROKKA_02479 +MVAERVEHGRALTGTTEARPDAAGAAGHAAAARTGAADAVVAPDARETGLRTYVVDTSVL +LSDPRAVLRFAEHEVILPLVVVSELEAKRADPDLGYFARTALRLLDDLRGRHGALDRAVP +ISPEGGTLRVELNHVSTDVLPLGIRGTDNDSRILAVAKAFADEGRDVTVVSKDLPMRVKA +AAMGLSADEYRHELVRDSGWRGTVTLTVEQELLDALYDDGEASLAGVPVDGTDGVGAGVE +ADGTGAGGSGVDRTGAEGPGAAVLPVNTGLVLLAPRGSALARVAEGGRALLVRGDQDVFG +LHGRSAEQRLAIDLLTDPAVGIVSLGGRAGTGKSALALCAGLDAVMERREHRKVVVFRPL +YAVGGQELGYLPGSEGEKMGPWAQAVFDTLGALVSPSVIDEVVDRGMLEVLPLTHIRGRS +LHDAWVIVDEAQSLERNVLLTVLSRMGRNSKVVLTHDVAQRDNLRVGRHDGIAAVVERLK +GHPLFGHVTLTRSERSPIAALVTEMLEDGRG +>PROKKA_02363 +MTLQADGTGRHGRGTGETGAEVREGAASDGRRSYVVDTSVLLSDPRALVRFAEHEVVLPL +VVVSELEGKRQDPDLGHAARHALRLLEDLRVRHGSLEDAVPFTAQGGTLRVELNHVSTDV +LPFGIRGTDNDSRILAVAKALADEGRDVTLVSKDLPMRVKAAAMGLAADEYRHELVRDSG +WRGAVSLRVDEDRLDSLYDDGRMGLHGIPLDEVAGSGVDAVPGEPAPTAVDLPVNTGLSL +TSPRAAGLARVREGGVATLVRGDADVFGLHGRSAAQRLAIDLLTDPSVGIVSLGGRAGTG +KSALALCAGLEAVMERREHRRVVVFRPLYAVGGQDLGYLPGTEGEKMGPWAQAVFDTLSA +IVSPSVIDEVVDRGMLEVLPLTHIRGRSLHDSWVIVDEAQSLERNVLLTVLSRMGRDSKV +VLTHDVAQRDNLRVGRHDGIAAVVETLKGHPLFGHVTLTRSERSPIAALVTELLEEGED +>PROKKA_00468 +MVAELVEHAQTRQEPSSRPGQARAEAGPAEATGLRTYVVDTSVLLSDPRALLHFAEHEVV +LPLVVVSELEAKRADPDLGYYARTALRLLDDLRGRHGALDQPVPITPEGGTLRIELNHVS +VDVLPLGIRGTDNDSRILAVAKALADEGATVTVVSKDLPMRVKAAAMGLAADEYRHELVR +DSGWRGTVSLSVAQERLDALYDDGEVDLAGVPLGTLTGTGVETGPEEAPAEADRLPVNTG +LVLTAPRGSALARVGEGGRACLVRGDRDVFGLHGRSAEQRLAIELLTDPSVGIVSLGGRA +GTGKSALALCAGLDAVMERREHRRVVVFRPLYAVGGQDLGYLPGSEGDKMGPWAQAVFDT +LGALVSPSVVDEVVDRGMLEILPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRN +SKVVLTHDVAQRDNLRVGRHDGIAAVVERLKGHPLFGHVTLTRSERSPIAALVTDLLEEG +RA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000493.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000493.fa new file mode 100644 index 0000000000000000000000000000000000000000..93d47c3b5afaed019fcff51d6a17264639bceef3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000493.fa @@ -0,0 +1,45 @@ +>PROKKA_00470 +MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA +AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA +TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA +EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG +INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL +RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA +FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV +IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE +>PROKKA_00188 +MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA +AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA +TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA +EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG +INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL +RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA +FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV +IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE +>PROKKA_02477 +MTAQNPEQQFRIEHDTMGEVKVPIDALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA +AAKANAELGVISQERADAIVAAADQVIAGEHDDQYPIDVFQTGSGTSSNMNTNEVLATLA +TRALKDAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTGALINELIPALDHLAVSLEKKE +KAFANIVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERVESSLPRVAEVPLGGTAVGTG +INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNVAYSIMKINNDL +RWMGSGPNTGLGEIFIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVSLSSTNGA +FELNVGIPVMAANLLESIRLLANTSRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV +IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDTALDTMSMTHPE +>PROKKA_02361 +MTAQNTEQQFRIEHDTMGEVKVPVDALYRAQTQRAVENFPISGKTLEPAHIHALAQIKKA +AAKANAELGVISQERADAIVAAADEVISGKHDGEYPIDVFQTGSGTSSNMNTNEVLATLA +TRRLKDAGSSEEVHPNDHVNASQSSNDVFPTSVHVAVTGALVNDLKPALEHLAESLERKA +EEFQGIVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIEASLPRVAEVPLGGTAVGTG +INTPQGFSARVIELLAEETGLPITEARNHFEAQANRDGLVEASGQLRNIAYSFIKINNDL +RWMGSGPNTGLGEIALPDLQPGSSIMPGKVNPVICEAAIMVAAQVIGNDTTISLSSTNGA +FELNVGIPVMAANLLESIRLLANTSRVMADKMIDGIEANEERCTFLAGASPSIVTPLNKV +IGYEAAAAIAKHAVKNKMTVREAVVDLGYVERGEVTEEQLDKALDTMSMTHPGE +>PROKKA_00470 +MTAENTDQQFRIEHDTMGEVKVPVNALYRAQTQRAVENFPISGKGLEPAHIHALAQVKKA +AAKANAELGIISQERADAIVAAADQVIAGDHDDQYPIDVFQTGSGTSSNMNTNEVLATLA +TRALKEAGSEDEVHPNDHVNASQSSNDVFPTSVHVAVTAALVNDLVPALDHLAVSLEKKA +EAFAGVVKSGRTHLMDATPVTLGQEFGGYAAQVRYGIERIQSALPRVAEVPLGGTAVGTG +INTPKGFSARVIELLAEETGLPLTEARNHFEAQANRDGLVEASGQLRNIAFSLMKINNDL +RWMGSGPNTGLGEIAIPDLQPGSSIMPGKVNPVICEAAIMVCAQVIGNDTTVALSSTNGA +FELNVGIPVMAANLLESIRLLANTTRVMADKMIDGIEANEERCAFLAGASPSIVTPLNKV +IGYEAAAKIAKHAVANKMTVREAVVDLGYVERGEITEEQLDKALDTMSMTHPE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000494.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000494.fa new file mode 100644 index 0000000000000000000000000000000000000000..e0aa7b7cd8884c401b1398e3889ea0062ee678bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000494.fa @@ -0,0 +1,25 @@ +>PROKKA_00471 +MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLAEGNRRFVAGEPSHPNQNAERRSDLTAGQ +APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL +GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD +HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV +>PROKKA_00189 +MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLAEGNRRFVAGEPSHPNQNAERRSDLTAGQ +APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL +GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD +HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV +>PROKKA_02476 +MSTENTATAAAAAHDDGAAGSRPTPQEAWETLAEGNRRFVAGDPGHPNQNAERRSTLTSG +QEPIAVIFGCSDSRLAAEIIFDVGLGDVFVIRTAGQVIDDAVLGSLEYSVDVLKIPLIVV +LGHDSCGAVTATVESYISGDMPPGFIRSLVERITPSVLAGRRRGLEEIDDFVAEHVDQTC +DRLVETSQAVRDAVEAGRTAVVGLTYSLAGGTAQPGRVLGALQV +>PROKKA_02360 +MTTAAETTPARPTPAEAWRTLQEGNRRFVAGTPGHPNQDSERRHGLTEGQAPIAVIFGCA +DSRLAAEIIFDVGLGDVFVVRTAGHVVDDAVLGSLEYAVDSLDVPLIIVLGHDSCGAVTA +TVESYISGTMPAGFVRSLVERITPSVLAGRRRGLEEVDDFVAEHVDQTCDRLLETSQSVR +AAVEAGRTAVVGLTYSLAEGTASPGRVHGRIEA +>PROKKA_00471 +MTPHTRPETTPAPDVVVPTSDLTPAEAWEVLVEGNRRFVAGEPSHPNQNAERRSDLTAGQ +APVAVIFGCADSRLAAEIIFDLGLGDVFVVRTAGHVIDDAVLGSIEYGVDVLEIPLVIVL +GHNSCGAVTATVESYISGTMPRGFVRPLVERIIPSVLAGRRRGLEEVDEFVAEHVDQTCD +HLLETSQSVRAAVESGRTAVVGLTYSLSEGTARPGRVHGDLAV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000496.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000496.fa new file mode 100644 index 0000000000000000000000000000000000000000..1a0689f0fd24623095ab8dfc5f40844a4c5fff99 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000496.fa @@ -0,0 +1,35 @@ +>PROKKA_00473 +MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD +TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA +VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR +PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT +GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA +DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR +>PROKKA_00191 +MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD +TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA +VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR +PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT +GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA +DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR +>PROKKA_02474 +MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD +TVSMAGTVVIGEGEKDEAPMLFNGEEVGDGSGAPVDVAVDPIDGTRLTAMGYNNALSVFA +VAERGTMFDPSAVFYMDKLVVGPEAADFVDLRLPVKQNVALVAKALDKPASQVTVCVLDR +PRHEGLVKEIREAGARVKFILDGDVAAAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT +GGVIQGRLAPTDETEKQKALDAGLDLDAVLSTNDLVTSDHCYFAATGITDGDLLRGVRFV +DGRVVTQSIVMRSWSGTVRTVDAEHDVRKWSKWLEDRGTRTGR +>PROKKA_02358 +MTSASSENTGYENHVPDRNLAMELVRVTEAAAIAASPWVGGGDKNRADGAAVDAMRAFMD +TVAMDGTVVIGEGEKDEAPMLFNGERVGDGKGASVDVAVDPIDGTRLTAMGYNNALSVFA +VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR +PRHEGLVKEIRAAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT +GGVIQGRLAPTDDAEKQKALDAGLDLDAVLTTDELVTSDHCYFAATGITDGDLLRGVRFA +GGRVHTQSIVMRSKSGTVRTVDAEHHVDKWSQWLKNRG +>PROKKA_00473 +MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD +TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA +VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR +PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT +GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA +DGRVHTQSIVMRSSSGTVRTVDADHDVKKWSKWLEDRDAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000497.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000497.fa new file mode 100644 index 0000000000000000000000000000000000000000..ef638be810efa5cd9cb07a410b3546ac9c09837a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000497.fa @@ -0,0 +1,40 @@ +>PROKKA_00474 +MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGARVGLDEV +VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPQ +RNYKDANHKPEMLLALTPFAAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI +SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP +DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHMDVP +ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV +TRGTASLALAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG +>PROKKA_00192 +MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGAHIGLDEV +VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPE +RNYKDANHKPEMLLALTPFSAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI +SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP +DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVP +ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV +TRGTARLVLAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG +>PROKKA_02473 +MHVLKPVIRDYAWGSPTLLARLQGREPTGRPEAEIWLGDHPGAPCGVVVGDGSVTGLDEL +TAADRERCLGPNVDTDRLPYLAKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPH +RNYKDANHKPEMLVALTHFSAMCGFRSPEVSSDSFEALAHALTEHADGDTSAVAVAAARI +SQTLAAGDLEDAFTAILDPESVWAAPGSVAQVVEVLRAAEDLAERDPSLATALEVAEHYP +DDPGVIVAILLNRVDLAPGQALHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTAKHVDVE +ELRRVVTFEAVPVPSTEPERVADSVVAFRPPFDEFELLQATLEDDAVRELDVHGPGIAVV +TRGSAHLGLAGQEVTLGPGESVFLPAAETATGPLAVRAADGAPATVHVTDLPRR +>PROKKA_02357 +MHLLEAVVRDYAWGSPTLLAELEGREPSGAPEAEKWLGAHPGAPCTVSGPEGRCGLDELI +AADPAPMLGEAARFGRLPYLMKLLAAGRPLSIQAHPTRERARAGFAAEEAAGVPVDAPHR +NYKDDNHKPEMIVALTPFSALCGFRRPEDAAATFERMADALAEWADGDATDVGIAARRIA +AHLAAEDVEAAFADILDPDAVWSAGGVDRLIEAVRAQPDLVAHDPALATALEVAEQCPGD +PGVLVTLLLNRVDLVPGQAVHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVPEL +RRVVAFAPLPVPYTDPVEDGAGVVRYRPPFEEFELTRLAADAGGPSAEARVAGPAIAVAV +DGPAVLACGADAVRLEAGAAVFLPAEETAAAPLTLSPATDDAPARVFVAALPTA +>PROKKA_00474 +MHVLKPVIRDYAWGSPTLLADLQGREPTGRPEAELWLGDHPGAPCVAVVADGARVGLDEV +VAADPERCLGPAAPEGRLPFLMKLLAAGAPLSIQAHPTLEQARAGFAAEEAAGVPVDAPQ +RNYKDANHKPEMLLALTPFAAMCGFRSPEVSSDSFEALARALTERADGDTSAVAVAAARI +SQALAAGDLEDAFTSILDPDSVWGAPGAVAQVVDVLRAAPDLAERDPSLATALEAAQHHP +DDPGVVVAILLNRVDLAPGQAIHLPAGNVHAYLHGLGVEVMAASDNVLRGGLTPKHVDVP +ELRRVVTFEALPVPSTEPERVADSVVAFRPPFEEFELLQATLEDDAVHGLDVHGPGIAVV +TRGTASLALAGQEIELGPGEAVFLPAAETASGPLAVRAAAGAPATVHVAGLPRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000498.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000498.fa new file mode 100644 index 0000000000000000000000000000000000000000..3aafb320d0d7d7693f14f89d495481a4fbf2cdf1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000498.fa @@ -0,0 +1,52 @@ +>PROKKA_00475 +MSSATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA +LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLI +RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN +ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF +DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL +IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR +RQQCMQAAMLEQFSPATVLTRFEGILAAGQQIVTTDLPQSQLGTFADLAERSRGQKMRRL +TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESVTAGSEPTGVSATPLLTVLAVVAQE +TQTPDVDEDDPATWPAPPTRTDGEPFTAEDLMTAEDLGQEDVLNHASSTNGLCVPAP +>PROKKA_00193 +MSPATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA +LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLM +RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN +ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF +DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL +IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR +RQQCMQAAMLEQFSPATVLTRFEGILAAGEQIVTTDLPQSQLGTFADLAERSRGQKMRRL +TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESATAGSEPTGVSATPLLTVLAVVAQE +TEAPDVDEDDPATWPAPPTRSDGEPFTAEDLMTAEDLGQEGVLNHASSTNGLCVPAP +>PROKKA_02471 +MSPATGSVPAGHAQPDPLRDPRVASPTERTRRALILTLLTLFVPGGAQVVAGSRPLGRAA +LRVTVAVWGVLLAGLLWWLVHRASLISLLARDGVLLVLAIALGLLAVGWAVLWIDTLRLI +RLHLLAPGARKATAVATVLALVLTSGALLYGGWATNAGRGALGSVFGDGPAVARTEGRYN +ILVMGGDAGEGREGLRPDSIHVASVDARSGAVVMFSLPRNLQNAPFTEGSPLWGVYPDGF +SCGDECILNALYTDVETNHPDLYPDAENPGAEAMMDAAGGILGLEISGYALMDMGGFAQL +IDAMGGVDLVTGGYVVHRGVRPDGEWGNIWWEPGEHHFDGKDALAFARSRHWSTDYARIR +RQQCMQAAMLAQFSPGTVLTRFEQILDAGQQIVTTSLPQSQLGTFVDLAERSRGQKMRRL +TIGPPDFGDTRDQFTTFPDYDLVHERVDEMLAEEPGQAGGATGGEAGHAAGVGSGASALP +LLTVLAVAAQEAVPDEVDEDDPATWPAPPTRPDGGAYTAEDLMLAEDLGQEDLLNHASST +NGLCAPGR +>PROKKA_02356 +MPASAASSPVLTRDPVRDPRQATGPERRRRAGILLLLTLLVPGGAQAVAGSRRWGRIALR +VTLAVWAAVLLALVLALTARAALVSVLANPVVLVLLGVVLVTLAIGWGLLWVDTFRLIRV +HLLGPRARAATAAATVVALVVTSGGLGYTAWMTQSGRGALGSIFGSGPAIEAADGRYNIL +VMGGDAGEDRVGLRPDSMHVASVDAETGAVTLFSLPRNLQNAPFTPDSPLWQAYPNGFDC +GDDCILNALYMDVEEKHKDLYPDAEHPGAEAMMDAAGGVLGLEITGYAMMDMAGFAQLVD +AMGGVDVVSGGYVTHRGARPDGTWGDIWWEPGTHHFGGDDALAFARSRKFATDYARIRRQ +QCMQAAMLQQFTPATVLTRFEGIVSAGTQIVTTNVPQSQLGTFVDLADRSRGYRMARLTI +GAPDFGTANDRFTTRPDYDLVHRRVAELLDEEPTKAGSASTAAPAASPGATPLLALTAAI +PAPLLVAEASPAATGTGGTTRPGVDPDDPSTWPSAPTGPNGEPYSAMELMRIQDAGDEAQ +LVRIASTNDLCAPGG +>PROKKA_00475 +MSSATGSVPAGHAQPDPLRDPRVASPTERTRRALILTALTLLVPGGAQLVAGSRRLGRVA +LRVTVTVWAVLILGLLWWLVSRASLISLMARDGVLLGLAVVLAALAVGWAVLWVDTFRLI +RPHLLAPGARKITAAVTALALVLTSGALLYGGWAANTSRGALGEVFQEGPAVPEAEGRYN +ILVLGADAGEGRQGLRPDSMHVVSVDARTGAIVMFSLPRNLQNAPFVEGSPLWDVYPNGF +DCGDECILNALYTDVEEHHADLYPDAEHPGAEAMKDAAGGILGLDVSGYALMDMGGFAQL +IDAMGGVDVVSGGYVVHRGVRPDGAWGNIWWEPGTHHFNGDDALAFARSRHWSTDYARIR +RQQCMQAAMLEQFSPATVLTRFEGILAAGQQIVTTDLPQSQLGTFADLAERSRGQKMRRL +TIGPPDFGDTGTHFTTYPDYDLVHRRVDEMLADESVTAGSEPTGVSATPLLTVLAVVAQE +TQTPDVDEDDPATWPAPPTRTDGEPFTAEDLMTAEDLGQEDVLNHASSTNGLCVPAP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000500.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000500.fa new file mode 100644 index 0000000000000000000000000000000000000000..55df77aa35c09a056e90747a8cedca5d32f5796f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000500.fa @@ -0,0 +1,25 @@ +>PROKKA_00478 +MLSDLWGRLTGMASLLWREVAKFGTVGAAAFVVDSLVFWWMMTGPLEGSNVKAKIVGGVV +ATLFSWVANRYWTFRDKRSSNKTRELVMFLIMNAIGLGIQAGCVAIAQYLMGVTDPTGLF +IAGNVIGLFFGTVFRYFAYRFWVFKEKLDVEPGFANDLAIITGQMPVLREDQLPPHGRHR +APDAGV +>PROKKA_00196 +MLSDLWGRLTGMASLLWREVAKFGTVGAAAFVVDSLVFWWMMTGPLEGSNVKAKIVGGVV +ATLFSWVANRYWTFRDKRSSNKTRELVMFLIMNAIGLGIQAGCVAIAQYLLGVTDPTGLF +IAGNVIGLFFGTVFRYFAYRFWVFKEKLDVEPGFANDLAIITGQMPVLREDQLRPRGRHR +TPDAGV +>PROKKA_02469 +MLSDLWSRLTGLVSMLWREVAKFGTVGAAAFVIDSLVFWWMMTGPLEGSNVKAKIVAGVV +ATLFSWVANRYWTFREKRSSNKTRELVMFLLMNAIGLGIQAGCVFIAQYLMGVTDPGGLF +IAGNVVGLFFGTVFRYFAYRFWVFKEELDVEPGFANDIAIITGQMPVLRDEQLHPHGRHE +ARGRPAERHVRRDDGPARHRAS +>PROKKA_02353 +MPTDLWHRFTGLVSMLWREVAKFGTVGAAAFVVDSAVFWWLMHGPLEGSNVKAKICAGVV +ATIFSWVANRYWTFRDKRQNNVVRELVMFLVMNAVGLGIQAGCVAIAQYGMGVTDPNGLF +IAGNVIGLFFGTVFRYFAYRFWVFKEELDEEPGFENDIAVITGQLPVLHAHDEHVPGLQH +RHPRHDVEDGSA +>PROKKA_00478 +MLSDLWGRLTGMASLLWREVAKFGTVGAAAFVVDSLVFWWMMTGPLEGSNVKAKIVGGVV +ATLFSWVANRYWTFRDKRSSNKTRELVMFLIMNAIGLGIQAGCVAIAQYLMGVTDPTGLF +IAGNVIGLFFGTVFRYFAYRFWVFKEKLDVEPGFANDLAIITGQMPVLREDQLPPHGRHR +APDAGV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000502.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000502.fa new file mode 100644 index 0000000000000000000000000000000000000000..6c3e3d418bbe65244ea800015fa8b10161cee257 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000502.fa @@ -0,0 +1,21 @@ +>PROKKA_00480 +MEQTQRVEDAHHADPAPAPRPRSVPSDWFLDPADPQAGVSGASLEDQATAFLTAHDLDGE +TGTPAATVTALFPGDARPVEAAPVSADWAAIPGVTTEPVEGELAWQADALCAQTDPEAFF +PEKGGSTRDAKRVCEACTVKDACLEYAMANDERFGIWGGLSERERRRLRRARA +>PROKKA_00198 +MEQTQRVEDTHRADPAPAPRPRSVPSDWFLDPADPQAGVSGASLEDQATAFLTAHDLDGE +TGTPAATVTALFPGDARPVEAVPVSQDWAAIPGVTTEPVEGELAWQADALCAQTDPEAFF +PEKGGSTRDAKRVCEACTVKDACLEYAMANDERFGIWGGLSERERRRLRRARA +>PROKKA_02467 +MEHTQRVEDTHRAESAQAAAPRPRGVPSDWFLDPADPLAGADAATLEDQATALLSAHDLE +DEAGTPSATVTALFPGDAGQPVEAAPVADDWAAIPGLVTEPVEGELAWQVDALCAQTDPE +AFFPEKGGSTRDAKRVCEACVVKDQCLEYAMENDERFGIWGGLSERERRRLRRARA +>PROKKA_02351 +MQNTQRVEDVARAERAPAASRSRGVPTDWFLDPADPTAGGRATAGLAAESLEDQATAFLA +AHDLDDAGTPAATVTALVPRPAEAPAVDDALVPDAWQPVPGVVMEPAEGELAWQVDALCA +QTDPEAFFPEKGGSTRDAKKVCAACDVRRECLDYAMANDERFGIWGGLSERERRRLRRER +G +>PROKKA_00480 +MEQTQRVEDTHRADPAQAPAPRPRSVPSDWFLDPADPQADVSGVSLEDQATAFLTAHDLD +GETGTPAATVTALFPGDARPVEAVPVSADWAAIPGVTTEPVEGELAWQADALCAQTDPEA +FFPEKGGSTRDAKRVCEACTVKDACLEYAMANDERFGIWGGLSERERRRLRRARA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000503.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000503.fa new file mode 100644 index 0000000000000000000000000000000000000000..4be386bce7704382003f016d4a2fd1e218b13ab4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000503.fa @@ -0,0 +1,22 @@ +>PROKKA_00481 +MARMTASASSDPLDPLPFRAGDAAGAEPGVEGGPAEAGVSSPTGRGGRDRRGRGLRHPRP +FGARSERGRGEALLTAVEKAVDRLGSLDAPGLRHVTARVERIPDRLDERLRELHAGRERD +EEALFARAERQGRDGVLITLFERPLRDAADPADLEGAVYGVALSRCADALGVDPQVLDPS +WGRG +>PROKKA_00199 +MARMTAPASSDPLDPLPFRAGDAAGAEPGVEGGPAKAGVSSPAGRGGRDRRGRGLRHPRP +FGARSERGRGEALLTAVEKAVDRLGSLDAPGLRHVTARVERIPDRLDERLRELHAGRERD +EEALFARAERQGRDGVLITLFERPLRDAADPADLEGAVYGVALSRCADALGVDPQVLDPS +WGRG +>PROKKA_02466 +MDRLAALEAPGLRHVTARVERIPDRLDERLRALRAGAERDEETLFARAERQGQDGVVITL +FERPLRDAADPEDLDGAVYGVALSRCAEALGVDPQVLDPGWGRA +>PROKKA_02350 +MARMPADPLAPLPPLPPARRDGRGPRPGLRRDVRGRGLRHPLPFGARAGRGRADALMDAV +EKAVDRLAGLQAPGLRRVAARLERIPDRLDERLALQRARAVADEEGLFGRAERDGADGVV +ITLFERPLTESADPADLEEAVYAVALSRCAAALGVDPQVLDPSWGRA +>PROKKA_00481 +MARMTASASSDPLDPLPFRAGDAAGAEPGVEGGPAEAGVSSPAGRGGRDRRGRGLRHPRP +FGARSERGRGEALLTAVEKAVDRLGSLDAPGLRHVTARVERIPDRLDERLRELHAGRERD +EEALFARAERQGRDGVLITLFERPLRDAADPADLEGAVYGVALSRCADALGVDPQVLDPS +WGRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000506.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000506.fa new file mode 100644 index 0000000000000000000000000000000000000000..7c6c6db53943b1d079da995d714a5949fea8c909 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000506.fa @@ -0,0 +1,40 @@ +>PROKKA_00484 +MASHQAGRGRDERAGAEDFDSGLDYGAFVEDDAADDPNRTQALPAMGRDDDGGAQHTSAL +SPEDLAALRGGDAAAADRRDAGRPAADADRDIVASRAVPEGGRRPLPGADELGPLSAAVG +ARAAGSSAAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAILAPLA +LVLATVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT +HQGAPLFTEVEVDHMTDVKTVLWIAAAALVVLLVVCALLIASLLRTSPGGVRRALFAGAV +WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVRDALIRLYPQQFWVDAAVVVGL +VTLLASLVTLVLTWPTRRRRELSADRREQLLRTRLRWAREDDAVVR +>PROKKA_00202 +MASHQAGRGRDERAGAEDFESGLDYGAFVQDDAADDPNRTQALPATGRDDDGGAQHTSAL +SPEDLAALRGGDAAAADRRDADRPAPDADRDIVASRAVPESDRRPLPGADELGPLSAAVG +ARAAGSSAAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAILAPLA +LLLAAVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT +HQGAPLFTEVEVDHMTDVKTVLWIATAALVVLVVVCALLIASLLRTSPGGVRRALFAGAV +WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVQDALIRLYPSQFWIDAAAAVGL +ISLLTALLTLVFTWPTRRRRERTADQRSAFESTRLRWAREEDAQLR +>PROKKA_02463 +MASHQAGRGREERAGAEDFESGLDYGAFAEDDAAEDPNRTQALPASGRDDAGVQHTSALS +PEDLAALRGGDAAAADGRAERSAERGMPDARERDIVASRAVPSSDRRPLPGADELGPLSA +AVGARSASGSSAADPADRYPQDASAAYAASSSAALQGPTPEERARLPKAGPRVAQVLLAI +LAPLALLLAAVRFVASPAFLWLEYHRPGFPADRFGFDTGDRMHYGSAGLDYVTNLAGSRY +LSSLTHQGEPLFTEAEVSHMTDVKVVLWIALAVLVALVVVCALLIAHLLRTSPGGVRRAL +FAGALWLPLALIALAVLAVLGWEIFFAGFHSLFFADGTWTFSVRDALIRLYPEQFWVDAA +LVVAAIAVIASLVTLVFTWPTRRRREMSADRRGQLLDTRLRWAREEDSPVR +>PROKKA_02347 +MASHTPGRSDGAGSGSSDFESGLDYGAFVEDDDAQPTQALPRTTEEHGAQRTLAFDRDEL +AAAAAGAGTGAGRSGAGSRAAGAAHGVAGEDITASRPAPAPAPSPASPWGADRYPSDATV +PASAPAAADTRTPEERARLPKAGPRLAQVLLAVLAPLVLLLGAVRLVATPLFLWLEYHRP +GFPADPYGFSTADRMTYGSAGLDYLHNLAGPRYLSELTFQGKPLLSEAAVSHMTDVKTVM +WIATAVLVLLGLACLLLALYLRRTSPGGVRRALFAGALGLLVVIVVLAAMAATGWQGFFA +GFHSLFFAEGTWTFSVSDPLIRLYPAQFWVDAAVAVAVLALIGIIAALVAGAPTRRRREM +SQDRRAQLEATRLRWAREDAHGVR +>PROKKA_00484 +MASHQAGRGRDERAGAEDFESGLDYGAFVQDDAADDPNRTQALPAMGRDDDGGAQHTSAL +SPEDLAALRGGDAAAADRRDAGRPAADADRDIVASRAVPEGDRRPLPGADELGPLSAAVG +ARTAGSSTAAPVDRYPEDGTAAPVAQAAALQGPTPEERARLPKAGPRLAQVLLAVLAPLA +LLLAAVRLVASPVFLWLEYHRPGFPADRFGFTLADRMHYGSAGLDYVTNLAGPRYLSSLT +HQGAPLFTEVEVDHMTDVKTVLWIATAALVVLVVVCALLIASLLRTSPGGVRRGLFAGAV +WLPLAVIALAVLAVLGWETFFAGFHSLFFADGTWTFSVRDALIRLYPQQFWVDAAVVVGL +VTLLASLVTLVLTWPTRRRRELSADHREQLLRTRLRWAREDDAVVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000507.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000507.fa new file mode 100644 index 0000000000000000000000000000000000000000..6ca6bf14378f34c4d9e3d7f9079fe0920636d71a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000507.fa @@ -0,0 +1,55 @@ +>PROKKA_00485 +MQNQSPVHESATELIGMPPADSNITDLIVTSCADRPDAPVYAVRNGAGGWVDVHFTAFLT +QVRAVAAGLIARGVQPGDRVGLFSPTSYAWAVLDQAVWFAGAVSVPIYETSSAHQVEHIV +TDSGLRVVAVGSEELGERVAEAAGHAGVDVATFPLTDAGLAELAEAGAFVSDDAVEHARS +LATLASPASIVYTSGTTGRPKGAVITHGNFVGAAINVLHFAREVVQWSPTTTSRTLLFLP +LAHVLAHAVQVICLYARIQVAHSGSPATLLGDLASFHPTWLLAVPRVFEKVEAGIEAKAQ +KSGTGPIYAAAKRTAIEWSTAVDEAEFGDGPGPSALLRARRALFDRLVYRKIREALGGEV +ISCVSGASALSPELVHFFRGAGIPIVEGYGLTETTAPATVNIPGAHRVGTVGLPVAGVTV +KIAEDGEILIRGPVVFDGYHGMPKASAEAMEDDFFRTGDIGALDEHGFLRITGRKKDVII +TAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALITLDAEAFTQWALDRELTLTPA +EAATDPTVLASIQEAVDQVNAGVSRAESIRRFRILDHPFTEDSGHVTQSQKLKRAQVIED +HAEDVEALYRR +>PROKKA_00204 +MQNQSPVHESATELVGMPPADSTITDLIVASCADRPDAPVYAVRNGAGGWVDVHFTAFLT +QVRAVAAGLIARGVQPGDRVGLFSPTSYAWAVLDQAVWFAGAVSVPIYETSSAHQVEHIV +TDSGLRVVAVGSEELGERVAEAAGHAGVDVATFPLTDAGLAELAEAGAFVSDDAVEHARS +LATLASPASIVYTSGTTGRPKGAVITHGNFVGAAINVLHFAREVVQWSPETTTSRTLLFL +PLAHVLAHAVQVICLYARIQVAHSGSPATLLGDLASFHPTWLLAVPRVFEKVEAGIEAKA +QKGGTGPIYAAAKRTAIEWSTAVDEAEFGDGPGPSALLRARRALFDRLVYRKIREALGGE +VISCVSGASALSPDLVHFFRGAGIPIVEGYGLTETTAPATVNIPGAHRVGTVGLPVAGVT +VKIAEDGEILIRGPVVFDGYHGMPKASAEAMEDDFFRTGDIGALDEHGFLRITGRKKDVI +ITAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALITLDSEALTQWALDRELSLTP +AEAATDPTVLASIQEAVDQVNAGVSRAESIRRFRILDHPFTEDSGHVTQSQKLKRAQVIE +DHAEDVEALYRR +>PROKKA_02462 +MPRVFEKVESGVATKAQKAGTGKVYQAARSTAITWSKALEEKKFGSGRGPSPALRARHAL +FDRLVYRKIREALGGEVRTCVSGASALSEELVHFFRGAGVPIVEGYGLTESTAPATVNVP +GAHRVGTVGLPVPGVTVKIAEDGEVLLRGPVMFSGYHGMPEASAESHAEDGFFRTGDIGS +LDEHGYLRITGRKKDVIITAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALVTLD +EEELTRWSLDRERSLTPAEAAKDPAVLETIQEAVDRVNEDVSRAESIRRIRILDHAFTED +SGYVTPSQKLKRAQVIEDYAEDVDALYRGR +>PROKKA_02345 +MQHASPISESSTDLYGLPAEDTNITDLILSSCAEDPRASVYAVRNGAGAWLDVRFDAFLG +QVRDVAKGLIAHGLQPGQRVALFAPTCYEWAVLDQAVWFAGAVSVPIYETSSAAQVAHIL +GDSQTHAAAVGGDELAATTREAARQAGIDVTVFPMSEAALRVLARDGAAVTDEQLEAART +TATLDDAASVVYTSGTTGRPKGAIITHRNFAAASINVLNFAAGVVDYHPGTNSRTLLFLP +LAHVLAHAVQVICLYARIQMAHSGSTKTLQEDMASFHPTWLLAVPRVFEKLEAGIAAKAE +DGGRGPVYHAAKRTAIEYSEALEAQTHEGGPGPSRALRARHAVFDTLVYGNVRKAFGGEV +LSCVSGASALSPELVHLFRGMGIPIVEGYGLTETTAPATVNIPAAYKVGTVGLPVAGATI +RIADDGEVLVKGPIVFAGYLRQPEATAESMDGDFFRTGDLGTLDEDGFLRITGRKKEVIV +TAGGKNVYPTPLEEIIRQHRLVQHVVVVGDDRPYVGALIVLDPDELKRWSLDRERTLTLE +EAVADEGVLAALQEAVDQANATVSRAESIRRIRVLDHELTEDSGHVTQSQKLKRAQVLAD +YADEIEQLYRGR +>PROKKA_00485 +MQNQSPVHESATELVGMPPADSNITDLIVTSCADRPDAPVYAVRNGAGGWVDVHFTAFLT +QVRAVAAGLIARGVQPGDRVGLFSPTSYAWAVLDQAVWFAGAVSVPIYETSSAHQVEHIV +TDSGLRVVAVGSEELGERVAEAAGHAGVDVATFPLTDAGLAELAEAGAFVSDDAVEHARS +LATLASPASIVYTSGTTGRPKGAVITHGNFVGAAINVLHFAREVVQWSPETTTSRTLLFL +PLAHVLAHAVQVICLYARIQVAHSGSPATLLGDLASFHPTWLLAVPRVFEKVEAGIEAKA +QKSGTGPIYAAAKRTAIEWSTAVDEAEFGDGPGPSALLRARRALFDRLVYRKIREALGGE +VISCVSGASALSPELVHFFRGAGIPIVEGYGLTETTAPATVNIPGAHRVGTVGLPVAGVT +VKIAEDGEILIRGPVVFDGYHGMPKASAEAMEDGFFRTGDIGALDEHGFLRITGRKKDVI +ITAGGKNVYPTPMEEALRQHRLIEHVVVVGENRPFVGALITLDSEALTQWALDRELSLTP +AEAATDPTVLASIQEAVDQVNAGVSRAESIRRFRILDHPFTEDSGHVTQSQKLKRAQVIE +DHAEDVEALYRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000508.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000508.fa new file mode 100644 index 0000000000000000000000000000000000000000..9f993c1cf9f297eadd0715b04b803d349f396c61 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000508.fa @@ -0,0 +1,51 @@ +>PROKKA_00486 +MEPVPATALAPRPAAVAADDGPFGVAALRARLGVSAAPLTRWHWILPLLVTVIAGVLRFT +NLAHPDQLIFDETYYPKDAYSLLESGYERRWGEDVNDAFARGEAEPLEGAAYVVHPPLGK +WLIGLGMLAFGPDNGVGWRFSAAVAGTLSVLLVALATQHLLRSVSLGAVAGLLLAVEGHH +LVMSRIGLLDIFLSFFVLAAFAALLADRVHGRRLLAERLAHDVARRGRDALASGPWLGWR +PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMSARRTAGVRRWAWAGVEKDGLYAF +VAVVGGGLVAYLASWTGWFVTEGGYYRDWHRDNPPEGVLAGLVPGPLRSLWHYHVESTTF +HQGLTSPHDYAANPWTWPFMGRPVSYYYEGAEPGEGICPADAAGACSAAITDIANPFVWW +TGLAAVLVCVWLLVRHRDWRAGALLGAYAAGQLVWSLWPERTMFFFYTIAYEPFLVMMIA +LALSLLLRPGRRPGPRWGSALVLAYVTIAVAVSLFFLPVWIGDVIPYDQWRWRMWFSSWI +>PROKKA_00205 +MEPVPATALAPRPAAVAVDDGPFGVAALRARLGVSAAPLTRWHWILPLLVTVIAGVLRFT +NLAHPDQLIFDETYYPKDAYSLLESGYERRWDEDVNDAFARGEAEPLEGAAYVVHPPLGK +WLIGLGMLAFGPDNGVGWRFSAAVAGTLSVLLVALATQHLLRSVSLGAVAGLLLAVEGHH +LVMSRIGLLDIFLSFFVLAAFAALLADRAHGRRLLAERLAHDVARRGRDALASGPWLGWR +PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMSARRTAGVRRWAWAGIEKDGLYAF +VAVVGGGLVAYLASWTGWFVTEGGYYRDWHRDNPPEGLLAGLVPGPLRSLWHYHVESTTF +HQGLTSPHDYAANPWTWPFMGRPVSYYYEGAEPGEGICPPDAAGACSAAITDIANPFVWW +TGLAAVLVCVWLLVRHRDWRAGALLGAYAAGQLVWFLWPERTMFFFYTIAYEPFLVMMIA +LALSLLLRPGRRPGPRWGSALVLAYVTIAVAVSLFFLPVWIGDVIPYDQWRWRMWFSSWI +>PROKKA_02461 +MEPVPATALAPRPAAVAVDGAPFGVAALRARLGVSAAPLTRWHWILPLLVTALAGVLRFT +NLAHPDQLIFDETYYPKDAYSLLQSGYERRWEEDVNDAFVRGEAEPLESAAYVVHPPLGK +WLIGLGMLAFGTDNGVGWRFSSAVAGTLSVLLVALVAQHLLRSVSLGAVAGLLLAVEGHH +LVMSRIGLLDIFLSFFVLAAFAALLADRAHGRQLLARRLAHDVARRGHAALATGPWLGWR +PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMAARRDAGVRDWARAGVVKDGLLAF +VAVVGGGLVAYLASWTGWFATEGGYYRMWHRDNPPEGPLAGLVPGPLRSLWHYHVESTTF +HEGLTSPHDYAASPWTWPFMGRPVSYYYRGGEPGQEVCPADAPSACSAAITDIANPLLWW +TGLIAVLVCLWLLIRHRDWRAGALLGAYLAGQVVWFLWPERTMFFFYTVAYEPFLILMIV +LALSLLLRPGRRPGPRWGSALVLAYAAAVVGVSLFFLPVWIGDVIPYDQWRWRMWFNSWI +>PROKKA_02344 +MACVPASSLTRRPAHALPAPADDAAAHPFGAAALRARLGVQAAVLTRWHWIVPLAVTVLA +GVIRFTNLAFPDKLIFDETYYPKDAYSLILSGYERRWAPDVDAAFAQGTAQPLDEPAYVV +HPPLGKWLIALGMLAFGPDNGVGWRFSAAVAGTLSVLLVTLVAQRLFRSVSLGALAGLLL +AVEGHHIVMSRIGLLDIFLSFFMIAAFAALLADRDHGRRLLASRLAEQVAAHDAGTRRGD +PLAFGPRLGWRPWRILAGALLGAGCAVKLSGLAFMAVFGILTVLWDMEARRTAGIRHWLR +AGVVRDGLPAFAAVVGAGLAVWLASWTGWFASEGGYYRRWAQDNPPEGPLSALLPGPLRS +LIHYQLEAFTFHEGLTSPHDYGSSPWTWPFMGRPVSYFYEGGKPGENGCPSTAADACSSA +ITDIANPFIWWTGLIAVLVCLAVLVRHRDWRAGALLGAYVAGQVVWFRWPERTMFFFYTV +AYEPFLILMIVLALSLLLRRGHRPGPRWGAVLVAAYLLVAVGVSLFFLPVWIGERIPYPQ +WSWRMWFSTWI +>PROKKA_00486 +MEPVPATALASRPAAVAVDDGPFGVAALRARLGVSAAPLTRWHWILPLLVTAIGGVLRFT +NLAHPDQLIFDETYYPKDAYSLLESGYERRWDEDVNDAFARGEAEPLEGAAYVVHPPLGK +WLIGLGMLAFGPDNGVGWRFSAAVAGTLSVLLVALATQHLLRSVSLGAAAGLLLAVEGHH +LVMSRIGLLDIFLSFFVLAAFAALLADRVHGRRLLAERLAHDVARLGRDALASGPWLGWR +PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMSARRTAGVWHWAWAGVEKDGLYAF +VAVVGGGLVAYLASWTGWFVTEGGYYRDWHRDNPPEGLLAGLVPGPLRSLWHYHVESTTF +HQGLTSPHDYAANPWTWPFMGRPVSYYYEGAEPGEGICPADAAGACSSAITDIANPFVWW +TGLAAVLVCVWLLVRHRDWRAGALLSAYVAGQLVWFLWPERTMFFFYTIAYEPFFVMMIA +LALSLLLRPGRRPGPRWGSALVLAYVTIAVAVSLFFLPVWIGDVIPYDQWRWRMWFSSWI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000510.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000510.fa new file mode 100644 index 0000000000000000000000000000000000000000..e86e9645827da45f9a302e94f43479d915bd8e70 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000510.fa @@ -0,0 +1,35 @@ +>PROKKA_00490 +MAHASETPLAYRAPAQQPDDDGGPRRDAHEEKSGRRRRLEYPPAPEPLPVPVVDNHTHLD +FRDGLVRVDVHQAMDAAEAVGVTGAVQVGCDIASARFTIAAIEAEPRLLGAVALHPNDAA +RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDEAGHAAQQESFRRHIRLAREL +GTALQIHDRDAHDDVVRILLEEAADGGLPPHVVFHCFSGGPDLARTCAEHGWHMSFAGPV +TFKANDELREALRIAPAELLLVETDAPFLTPHPHRGRPNAPYLIPLTLRGMAETRGDDVA +ALARAVSENTARVYGSF +>PROKKA_00211 +MAHASETPLAYRAPAPQPDDDGGPRRDAHEEKSGRRRRLEYPPAPEPLPVPVVDNHTHLD +FRDGLVRVDVHQAMDAAEAVGVTGAVQVGCDVASARFTIAAIEAEPRLLGAVALHPNDAA +RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDETGHAAQQESFRRHIRLAREL +GTALQIHDRDAHDDVVRILLEEAADGGLPPHVVFHCFSGGPDLARTCTEHGWHMSFAGPV +TFKANDELREALRTAPAELLLVETDAPFLTPHPHRGRPNAPYLIPLTLRGMAETRGDDVD +ALARAVSENTARVYGSF +>PROKKA_02457 +MAHASETPLAYRAPAQQPDDDGGPRRDAREEKSGRRRRLEFPPAPEPLPVPVVDNHTHLD +FRDGLVRVDVHQAMDAAEAVGVVGAVQVGCDVASARFTIAAIEAEPRLLGAVALHPNDAA +RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDETGHAAQQESFRRHIRLAREL +GTALQIHDRDAHDDVVRILLEEAAEGGLPPHVVFHCFSGGPELARTCAEHGWHMSFAGPV +TFKANDELREALRIAPAELLLVETDAPFLTPHPHRGRPNAPYLVPLTLRGMAETRGDDVD +ALARAVSENTARVYGSF +>PROKKA_02341 +MATTTSAQSASTQSASTEPGIPSAYRPPATPADLGDGPARDTREEKSGRKRRLEYPPAPE +PLPVPVVDNHTHLDFRDGLVRVDVHQAMDAAEAVGVVGAVQVACDVESARFTVEAIEAES +RLLGAVALHPNDAARLTARGEFEEAFAVIAELAEHPRVRAVGETGLDFFRTTDEAGHAAQ +EESFRRHIRLARELGKALQIHDRDAHDDVVRVLLEEEADGGLPPHVVFHCFSGGPDLART +CAERGWHASFAGPVTFKANDDLRDALRLLPRELVMVETDAPFLTPHPHRGRPNAPYLIPV +TLRGMAEARGEEVAELAAAVAENTARVYGEF +>PROKKA_00489 +MAHASETPLAYRAPAQQPDDDGGPRRDAREEKSGRRRRLEYPPAPEPLPVPVVDNHTHLD +FRDGLVRVDVHQAMDAAEAVGVVGAVQVGCDVASARFTIAAIEAEPRLLGAVALHPNDAA +RLAERGEFEEAFAQIAELARHPRVRAVGETGLDYFRTQDEAGHAAQQESFRRHIRLAREL +GTALQIHDRDAHDDVVRILLEEAADGGLPPHVVFHCFSGGPELARTCAEHGWHMSFAGPV +TFKANDELREALRIAPAELLLVETDAPFLTPHPHRGRPNAPYLIPLTLRGMAETRGDDVD +ALARAVSENTARVYGSF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000511.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000511.fa new file mode 100644 index 0000000000000000000000000000000000000000..9a2940aeb6c1245125ac2fa6b1495e15206814d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000511.fa @@ -0,0 +1,60 @@ +>PROKKA_00491 +MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASILPLVSLLTSGELG +SPALEGLLARFGAVTVPEQTVAFAVVIVLAFLLKAILVLAFRWWTMGFTNQNLIRTSATL +LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVTVVVGVAM +PLTGLGMALYFLAVAWVIKTVIRRPASRLGWTLVTAGERANTAALQGLENYKDVKIRGND +SAFMEEYRAARMESAEATRLKMILTMMPRYVLEVAFVAAIAALVAVAFIQGRGGEAFGSL +ALLAMAGFRVLPSMAALMATTNEIRTSWPAFERTTAELAAAQPVLHAADRPYERITFEES +IEVRDASFTYPGKAEPVLRDIDLRIPFGSSYAFVGGSGAGKTTLVDLVIGFHHAQRGGVY +VDGVELEANPRGWWDNVAFVPQSVTVVNGTVLHNVLLDVEAAQTADRAEVERVLREAQLG +QWLDELPDGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT +EVIESLRGRITVIVVAHRLSTVKRCDQIVLMDQGRIIGQGTFAGLQETSPEFRELVRLGD +LST +>PROKKA_00212 +MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASIIPLVSLLTSGELG +SPALEGLLARFGAVTVPEQTVAFAVVIVVAFLLKAILVLAFRWWTMGFTNQNLIRTSATL +LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVAVVVGVAM +PLTGLGMALYFLAVAWVIKTVIRRPASRLGWTLVTTGERANTAALQGLENYKDVKIRGND +SAFMEEYRAARMESAEAMRLKMILTMMPRYVLEVAFVAAIAALVAVAFIQGRGGEAFGSL +ALLAMAGFRVLPSMAALMATTNEIRTSWPAFERTTAELAAAQPVLHAADRPYERITFEEA +IEVRDASFTYPGKAEPVLRDIDLRIPFGSSYAFVGGSGAGKTTLVDLVIGFHHAQRGGVY +VDGVELEANPRGWWDNVAFVPQSVTVVNGTVLHNVLLDVEAAQTADRAEVERVLREAQLG +QWLDELPDGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT +EVIESLRGRITVIVVAHRLSTVKRCDQIVLMDHGRIIGQGTFAGLQETSPEFRELVRLGD +LST +>PROKKA_02456 +MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASILPLVSLLTSGELG +SPALEGLLARFGAVTVPEQTVAFAVVIVLAFLLKAILVLAFRWWTMGFTNQNLIRTSATL +LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVAVVVGVSM +PLTGLGMALYFLAVAWVIKAVIRRPASRLGWTLVTTGERANTAALQGLENYKDVKIRGND +SAFMEEYRAARAESAEATRLKMILTMMPRYVLEVAFVAAIAALVAVAFVQGRGGEAFGSL +ALLAMAGFRVLPSMAALMATTNEIRASWPAFERTTAELADAQPVLDAADRPYERLEFARE +IEVRGASYTYPGSDEPVLRDIDLTIPFGTSYAFVGGSGAGKTTLIDLLIGFHHAQDGAVL +VDGVELEANPRGWWDNVAFVPQSVTVVNGSVLHNVVLDLEAAETADRAAVEQVLRDAQLG +EWLDALPEGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT +EVIESLKGRITVLVVAHRLSTVKHCDQIVLMDQGRIIGQGTFRGLQETSPEFQELVRLGD +LSA +>PROKKA_02340 +MVTRLLKSRLPEGTQYLVDRPMRIRLGFVVLGSILVALLEMAALASILPLVNLLTTGSPG +APVITELLASVGAVSVAEQTVAFAGVIVVAYLLKAVLVLSFRWWTMGFTNKNLIQTSAKL +LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTLLTEAVTLLAVGIVVGVTM +PLTALGMGAYFLVVTLIIRHVIRKPASQLGWTLVVTGERANTAALQGLENYKDVKVRGND +SAFMDEYVDARRENAEAIRLKMILTMMPRYVLEVAFVAAIAGLVAVAFASGRGDQAFGSL +ALLAMAGFRLLPSIASVMATSNEIRASWPAFERTVAELKDAQPVLDAADRPYDRLPFERS +LEARNASFTYPGKDEPVLKGIDLSIPFGASYAFVGGSGAGKTTLVDLLIGFHHAQQGGVY +VDGVELQADPRGWWDNVAFVPQSVTVVNGSVLHNVVLDIEAARTADRTEVERVLRDAQMG +DWLDALPDGLDTVVGEGAVGVSGGQRQRLGIARALYRRPRLLVLDEATSALDNVTERKVT +DVIESLKGRITVIVVAHRLSTVKHCDQVVLMDEGRILDQGTFAGLQETSPEFQELVRLGD +LSS +>PROKKA_00490 +MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASILPLVSLLTSGELD +SPALEGLLARFGAVTVPEQTVAFAVVIVLAFLLKAILVLAFRWWTMGFTNQNLIRTSATL +LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVAVVVGVAM +PLTGLGMALYFLAVAWVIKTVIRRPASRLGWTLVTAGERANTAALQGLENYKDVKIRGND +SAFMEEYRAARMESAEATRLKMILTMMPRYVLEVAFVAAIAALVAVAFIQGRGGEAFGSL +ALLAMAGFRVLPSMAALMATTNEIRTSWPAFERTTAELAAAQPVLHAADRPYERVTFEEA +IEVRDASFTYPGKAEPVLRDIDLRIPFGSSYAFVGGSGAGKTTLVDLVIGFHHAQRGGVY +VDGVELEANPRGWWDNVAFVPQSVTVVNGTVLHNVLLDVEAAQTADRAEVERVLREAQLG +QWLDELPDGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT +EVIESLRGRITVIVVAHRLSTVKRCDQIVLMDQGRIIGQGTFAGLQETSPEFRELVRLGD +LST diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000512.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000512.fa new file mode 100644 index 0000000000000000000000000000000000000000..4b3d0b72e705fa61280eb0c91558e83f83fc22fd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000512.fa @@ -0,0 +1,34 @@ +>PROKKA_00492 +MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV +LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS +EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG +PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPTGGASRREVFA +VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR +AAEVSA +>PROKKA_00213 +MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV +LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS +EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG +PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPAGSTSRREVFA +VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR +AAEEVVA +>PROKKA_02455 +MIDPNTIRRIVQAAGVGPDEHVLEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAERLPHTV +QEFRPASADALAVLHADALRMTAADLDAVRPAAAPGGPTALVANLPYNVAVPVLLHALAE +LPGLRHGLVMVQEEVADRLAAGPGSRVYGVPSAKAAWYAQVDKAGTIGTQVFWPAPRIHS +GLVAFTRREPPTSAVSRAETFAVVDGAFAQRRKTLRAALAGWAGSPQAAEDALVAAGVDP +RTRGEALGIEAFARIAEHGPRRAAGEGSA +>PROKKA_02339 +MVPPPDAPATAPLLSAADVRRLAAELDLRPTKQWGQNFVIDPNTIRRIVAAADLAPDEHV +LEIGPGLGSLSLGLLDAASAVTAVEIDPVTAARLPATAAEFRPERAADLAVLHADAMTLT +AEGLDSVRPAGAASGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG +PGSRVYGVPSAKAAWYADVRKAGVIGTQVFWPAPRIHSGLVAFTRREPPTQAVDRREVFA +VVDAAFAQRRKTLRAALATWAGSPALAEEALVAAGVDPKARGEALDIAAFARIAEHRPEA +AS +>PROKKA_00491 +MVQPSPHPAPAPLLSAADVRRIAAELDLRPTKQWGQNFVIDPNTIRRIVQAADVTADEHV +LEIGPGLGSLTLGLLDAAAAVTAVEIDPVTAARLPRTAAEFRPGAEDALAVLHADAMTLS +EQALAEVRPAAAAGGPTALVANLPYNVAVPVLLHALAVLPGLRHGLVMVQEEVADRLAAG +PGSKVYGVPSAKAAWYADVRKAGTIGTQVFWPAPRIHSGLVAFTRREPPAGGASRREVFA +VVDAAFAQRRKTLRAALASWAGSPQAAEDALVAAGVDPRARGEALDIAAFARIAEHGPRR +AAEEVVA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000513.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000513.fa new file mode 100644 index 0000000000000000000000000000000000000000..1ddb2b0d22c14227fd1e48d5d22dbd620e249ad1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000513.fa @@ -0,0 +1,35 @@ +>PROKKA_00493 +MTTEDLGLDPTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD +GRITVGPSGRHISLVDTQDVPWDERNLAHRAAAHLRHTLGLDPDSHGVHLEVAKQVPVAG +GMGGGSADAAAALLACSALWETGHTRAELAELAAPLGADVPFSVLGGAAVGLGTGVELTP +VAARTPVHLVLVPADAGLSTPVVFQTLDELRREGHLPDGPPRPEVNEAVLRALTAADPLE +LATAMDNDLQTPAVVLFPELSDVLDLGLDEGALRGMVSGSGPTLLFVAQDEASALRLASA +IEERTGVRALPVHGPVPGAHVL +>PROKKA_00214 +MTTEDLGLDPTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD +GRITVGPSGRHISLVDTQDVPWDERNLAHRAAAHLRRTLGLDPDTHGVHLEVAKQVPVAG +GMGGGSADAAAALLACSALWETGHTRAELAELAAPLGADVPFSVLGGAAVGLGTGAELTP +VAARTPVHLVLVPADAGLSTPVVFQTLDELRREGHLPDGPTRPEVNEAVLRALTAADPLE +LATAMDNDLQTPAVVLFPELSDVLDLGMDEGALRGMVSGSGPTLLFVAQDEASALRLASA +IEERTGVRALPVHGPVPGAHVL +>PROKKA_02454 +MSEARAGLSGTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD +GRVTVGPCPRQVSLVDSHDVPWDERNLAHRAAVHLRTALGLDEATHGVHLDVAKQVPVAG +GMGGGSADAAAALLACSVLWETGHTRSELAELAAPLGADVPFAVLGGAAVGLGTGAELTP +VAARTPVHLVLVPADAGLSTPVVFGTLDELRRDGHVPEGAAHPEVNQEVVRALTAADPLA +LATVMDNDLQTPAVALFPDLGDVLDLGLDEGALRGMVSGSGPTLLFVVPDEHSALSLATA +VEERTGVRALPVHGPVAGAHVL +>PROKKA_02338 +MSGLPGPSARHVTVRAPGKVNLSLRVGPPRPDGYHPVASVYLAVSLAETVTAVARPDGDA +RITLAESTRQPSSVDTRDVPWDERNLAHRAALHLRQSLGLAPETHGVHLEVSKQVPVAGG +MGGGSADAAAALLACSVLWDTGLTRSELAELAAPLGADVPFAVTGGAAVGRGTGSELTPV +AARRPVHLVLVPADAGLSTPIVFRTLDELRSLGRAPEGQGEPAVDADVVRALAQADPLAL +ALAMENDLQTPAVTLFPELSDVMDVGLDEGALRAMVSGSGPTLLLLAHSEQDAARLATAV +QERTGVAALAVHGPVPGAHVL +>PROKKA_00492 +MTTEDLGLDPTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIARTD +GRITVGPSGRHISLVDTQDVPWDERNLAHRAAAHLRRTLGLDPDTHGVHLEVAKQVPVAG +GMGGGSADAAAALLACSALWETGHTRAELAELAAPLGADVPFSVLGGAAVGLGTGAELTP +VAARTPVHLVLVPADAGLSTPVVFQTLDELRREGHLPDGPTRPEVNEAVLRALTAADPLE +LATAMDNDLQTPAVVLFPELSDVLDLGMDEGALRGMVSGSGPTLLFVAQDEASALRLASA +IEERTGVRALPVHGPVPGAHVL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000514.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000514.fa new file mode 100644 index 0000000000000000000000000000000000000000..4e68621a4ee0d824e9dba51c57de40db59163fd4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000514.fa @@ -0,0 +1,60 @@ +>PROKKA_00494 +MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR +VTRRGGVRVGVLDQQDRLDPEHTVRQAVVGDVDDHVWASDPKVRDVLGGLLDGFDLEQSV +RGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKPRWRPTDGGLVVVT +HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWVLARAERSRQAAVTEQKRQQLVKKELAWL +RRGAPARTSKPKFRIEAANAIIEDVPAPRDSVSLAKMATARLGKDVLDLEHVSLTLGEKP +ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRIAPDSGRVKRGKTVVSATLTQDVKE +LDDVAHLRVAEVMAREGSSFQVGDREMSSGQLLEMLGFGTSRQWTQVSELSGGERRRLQL +LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL +GDGKVRGLPGGVDQYLELRAAMDEAGGPARGAGPVRGRNDVVGTCAGMGGPEEDTGPTEA +ERRLARKEMARLEKQMTRLRDRRSGLEARMAALGQAQDFDALTAASADLKDLDAQLDVLE +EEWLRAAELAEGD +>PROKKA_00215 +MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR +VTRRGGVRVGVLDQQDRLDPEHTVRQAVVGDVDDHVWASDPKVRDVLGGLLDGFDLEQSV +RGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKQRWRPTDGGLVVVT +HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWVLARAERSRQAAVTEQKRQQLVKKELAWL +RRGAPARTSKPKFRIEAANAIIEDVPAPRDSVSLAKMATARLGKDVLDLEHVSLTLGEKP +ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRIAPDSGRVKRGKTVVSATLTQDVKE +PDDVAHLRVAEVMAREGSSFQVGDREMSSGQLLEMLGFGTSRQWTQVSELSGGERRRLQL +LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL +GDGKVRGLPGGVDQYLELRAAMADAGGPARGAGVARGRNDVVGTCAGMGGPEEDTGPTEA +ERRLARKEMARLEKQMTRLRDRRSGLEARMAELGQAQDFDALTAASADLKDLDAQLDVLE +EEWLQAAELAEGD +>PROKKA_02453 +MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR +VTRRGGVRVGVLDQQDRLDPTHTVRQAVVGDVEDHVWASDPKVRDVLGGLLDGLDLEQTV +EGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKDRWRPTDGGLVVVT +HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWILARAERARQAAVVEQKRQQLMKKELAWL +RRGAPARTSKPKFRIEAANAIIADVPEPRDSVSLAKTATARLGKDVLDLEHVGLSLGEKR +ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRLEPDSGRVKRGKTVVTATLTQDVKE +LDEVAHLRVAEVMAREGSAFQVGDKEMSAGQLLEMLGFGTSRQWTQVSELSGGERRRLQL +LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL +GDGKVRGLPGGVDQYLELRAAMDAAGASGGPARGAGAARGRNDVVGTCAGMGGPEEDTGP +TEAERRLARKEMARLEKQMTRLRDSRSVLEARMAELGQAQDFDALTAASADLKDLDAQLD +VLEEEWLQAAELTEGD +>PROKKA_02337 +MAHLLGAENIGISFGTRTVLDGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR +VTRRGGVHVGVLDQRDVLDPQDTVRRAVVGDVEDHVWASDARIRDVLGGLLAGMDLEQRV +EGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLAGHLNARWRPNDGGLVVVT +HDRWFLDAVCTRTWEVHDAAVDPFDGGYAAWILARAERARQAQVTEQKRQQLMKKELAWL +RRGAPARTSKPKFRIEAANAIIADVPEPRDTVSLAKTATARLGKDVIDLEDVTLTLGDRT +ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRLQPDSGRMKRGKTVVSATLTQDVKE +LDEVADLRVAEVMAREGSAFQVGDREMSPGQLLEMLGFGPTRQWTAVSELSGGERRRLQL +LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL +GDGRVRDLPGGVDQYLELRVLMDDAGGAAPAPGSSRGRGDAQGTCAGMVVDIPEVSEAER +RQARKDMARLERQMQRLRESRGGIEARMAELGQAQKYDELGAATAELTAVDAELEDLEEQ +WLEAAERDA +>PROKKA_00493 +MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR +VTRRGGVRVGVLDQQDRLDPEHTVRQAVVGDVDDHVWASDPKARDVLGGLLDGFDLDQPV +RGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKQRWRPTDGGLVVVT +HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWVLARAERSRQAAVTEQKRQQLVKKELAWL +RRGAPARTSKPKFRIEAANAIIQDVPAPRDSVSLAKMATARLGKDVLDLEHVSLTLGEKP +ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRIAPDSGRVKRGKTVVSATLTQDVKE +LDDVAHLRVAEVMAREGSSFQVGDREMSSGQLLEMLGFGTSRQWTQVSELSGGERRRLQL +LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL +GDGKVRGLPGGVDQYLELRAAMDDAGGPARGAGAARGRNDVVGTCAGMGGPEEDTGPTEA +ERRLARKEMARLEKQMTRLRDRRSGLEARMAELGQAQDFDALTAASADLKDLDAQLDVLE +EEWLQAAELAEGD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000518.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000518.fa new file mode 100644 index 0000000000000000000000000000000000000000..bce2571fa67070e9d2388ffd361ec36b4b24eeab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000518.fa @@ -0,0 +1,40 @@ +>PROKKA_00503 +MPGAQGEDEAMSETTALRIRTGLDAVTVSGLTGDERAEVIASWARCGVEAVEPPARADAH +RDADTARPWLQWHEDLVFLATSRTIESARGTHLLFHAACLAAPDTGAAMVLVAASGTGKT +TATRRLGPHFAYLTDETAIIAPDGLTVTPYPKPLSLLGSRGVRPKTQRGPDDLGLGPTLP +DARLARIAVLDRVRDPAGPVTPRAEAIELVAALEALVPQTSSLSLLPRGLVTLCRVLDTV +GGAQRLVYAEAEDLRDVVDGLLAAPPTSVTPAWEALTEEELRASVGAAAPGAVSRCAVDD +GILTDSGRLVLLASDRLVVLEGLGPSVWLLLDESRTAADVVACLRAEGPVPEDAEARVRK +AMDALVSAGLATAG +>PROKKA_00223 +MPGAQGEDEAMSETTALRIGTGLDAVTVSGLTGDERAEVIASWARCGVEAVEPPARADAH +RDADTARPWLQWHEDLVFLATSRTIESARGTHLMFHAACLAAPDTGAAIVLVAASGTGKT +TATRRLGPHFAYLTDETAIIAPDGLTVTPYPKPLSLLGSRGVRPKTQRGPDDLGLGPTLP +DARLARIAVLDRVRDPAGPVTPRAEAIELVAALAALVPQTSSLSLLPRGLVTLCRVLDAV +GGAQRLVYAEAEDLRGVVDGLLAAPPTPVTPAWEALTEEELSASVGVATPGAVSRCAVDD +GILTDSGRLVLLASDRLVVLEGLGPSVWLLLDEPRTAADVVARLRAEGPVPEDAEARVRE +AMDALVTAQLATTG +>PROKKA_02447 +MPAAPPDPSAAPVREALRIGAGLDAVTVSGLTGAERDELLRSWARCGVETVELTEDADAH +RGPEHPRSWLDWHENLVFLATSRAIESARGTHLMFHAACLAAPDTGAAIVLAAASGTGKT +TATRRLGPHYAYLTDETAMVDPADLSVTPYPKPLSLLEPGGSRPKTQRGPDELGLGLTRA +DAVLARIAVLDRVREAAAPVPARAEPMDVVTALQHLVPQTSSLSLLPRGLVALCTLLDAL +GGVQRLVYAEADDLRPVIDGLLAAAPQPVDPAWEPLDAAELAASEGAAEPGAVRRAAAAD +GILTADGRLVLLAGTTLTVLDGIGPAVWFALESPLTPERIVARLAEDGPVPADAAERVAE +AVAALESAGLLVTTPQGAGPEADALRS +>PROKKA_02331 +MTDPRRGGRAVRIPAGDGSTTAAGLDETGVRTLLDAWRRCGAEEVAAPAEGAAAYWEATG +WDWFHENLVHSATTAAITAGVGRRLLFHGACLADPGTGSAVALVAASGTGKTTATRRLGP +HYAYLTDETVIVAPDTLEVTPFPKPLSLLGPSGVRPKTQVSPDELGLGDAVPARLARLAV +LDRVRDVDGPVTARAETMGLGDALIAVVPQTSSLARLPRGLRELCRVIDRLGGVQRLVYA +EADGLRPVVDELLAAAPEPLEPAWEPLTPAELAASRETGDAAAGAARREAVDDGIVTDDG +RLILLAGPQLAALEGLGPVVWLMLEEPLTNAQIVERLAAEGPVPDDAADRVADAVTALAE +SGLVRI +>PROKKA_00502 +MPGAQGEDEAMSETTALRIGTGLDAVTVSGLTGDERAEVIASWARCGVEVVQPPTHTDAH +RGAHTASPWLQWHEDLVFLATSRAIESARGTHLLFHAACLAAPDTGAAMVLVAASGTGKT +TATRRLGPHFAYLTDETAIIAPDGLTVTPYPKPLSLLGSRGVRPKTQRGPDDLGLGPTLP +DARLARIAVLDRVRDPAGPVTPRAEAIELVAALEALVPQTSSLSLLPRGLVTLCRVLDTV +GGAQRLVYAEAEDLRDVVDGLLAAPPTPVTPAWEALTEEELRASVGAAVPGAVSRCAVDD +GILTDSGRLVLLASDRLVVLEGLGPSVWLLLDESRTAADVVARLRAEGPVPEDAEARVHE +AMDALVTAELARTG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000520.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000520.fa new file mode 100644 index 0000000000000000000000000000000000000000..1cbe717f96426785366bdd049c95adde1510d0d8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000520.fa @@ -0,0 +1,35 @@ +>PROKKA_00505 +MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG +MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL +EAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA +LPQVPRRDELVFVGSRYPNRVELLARLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP +AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE +VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA +>PROKKA_00225 +MSATGYTVAAPPEARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG +MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL +DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA +LPEVPRRDELVFVGSRYPNRVELLTRLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP +AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE +VLVFEDADHLIELGRRIVADPAWGARIREAGRRRSHVEHTFAHRAAMAQGWWA +>PROKKA_02445 +MSGTGYTVPARGARGTGRAERLFLVSPAFHGYHRSIARAWAAQGFDVTVHCYDAYATVPM +KLRNKALLELPQKAGVDRTAARVAWDTERAVAALRAARPDRVLVIKGDSLGEAFWSEVVE +AGLPRLLWLYDDLSRHDYSPEFLRAIGPVLSYARSEAEQLAGEGVDAHYLPNGFDPDMAL +PSLPRREELVFVGSRYPNRVELLTTLAEAGVPVRAYGRQWSHHPVDRLRTWEVTRPALPA +ERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYEPGEEV +LVFENPEHLVELGRRVVAEPSWGERIREAGRSRSHAEHTFAHRAALAQEWWT +>PROKKA_02329 +MSAGTYTIAARGERPVSGRPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYADLG +MKLRNKLALELPQKAGLDRTAARVAWDTDRAVAALRAAAPDRVLVIKGDSLGDAFWDEVT +GRALPRMLWLYDDLSRHDYSMDFLRGIGPVLSYARSEAESLAAQGVDAHYMPNGFDPEMV +LPAVPRTEELVFVGSRYPNRVELLRALASAGVPVRAYGRQWSHHPVDRLRTWELSRPDLP +AERDIPLAEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRPDVAEFYVPGEE +VLVFEDTEHLVELGRRIVAEPAWGDRIRAAGRRRSHAEHTFSHRARMAQEWWA +>PROKKA_00504 +MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIASAWAAQGFDVAVHCYDAYATLG +MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSAIL +DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA +LPQVPRRDELVFVGSRYPNRVELLSRLTAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP +AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE +VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000522.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000522.fa new file mode 100644 index 0000000000000000000000000000000000000000..23169c41d3c6ab72185ffec019e3a03b894864b5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000522.fa @@ -0,0 +1,30 @@ +>PROKKA_00507 +MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAEEDLHVVVSTDSAEIAEVAL +RYGADVPGLRPAHLAQDSTPTEPVIEHVLAAERAAGVEPEGVMLLQATSPLRLPGTLDRA +VRQFRDTGVDSLVGVVPVSPFLWRHPEDPDGEPIPDFDVTARKRRQDMTRTDLRFRENGS +LYVTRPWVYDRLHNRLGGRIGLLELDDLEGVDIDTELDFALAEQQMDQYLAVHKVLRHRS +DLGAPRTAETPTTGPNRTPGGAQ +>PROKKA_00227 +MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAGEDLHVVVSTDSAEIAEVAL +RYGADVPGLRPAHLAQDSTPTEPVIEHVLAAERAAGVEPEGVMLLQATSPLRLPGTLDRA +VRQFRDTGVDSLVGVVPVSPFLWRHAGDPDGEPIPDFDVTARKRRQDMTRADLRFRENGS +LYVTRPWVYDRLHNRLGGRIGMLELDDLEGVDIDTELDFALAEQQMDQYLAVQKVLQHRP +DLGAPRTAETPTTGPNRTLGGTQ +>PROKKA_02443 +MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAEADLHVVVSTDSEEIAEVAR +RYGADVPGLRPAELAQDETPTEPVVEHALAAERAAGVEPEGVMLLQATSPLRLPGTLDRA +VAQFRETGVDSLVGVVPVSPFLWRHAADPADPPVCDFDVAHRKRRQDMDRPDLRFRENGS +LYVTRPWVYDELHNRLGGRIGMFELDDLEGVDIDTELDFALAEQQMDQYLAVHKVLQRVP +DRTQLHGTSTATLGDAL +>PROKKA_02327 +MSILCVIPVRGGSRGLPGKNIRMLGGHPLVAWTIQAALDAEADLHVVVSTDSEEIAEVAR +KYGADVPALRPAELARDDTPTEPVVEHALAAERARGVEPEAVMLLQATSPLRLPGTLDRA +VAAFREPGVDSVVGVVPVSPFLWRHAADPAAAPVADYDVDGRKRRQDMDRADLRFRENGS +LYVTAPWVYDERHNRLGGRIALLELDDLEGVDIDTELDFALAEQQMDQYLAVQKLLQTRP +DLTRTAGGAL +>PROKKA_00506 +MSILCVIPVRGGSRGLPGKNIRLLGGHPLVAWTIQAALEAEEDLHVVVSTDSAEIAEVAL +RYGADVPGLRPAHLAQDSTPTEPVIEHVLAAERAAGVEPEGVMLLQATSPLRLPGTLDRA +VRQFRDTGVDSLVGVVPVSPFLWRHPEDPDGEPTPDFDVTARKRRQDMTRADLRFRENGS +LYVTRPWVYDRLHNRLGGRIGMLELDDLEGVDIDTELDFALAEQQMDQYLAVQKVLQHRP +DLGAPRTAETPTTGPNRTLGGTQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000523.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000523.fa new file mode 100644 index 0000000000000000000000000000000000000000..439e2845a7d6d144d3811b6028c7bd9fbf5b2a48 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000523.fa @@ -0,0 +1,70 @@ +>PROKKA_00508 +MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLLAQPE +ASLDVAAADVAHRDPATAPLGATPAEMREALPAGALHLPLLDERGRLTALAINREAELRI +GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA +TAGEDLGAQRTLDELAKFSLSAEDMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV +KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIREAAALVRSFGVPFAMLHAQSTYPA +PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK +VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLRVGATITAD +DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFEFRRPWGLPVR +YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFSEPMPMGFTTHLPDIFSGDFLVDLASD +DDAVWERSIAEVQRTIDITRDLKRWFPHEEEPIMVITMGGFTLDRHIRPEERLPKYERIA +EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL +SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS +FIPEIWQGHINNGEGFWTALDRLEQWL +>PROKKA_00228 +MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLLAHPE +ASLDVAAADVAHRDPATASLGASPDEMREALPAGALHLPLLDERGRLTALAINREAELRI +GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA +TAGEDLGAQRTLDELAKFSLSAADMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV +KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIRESVALVRSFGVPFAMLHAQSTYPA +PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK +VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLQAGVTITAD +DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFQFRRPWGLPVR +YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFREPLPMGFTTHLPDIFSGDFLVDLASD +DDAVWERSIVEVQRTIDITRDLKRWFPNEEEPIMVITMGGFTLDRHIRPEERRPKYERIA +EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL +SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS +FIPEIWQGHINNGEGFWTALDRLEQWL +>PROKKA_02442 +MITERHLTPYLVFPEDSLLVALQKMTDNRERIVFVVDSHGFLAGSLTDGDFRRWLLANPG +ASLEVAAVEAANRTPATGPVGASPAEVLAALPAGALHLPLLDERGRLAALAINRESELRI +GEHRIGPGRPAFLIAEIGNNHQGSVDLARELVDLAVEAGADAVKFQLRDMDALYRQSGAG +TAGEDLGAQRTLDELAKFSLPAEDMVRVFDHVRDAGVALMCTPWDAPSMRVLAQYPVDGV +KIASADLTNHGLLRDAAAARLPMVLSTGMSREDEIKEAVELVRSSGVPFAVLHAQSTYPA +PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVPLAAVARGASIIEKHFTVDRGLEGNDHK +VSLLPEEFAQMVRQTREIEESIGVAAERVVSTGEAMNRINLAKSLVAARPLAAGETVTED +AVTVKSPGRGLQPNELPRLVGRTLHRDMAEGDFFFAGDLTDTVPTGRQFEFRRPWGLPVR +YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFTEPLPMGFTTHLPDIFSGDFLVDLASD +DDAVWERSIAEVQRTIDITRDLKRWFPKEEAPIMVITMGGFTLDRHIAPAERQAKYDRIA +EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL +SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS +FIPEIWQGHINNGEGFWTALDRLEQWL +>PROKKA_02326 +MIIERHLTPYLVFPEDSLTVALQKMTDNRERIVFVVDTHGFLQGSLTDGDVRRWLLAHPG +AALDSPAVAAANPSPATGLVGDAPSSVLAALPEGALHLPLLDERGHLTALAINRESELRI +GSHRVGEGRPAFLIAEIGNNHQGSVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA +TAGEDLGAQRTLDELAKFSLSVDDMVKVFDHTRAAGVALMCTPWDAPSMQVLADYPVDGV +KIASADLTNHGLLRDAASRGIPMVLSTGMSREEEIQESAALVRSYGVPFAMLHAQSTYPA +PYKDVNLAYLDRLAEIAQAPVGYSGHERGFHVALAAVVRGASIIEKHFTIDRSLEGNDHK +VSLLPDEFAQMVRQTREIEESIGVAGERVVSTGEAMNRINLAKSLVAARSLTAGDVVAEA +DVTVKSPGRGLQPNQLPQLVGRTLHRDLEEGDFFFAGDLTDSVPTGRQFEFRRPWGLPVR +YHDYAALTKDCTPDFLEFHFSYKDLEIDIDTVFREPMPGGFTTHLPDIFAGDFLVDLASM +DEQVWERSIAEVQRTIDITRDLKRWFPSEEAPIMVITMGGFTLDRHIRPEERQPKYERIA +EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL +SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS +FIPEIWQGHINNGEGFWTALDRLEQWL +>PROKKA_00507 +MIIERRLTPYLVFPEDSLLAALQKMTDNRERTVFVVDSHGFLVGSLTDGDVRRWLVAHPE +ASLDVAAADVAHRDPVTAPLGASPAEMREALPTGALHLPLLDERGRLTALAINREAELRI +GGHRIGEGHPAFLIAEIGNNHQGDVDLARRLVDLAVEAGADAVKFQLRDMDALYRQSGAA +TAGEDLGAQRTLDELAKFSLSAEDMVRVFDHVREAGVALMCTPWDAPSMRVLREYPVDGV +KIASADLTNHGLLRDAAASGLPMVLSTGMSREEEIRESVALVRSFGVPFAMLHAQSTYPA +PYKDVNLAYLDRLAEIAQTPVGYSGHERGFHVALAAVARGAAIIEKHFTVDRGLEGNDHK +VSLLPEEFAQMVRQTRDIEESIGVGTERVVSTGEAMNRINLAKSLVAARPLQAGATITAD +DVTVKSPGRGLQPNELPRLVGRTLHREMAEGDFFFAGDLTDTVPTGRQFQFRRPWGLPVR +YHDVEALTKDCTPDFLEFHFSYKDLEIDIDSVFTEPMPMGFTTHLPDIFSGDFLVDLASD +DDAVWERSIAEVQRTIDITRDLKRWFPNEEEPIMVITMGGFTLDRHIRPEERLPKYERIA +EAVQRLDTSGIRIAAQTLPPFPWLMGGQQYHNLFMDPDDTVAFVEATGVPLCLDISHSKL +SATFLGIPFSEMVEKLAPHTIHLHLVDATGVDGEGPQIGEGDVDWPVLCEQLDRLAPGVS +FIPEIWQGHINNGEGFWTALDRLEQWL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000525.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000525.fa new file mode 100644 index 0000000000000000000000000000000000000000..8729f0d7118e4452570acadc293f2eda014a8b6a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000525.fa @@ -0,0 +1,35 @@ +>PROKKA_00512 +MTETPLAPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEAHVVVDGDVDGSEGMLAQLA +AEHPGLDLSWTVFGENRGRVAALNAGADATSGRILIRADDDLEPGPHYIRDHVAAHAGGS +GGVIGLTANVLPDSAYQRVYGDAQDEAHRRHAYALPAEQQWRHWAGNVSVPRTLHEELGG +YDPDYRRYGWEDVDFGYRLHAAGYPVEIRPELETRHHAAAVTTYTKARRALHSGSARQIF +IAKHGADALGGDRAPGGPWGAAVRAVAALSTERTIQYSSAVVERAAAVLPAPIARKLIAL +QVEAAAETGRTRPGRARRQF +>PROKKA_00232 +MTETPLTPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEVHVVVDGDVDGSEAVLGQLA +AERPGLDLSWTVFPENRGRVGALNAGADATSGRILIRADDDLEPGPHYIRDHVAAHSGEP +GGAIGLYLNVLEPTPYQRAYGDTQDVLHREHAYALQADQQWRHWAGNVSVPRALHQQIGG +YDPDYRQYGWEDIDYGYRLHAAGYPVVIRPELETRHHAAAVTTHSKAVRALHGTAARNLF +VGKHGAAPLGTIGAPRGVWGAAVRLVAWGTTEATLTRSSALIDAVADHLPRGLARRLIAL +QVEGAAEAGRAHPHRAQRSI +>PROKKA_02439 +MTETPLTPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEVHVVVDGDVDGSEAVLAQLA +AEYPGLDLSWTVFGENRGRVAALDAGADATSGRILIRADDDLEPGPHYIRDHVAAHDDVQ +RGVIGLTANVLPDSAYQRVYGDAQDEAHRRHAYALPAEQQWRHWAGNVSVPRVLHEELGG +YDPDYRRYGWEDVDFGYRLHAAGYPVEIRPELETRHHAAAVTTSTKARRALHSGSARQIF +IAKHGADALGGDRAPGGLWGAAVRAVATLSTERTIQYSSAVIERAAAVLPAPIARKLIAL +QVEAAAETGRTRPGRARRQF +>PROKKA_02322 +MSDQTAYEASVIVPSRGGAGRLPRLIGALAAQEEAPPFDVHVVVDGDVDDSASALERLAA +AHPDLPLTWTVFEENRGRVAALNAGADATTGRILIRADDDLEPGVHYIRDHVAAHAEGPG +GAIGLYLNILESTPYQRVYGDAQDVLHREHAYALPADQQWRHWAGNVSVPRAVHEELGGY +DPDYRQYGWEDIDFGYRLHAAGYPVRIRPELATSHHAAAVTTYSKAVRALHGTAARNLFI +QKHGAEVLGGVDAPRGLWGAAVRLVALGATEGSLTRSSALIDAIADRVPITVARKLIALQ +VEGASEAGRAYPERAQRPI +>PROKKA_00511 +MTETPLTPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEVHVVVDGDVDGSEGMLAPLA +AEHPGLDLSWTVFGENRGRVAALNAGADATSGRILIRADDDLEPGPHYIRDHVAAHDDVQ +RGVIGLTANVLPDSAYQRVYGGAQDEAHRRHAYALPAEQQWRHWAGNVSVPRALHEELGG +YDPDYRRYGWEDVDFGYRLHAAGYPVEIRPELETRHHAAAVTTYTKARRALHSGSARQIF +IAKHGADALGGDRAPGGPWGAAVRAVAALSTERTIQYSSAVVERAAAVLPAPVARKLIAL +QVEAAAETGRTRPGRARRQF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000527.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000527.fa new file mode 100644 index 0000000000000000000000000000000000000000..71e0b1ef41e81c20805573bf7d5cb0425644c641 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000527.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000528.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000528.fa new file mode 100644 index 0000000000000000000000000000000000000000..155ffbd5a1c8ac55301b2c578814976d29e80ee5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000528.fa @@ -0,0 +1,45 @@ +>PROKKA_00522 +MRITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAEHPRLAALAPVQNNISFNDA +VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY +QTLEPDTAYTYLVNDHWSADAQGRYTFLNLADPTAAIAWPIPLEDAELSDKDRAHPMLAD +VTPMPSAPILVLGAGGQLGRALVARAEAAGIPVEAHGRDTWDMTDPASWPREHFRGLRAV +VNASAMTAVDAAETPEGRAQAWAVNAAAVAELARRCTKAGVPLAHVSTDYVFDGALPVGQ +EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP +AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA +RVSATTTAAYLAGKEGVAPRPTNSALDLGPLAAVGYTAPDQRERLRDHLTEFKAGTC +>PROKKA_00244 +MRITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAGHPRLASLAPVQNNISFNDA +VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY +QTLEPDTAYTYLVNDHWSADAQGQYTFLNLADPTAAIAWPIPLEDAELSDKDRAHPMLAD +VTPMPPAPILVLGAGGQLGRALVVRAEAAGIPVEAHGRDTWDMTDPASWPREHFRGLRAV +VNASAMTAVDAAETPEGRAQAWAVNATAVAELARRCTEAGVPLAHVSTDYVFDGTLPVGQ +EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP +AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAG +HVSATTTAAYLAGKEGVAPRPTNSALDLGPLAAVGYTAPDQRERLRTYLRR +>PROKKA_02427 +MKITETAIPGLLVIDLDVHGDNRGWFKENWQREKIRALAAEHPRLATLAPVQNNISFNDA +VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY +QTLEPDTAYTYLVNDHWSADAQSQYTFLNLADPTAAIAWPIPLEEAELSDKDRAHPMLAD +VTPMPPAPILVLGAGGQLGRALVARAEAAGIPVEAHDRTTWDLEDPDSWPREHFRGLRAV +VNASAMTAVDAAETPEGRAQAWAVNATAVAELARRCAEAGVPLAHVSTDYVFDGTLPVGQ +EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGRNFVATMASLAERGIDP +AVVDDQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA +RVSATTTAAYTAGKEGVAPRPTNSALDLGPLAVVGYTAPDQRGRLRDHLSELTGDAR +>PROKKA_02310 +MKITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAEHPRLASLAPVQNNISFNDA +VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY +QTLEPDTAYTYLVNDHWSADAQGQYTFLNLADPTAAIAWPIPLEDAELSDKDRAHPMLAD +VTPMPPAPILVLGAGGQLGRALVARAEAAGIPVEAHGRDTWDMTDPASWPREHFRGLRAV +VNASAMTAVDAAETPEGRAQAWAVNATAVAELARRCTEAGVPLAQVSTDYVFDGTLPVGQ +EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP +AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA +RVSAATTAEYMAGKEGAAPRPTNSALDLGPLAAVGYTAPDQRERLRDHLSEAAGGTR +>PROKKA_00522 +MRITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAEHPRLASLAPVQNNISFNDA +VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY +QTLEPDTAYTYLVNDHWSADAQGQYTFLNLADPTAAIAWPIALEDAELSDKDRAHPMLDD +VVPMPPAPILVLGAGGQLGRALVARAEAAGIPVEAHGRDTWDMADPASWPREHFRGLRAV +VNASAMTAVDTAETTEGRAQAWAVNATAVAELARRCTEAGVPLAHVSTDYVFDGALPVGQ +EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP +AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA +RVSATTTAAYLAGKEGVAPRPTNSALDLGPLAAVGYTAPDQRERLRDHLTEFKAGTC diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000529.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000529.fa new file mode 100644 index 0000000000000000000000000000000000000000..3176ee7124b33b3345c6812ba61a011e307a8bb4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000529.fa @@ -0,0 +1,25 @@ +>PROKKA_00526 +MSDQLKIKVTRRTDFGKGAARQARRAGLIPAVVYGHGQDPVHLLLPAQETTLAVRNPNAL +LTVVNEAGEEHLVLPKDIQRHAIKDTVDHLDLIEVRRGEKVVVEVTVQVEGEVAPGTEYV +LDYATVPVEADATDLPEVVTISIEGREAGDHVYAPDVQVPAGATLQLEDDIVIATVNEVV +EQDLGDESVQEEQAAESAED +>PROKKA_00247 +MSDQLKIKVTRRTDFGKGAARQARRAGLIPAVVYGHGQEPVHLLLPAQETTLAVRNPNAL +LTVVNEAGEEHLVLPKDIQRHAIKDTVDHLDLIEVRRGEKVVVEVTVQVEGEVAPGNDYV +LDYVTVPVEADATDLPEAVTISVEGREAGDHVYAPDVQVPAGATLQLEDDIVIATVSEVV +EQDLGDESVQEEQAAESAEGESEGSED +>PROKKA_02425 +MSDKIKVTRRTDFGKGAARQARRAGLIPAVVYGHGQDPIHLLLPAQETTLAVRNPNALLT +VVNEAGEEHLVLPKDIQRHALKDTVEHLDLIEVRRGEKVVVDVTVHVEGEVAKGNDYVLD +HVTVPLEAEATHLPESVTISVEGREAGEHVYATDVQVPAGTTLQLEDEIVIATVSEVVEQ +DLGDESVQEEQAAEGEAAEGESAEGESEGSED +>PROKKA_02308 +MSDQIKLKVTRRTDFGKGASRQARRAGQIPAVVYGHGAEPIHLLLPAQETTLAVRNPNAL +LTVVNEAGEEHLVLPKDIQRHPIRQTVDHLDLIEVRRGEKVVVEVPVHVEGELSTAVDAE +YVLDYPTVPVEAEATDLPENVLISVEGREPGQHVYATDVQVPAGVTLQLEDEIVIATVSE +VVEQDLGDESVQEEQAAESAEGAEGEGESEGSEESAEGESEGSED +>PROKKA_00526 +MSDQLKIKVTRRTDFGKGAARQARRAGLIPAVVYGHGQEPVHLLLPAQETTLAVRNPNAL +LTVVSEAGEEHLVLPKDIQRHAIKDTVDHLDLIEVRRGEKVIVEVTVQVEGEVARGNEYV +LDYVTVPVEADATDLPEAVTISVEGREAGDHVYAPDVQLPAGATLQLEDDIAIATVNEVL +EQDLGDESVQEEQAAESAEGESEGSED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000530.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000530.fa new file mode 100644 index 0000000000000000000000000000000000000000..c2d830221ed008b9bc160c3c938fe23b549056b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000530.fa @@ -0,0 +1,25 @@ +>PROKKA_00527 +MTTGTTLIVGLGNPGPEYERTRHNVGQMVADELASRMGVGFTRHRAGAVVATGRLGIGGP +RVVLAKSTGYMNVSGRPVSALAAFYGIGPEDLVVVHDELDIPFDTLRLKRGGGEGGHNGL +KSITASLGTKDYARVRVGIGRPPGRMDVADFVLRPFTKPEQDALPLHVDRAADAVEKLVT +DGLEPAQQAFH +>PROKKA_00248 +MTTGTTLIVGLGNPGPEYERTRHNVGQMVADELASRMGVGFTRHRAGAVVATGRLGIGGP +RVVLAKSTGYMNVSGRPVSALASFYGIGPEDLVVVHDELDIPFDTLRLKRGGGEGGHNGL +KSITASLGTKDYARVRVGIGRPPGRMDVADFVLRPFTKPEQDVLPLHVDRAADAVEKLVT +DGLAPAQQAFH +>PROKKA_02424 +MSAGTTLIVGLGNPGPEYERTRHNVGQMVADELASRMGAGFTRHRAGAVVATGRLGIGGP +RVVLAKSTGYMNVSGRPVSALASFYGVGPEDLVVVHDELDIPFDALRLKRGGGEGGHNGL +KSITASLGTKDYARVRVGIGRPPGRMDVADFVLRSFSKPEQDALPLHVDRAADAVEKLVT +DGLEAAQQAFH +>PROKKA_02307 +MTGTTLIVGLGNPGPEYERTRHNVGHMVAGELASRMGVGFTRHKAGAVVATGRLGIGGPR +VVLAMSTGYMNTSGRPVSALTNFYDVAPEDLVVVHDELDIPFETLRLKRGGGEGGHNGLK +SITASLGTKDYHRVRVGIGRPPGRMDVADFVLKPFTKQEQELLPLHVDRAADAVEKLVTD +GLEAAQQAFNS +>PROKKA_00527 +MTTGTTLIVGLGNPGPEYERTRHNVGQMVADELASRMGVGFTRHRAGAVVATGRLGIGGP +RVVLAKSTGYMNVSGRPVSALASFYGIGSEDLVVVHDELDIPFDTLRLKRGGGEGGHNGL +KSITASLGTKDYARVRVGIGRPPGRMDVADFVLRPFTKPEQDVLPLHVDRAADAVEKLVT +DGLEAAQQAFH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000532.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000532.fa new file mode 100644 index 0000000000000000000000000000000000000000..862108fc6b8e7827c24fca7196ae9ec77239dcc4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000532.fa @@ -0,0 +1,37 @@ +>PROKKA_00530 +MSALWAVALIMLLSGTAKLRSGEDVQATFTRLRVPRPFAAPALARAFPWLELLLAAALLQ +PFTPLRPVVGLAAVALFAAFLALVVRAQDDGVSCGCFGEASAAPISRTTVVRNVVFLVLA +VLALVEGIVSLAVHGAGLAWQPLTAFGAGAWAWALLVTVLLTTAAFLAGRESVPAAPDAA +PATPEAPATPEAPDAADPVGEAEPERRPFPDAVVVADGEYTGLHRLVQDGAVVALRLSTG +CGSCARVIERLDEFKDALGPVRLRVLMPQRAPGADGAIRSGAVDASLVLADPDGAASQAI +GLHSFPTAVLLGTDRLTAGGPVGGADDVLAFLEEIREIMTTELPAATDGSTATPEVRA +>PROKKA_00251 +MSALWAVALIMLLSGTAKLRSGEDVQATFTRLRVPRPFAAPGLARAFPWLELLLAAALLQ +PFTLLRPVVGLVAVVLFAAFLALVVRAQDDGVSCGCFGEASAAPISRTTVVRNVVFLALA +VLALAEGIVSLAVHGAGLAWQPLTAFGAGAWAWALLVSVLLATAAFLAGRESVPAAPDAV +PAMPTPEAPAAVDPAAVDPADGDPADAAEPERHPFPDAVVVADGEYTGLHRLVADGAVVA +LRLSTGCGSCARVIERLDEFTDALGPVRLRVLMPQRAPGAEGAIHSGAVDASLVLADPAG +AASQALGLYSFPTAVLLGTDRLTAGGPVGGADDVLAFLEEIREIMTTELPAATDGSTATP +EVRA +>PROKKA_02422 +MPALWAVALILLLSGTAKLRSGEDVQATFTRLRVPRPFAAPALARAFPWLELLLAAALLQ +PFTQLRPVVGLVAVALFAAFLALVVRAKGDGVSCGCFGEASAAPISRTTVVRNVVFLVLA +VLALAEGIVSLAVHGGGLAWQPLTAFGAGAWAWALLVSVLLATAAFLAGRESVPAAPDAA +PAASTPEAPAAVDPADGAEPERHPFPDALVIEDGRYTGLHALASRGAVVALRLSAGCGSC +SRVIARLDEFRASLGPVRLRVLMPQHEAGATPSASTGAIPEDLVVDDPNGAAARGLGLTS +YPMAVLLGTDLLTAGGPVGGADDVLAFLEEIRDIMAAEAPAAPAAPARSPASDTPTPEVR +A +>PROKKA_02304 +MSALWAVALIMLFSGAAKLRSREDVGAVFTRLKVPAPWNDARLARAFPWLELLLALALVQ +PFTVLRPLVGLAAVALFVAFLVLVVRATGDGVSCGCFGEASAAPITGQTVVRNVLFLLLA +VMALFEGVASLAVHGIATEWLPLTAFGEDVTAWTVVVTLLLAAAAVLVGRESVPAAASAV +PVPAAGVPGSAAPAPAEGQGDEPERRPFPVAAVQQGGAFVTLHQLVIPGAVVALRLSVGC +GSCSAVIARLPELVERLGPIRVRVLMPQTVPGGELRHGTIPAELVLEDPAGAAAGGLGLT +GFPSAVLLGADGMTAGGPVFGADEVIAFLEEIGEIVATELPAAAEGSHRP +>PROKKA_00530 +MSALWAVALIMLLSGTAKLRSGEDVQATFTRLRVPRPFAAPGLARAFPWLELLLAAALLQ +PFTLLRPVVGLVAVALFAAFLALVVRAQDDGVSCGCFGDASAAPISRTTVVRNVVFLALA +VLALAEGIVSLAVHGAGLAWQPLTAFGAGAWAWALLVSVLLATAAFLAGRESVPAAPDAV +PATPTPEAPAVADPADGAEPERHPFPDAVVVADGEYTGLHRLVQDGAVVALRLSTGCGSC +ARVIERLDEFKDALGPVRLRVLLPQYAPGAEGAIRSGAVDASLVLADPAGAASQALGLHS +FPTAVLLGTDRLTAGGPVGGADDVLAFLEEIREIMTTELPAAMDGSTATPEFRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000533.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000533.fa new file mode 100644 index 0000000000000000000000000000000000000000..329a14b7998362aa8f3d62803f0b78fcd935a0da --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000533.fa @@ -0,0 +1,110 @@ +>PROKKA_00531 +MSAPETTPVLAPLLPRLRAERALEAAAASASRPLEARGVELEIGLPDGARAPLLTVLAEA +LAEGHGERAAVLVVTATTREAEDLVTDLAAWAPAGAAALFPSWETLPHERLSPRSDTVGA +RLAVLRRLAHPEEHAEGPLRIVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAAL +ADAAYSRVDMVSRRGEFAVRGGLIDVFPPTEDYPVRIEFFGDEVEQMRWFSVADQRSLED +TTEDGSGHPSELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLS +PLLAEAMTSLPRMLPTGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDV +AEADQSAAGGFLTVAELRAAALEQDQGFWSVTALVSDAELLPDAATLRATLGVPQTFSGD +IEAMVAHTRVRLAEGWHAVVLTDGPGSARRLAELNAEAGLTASVVDGPLPADLAPGRVSI +ATAPVGSGFTIPDAQIALITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLTLQPGGHVV +HSQHGIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDL +ISTYVGGETPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQ +GELEEAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGK +QVAVLVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVIEGLAHGEVDVVIGT +HRLLSDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGI +RETSTLATAPEERHPVLTSVGPYSDQQVTAAIRRELMREGQVFYVHNRVTTIDKVAKRIA +ELVPEARIAVAHGKMSEARLEQIMVDFWERKFDVLVSTTIIETGLDIANANTLIVEDAHR +YGLSQLHQLRGRVGRGRERAYAYFLYDPQKPLGEVALERLKAVATHNELGAGMQLAMKDL +EIRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHD +YVPGERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPEPVEALVAVARFRNRARAAGV +TEVMLLGQNVKFGPAADLPESRQMRLTRMYKGAQVKPALNGVLIPRPKTKPVMGQDLVDV +PLLEWAQQVVDAIFAPEG +>PROKKA_00252 +MSAPETTPVLAPLLPRLRAERALEAAAASAARPLESRGVELEIGLPDGARAPLLTVLAEA +LAEGHGERAAVLVVTATTREAEDLVTDLAAWAPAGTAALFPSWETLPHERLSPRSDTVGA +RLAVLRRLAHPEEHAEGPLRVVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAAL +ADAAYSRVDMVSRRGEFAVRGGLIDVFPPTEDYPVRIEFFGDEVEQMRWFSVADQRSLED +TTEDGSGHPSELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLS +PLLAEAMTSLPRMLPAGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDV +AGADQSAAGGFLTVAELRAAALEQDQGFWSVTALVSDDELLPDAATLRATLGVAQTFSGD +IEAMVAHTRVRLAEGWHAVVLTDGPGSARRLAELTTEAGLTAAVVDGPLPADLAPGRVSI +ATAPVGSGFTIPDAQIALITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLTLQPGDHVV +HSQHGIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDL +ISTYVGGETPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQ +GELEEAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGK +QVAVLVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVVEGLAHGEVDVVIGT +HRLLSDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGI +RETSTLATAPEERHPVLTSVGPYSDQQVTAAIRRELMREGQVFYVHNRVTTIDKVAKRIA +ELVPEARIAVAHGKMSEARLEQIMVDFWERKFDVLVSTTIIETGLDIANANTLIVEDAHR +YGLSQLHQLRGRVGRGRERAYAYFLYDPQKPLGEVALERLKAVATHNELGAGMQLAMKDL +EIRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHD +YVPGERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPEPVEALVAVARFRNRARAAGV +TEVMLLGQNVKFGPAADLPESRQMRLTRMYKGAQVKPALNGVLIPRPKTKPVMGQDLVDV +PLLEWAQQVVDAIFAPEG +>PROKKA_02421 +MPPRPPPVVAPLLPRLRAERAIEAAAASAARPLEARGVELEIGLPDGARAPLLTVLAEAL +AEGHGERAAVLVVTATTREAEDLVTDLAAWAPAGAAALFPSWETLPHERLSPRSDTVGAR +LAVLRRLAHPEEHAQGPLRIVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAALA +DAAYSRVDMVSRRGEFAVRGGLIDVFPPTEDHPVRIEFFGDEVEQMRWFSVADQRSLEDT +TEDGSGHPTELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLSP +LLAEAMTSLPRMLPTGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDIA +GADQSAAGGFLTVAELRAAALEQDQGFWSVTALAPDDELLPDAATLRSTLGVPRTFAGDM +EAMVEHTRTRLAEGWHAVILTDGPGSARRLAELHADAGLTASVADGPVPAEPAPGRVTIA +TAAVGAGFTVPDERLAVITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLALQPGDHVVH +AQHGIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDLV +SSYVGGEAPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQS +ELEEAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGKQ +VAVLVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVVEGLAHGEVDVVIGTH +RLLSDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGIR +ETSTLATAPEERHPVLTSVGPYSDQQVTAAIRRELMREGQVFYVHNRVTTIDKVARRIAE +LVPEARIAVAHGKMGEARLEQIMVDFWERRFDVLVSTTIIETGLDIANANTLIVEDAHRY +GLSQLHQLRGRVGRGRERAYAYFLYDAQKPLGEVALERLKAVATHNELGAGMQLAMKDLE +IRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHDY +VPGERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPDPVEALVAVARFRNHARAAGIT +EVMLLGQNVKFGPAADLPESRQMRLARMYKGSQVKPALNGVLIPRPKTKPVMGQDLVDVP +LLEWAQQVIDAIFAPEG +>PROKKA_02303 +MSPADVTAPVPVLAPLLPVLAREPAFEAAAASAARALPARGQELEIGLPDGARAPLFAHL +ADALAAGHGADAVLLVVTATAREAEDLIGDLAAWADPASVALFPSWETLPHERLSPRSDT +VGARLDVLRRLAHPGEDGRPPLRVVVAPVRSVIQPLVRGLGELAPVHLRVGQERDFDAVV +QDLADAAYARVDMVSRRGEFAVRGGLIDVFPPTADHPVRVEFFGDEVEQMRWFSVADQRS +LQDTSEDGSGHPTELHAPPCRELLVTPSVQERARALMARLPGAADMLERIAEGQAVEGME +SLSPLLADGMTSLVHLLPEGSLTLLVEPERIRSRADDLLATNEEFLAAAWAGAAQGAQAP +VDLGADQSAAGGFLTLAELREAVLEERQGHWSTTALSPDAELLPDASALRSSLGVPTTFG +ADMEAMVRFTRERLADGWSVVLLTDGPGSARRLAELHADAGLTASVLDGPVDPAPAPGRV +RVATAAVGTGFTDPETKLAVVTEQDLFGRHRTAGTRAAGGKLARRRRNAVDPLALQPGDF +VVHSQHGIARFVELQRRPVTGGARKRPGEEESYREYLVLEYAPSKRGAPGDRLFVPTDQL +DLISQYVGGEAPALSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMATRGHSFAPDTP +WQAELEEAFPYIETPDQLTTIEEVKKDMESPVPMDRLVSGDVGFGKTEVAVRAAFKAVQD +GKQVAVLVPTTLLARQHHQTFTDRFAGFPVTVAALSRFQTAKESKEVVEGLAAGEVDVVV +GTHRLLSKEVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLT +GIRETSTLATAPEERHPVLTSVGPYTDQQVIAAIRRELMREGQVFYVHNRVTTIDKVASR +LAQLVPEARIAVAHGKMSESRLEQIMVDFWEKRFDVLVSTTIIETGLDIANANTLIVEDA +HRYGLSQLHQLRGRVGRGRDRAYAYFLYDAQKPLGEVAMERLKAVAQHNELGAGLQLAMK +DLEIRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLP +HDYVPGERLRLEMYRSLATAVDDAAVDAVVEEMKDRYGPLPEPVQALVAVARFRNRAREA +GVTEVMLLGQNVKFGPAADLPESRQLRAQRMYKGAQLKPALNALLIPRPKTKPVMGQDLV +DAPLLEWADQVVQAIFAPEPVSAG +>PROKKA_00531 +MSAPVLAPLLPRLRAERAIEAAAASASRPLEARGVELEIGLPDGARAPLLTVLAEALAEG +HGERAAVLVVTATTREAEDLVTDLAAWAPAGAAALFPSWETLPHERLSPRSDTVGARLAV +LRRLAHPEEHAEGPLRIVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAALADAA +YSRVDMVSRRGEFAVRGGLIDVFPPTEDYPVRIEFFGDEVEQMRWFSVADQRSLEDTTED +GSGHPSELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLSPLLA +EAMTSLPRMLPTGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDVAGAD +QSAAGGFLTVAELRAAALEQDQGFWSVTALVSDAELLPDAATLRATLGVAQTFSGDIEAM +VAHTRVRLAEGWHAVVLTDGPGSARRLAELNAEAGLTASVVDGPLPADLAPGRVSIATAP +VGSGFTIPDAQIALITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLTLQPGDHVVHSQH +GIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDLISTY +VGGETPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQGELE +EAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGKQVAV +LVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVVEGLAHGEVDVVIGTHRLL +SDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGIRETS +TLATAPEERHPVLTSVGPYSDQQVIAAIRRELMREGQVFYVHNRVTTIDKVAKRIAELVP +EARIAVAHGKMSEARLEQIMVDFWERKFDVLVSTTIIETGLDIANANTLIVEDAHRYGLS +QLHQLRGRVGRGRERAYAYFLYDPQKPLGEVALERLKAVATHNELGAGMQLAMKDLEIRG +AGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHDYVPG +ERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPEPVEALVAVARFRNRARAAGVTEVM +LLGQNVKFGPAADLPESRQMRLTRMYKGAQVKPALNGVLIPRPKTKPVMGQDLVDVPLLE +WAQQVVDAIFAPEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000535.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000535.fa new file mode 100644 index 0000000000000000000000000000000000000000..c9423d8b4176537c970b199f1249357115826c04 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000535.fa @@ -0,0 +1,30 @@ +>PROKKA_00533 +MGERATRQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDHRRSS +DVDLLVHPADATAVIELLRSHGWEPVATFSEGSIFQHAATLWHDQLGYVDVHRLFPGLGA +SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE +SWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRSAATA +RERAVLVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR +>PROKKA_00254 +MGEHATGQRPAAPPSLDLEVRVRLAHARITHLLERAGIRGLHLKGYATEPGVYPDHRRSS +DVDLLVPPADAAAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFPGLGA +SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE +SWAALREEARRLDAGAAWHVATGEAADGVDTRQLTLFAALHESQSGLELFRTRWRSAATV +RERAALVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR +>PROKKA_02419 +MTETGTTDQRAAAQPALDLAVRVRLGHARIAYVMEEAELRGLHVKGYAAEPGVYRGRRSS +SDVDLLVHPSDAAAAVELLASHGWAPVADFSEGSIFEHAATLWHDHLGYVDVHRLFPGLG +TDAARTFDALWAERTTRVIAGRPVPVPGPVHQRLVVIVHAARDSHRGALDVRHIRDTSSP +AEWDALRQEARRLHATAAWHVATGEDADGMDAHDLALFEALQDDESGLDLFRTRWRTAHS +ARERARLVLHTLPVNRPHLQMRLGHAPTRADLWREQRSRATALARWAWTRGVRRGR +>PROKKA_02301 +MTAAPAPLETRVRLAHARITHLMAAAGVRSLHIKGYAMGPGVYAGGRTSSDVDLLVHPAD +LSHALDALTSHGWRRIADFAEGSVFEHAATLWHDQLGYVDVHRRLPGLGRSPVDAFEALW +GERTTTVVAGHAVPVPSLRHQRLVVLVHGARDAGRGRFDVDHLRHTLDAGQWAELRVQAQ +ILGAGAAWSIATGETDVAGVDEREALLLSAVRGDESGIRLLATRWHAARGWRERLHLLVR +TVPVNRAHLQMRLGRPPTTADVLREQASRGAALTRWAAGKAVPRVGR +>PROKKA_00533 +MLAAMGERATGQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDH +RRSSDVDLLVPPADADAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFP +GLGASPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRES +LPAESWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRS +AATVRERAALVARTIPVNRPHLQMRLGRPVTRADLWREQGARLGALAGWAWTKAVRRDR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000536.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000536.fa new file mode 100644 index 0000000000000000000000000000000000000000..5a3ebaab7e0b1f7c9bb103bc49d41f505f2f3c20 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000536.fa @@ -0,0 +1,32 @@ +>PROKKA_00534 +MSRDHRPPIRNPFLPPTPEEPEVPARDGGHPAGDGGDADAPAASTAREDRLAEFRLGPAF +RPHPADRVPGPVPSARVLVVCTGNICRSAYVEYALQAQLNALLGDRGRAEVTSAGTEPNQ +ALTVPGPLLDRAPSRRVRAALTQHRPQQLTGRSLAGQDLVLTATDDHLDEVLREDPAAVR +RTFTILGMGTLLRDHGEELAAAVPPGAGVTALVTALAALRSRLIAHGERPDADLPDPFRG +PAEGYAAMAQTAQPIVELLAWEIARALDGDLVEEEPTGA +>PROKKA_00258 +MSRDHRPPIRNPFLPPTPEEPEVPARDGGHPAGDGGDADAPAASTAREDRLAEFRLGPAF +RPHPADPATPRQRATPTERTVAPAPVRAAEPASPASPAGRVPGPLPSARVLVVCTGNICR +SAYVEYALQAQLNALLGDRGRAVVTSAGTEPNQALTVPGPLLDLAPSRRVRAALTQHRPQ +QLTGRSLADQDLVLTATDDHLDEVLREDPAAVRRTFTILGMGTLLRDHGEELAAAVPPGA +GVTALVTALAELRSRLIAQGERPDADLPDPFRGPAEGYAAMAQTAQPIVELLAWEIARAL +DGDLVEEEPTGA +>PROKKA_02415 +MSQDRRAPIRNPFLEPGASVPGAPPRRADADPEDRLAEFRLGPAFGGRPAQPRRPQGFGG +RTAPGEGTTTTPRPDGTAAAEPADTAAEPVDTAAEPAANPKTARPAESAEAADAPAPAPA +PLPTVRVLAVCTGNICRSAYVQHTLQAQLNALLGDRGRAEVTSAGTEPNQALTVPEPLRE +LSPSRRVRAALTEHRPQQLTAASLWGQDLVITAADDHLEEVLREDPGAVRRTFTVRGIGT +LLGEHGEEIAAAVPPGAGLAALVDAMADLRVRLIGRGEEPDADLPDPFRGPAEGYAQMVE +TARPIVELLAWEIARALDGDLVEDDEPTRV +>PROKKA_02297 +MSWFERPALRSPFAAAPGMDAPADDGAGGPLRILTVCTGNICRSAWAHHVLQARLDAALG +ADVVEVSSAGTGPNQALAVPEELLTLAPDAGVRAALAAHRPRRLTARVLAGQDLVLTATE +AHRDAVVREAPAALRRSATLLDAGALLADPDAVAPGGGGRALVAALEAARREGRGLDAGR +RGLFPAGRRAADLADPFRGPAEGYTEMTRALEPALAAVEAAVVRAVEPAR +>PROKKA_00537 +MSRDHRPPIRNPFLPPTPEEPEVPTRDGGHPAGDGGDAGAPAAATAREDRLAEFRLGPAF +LPHPADPAAPRQHATPAERAVAPATAAAAEPASPAAPADRVPGPLPSARVLVVCTGNICR +SAYVEYALQAQLNALLGDRGRAVVTSAGTEPNQALTVPGPLLDLAPSRRVRAALTQHRPQ +QLTGRSLADQDLVLTATDDHLDEVLREDPAAVRRTFTILGMGTLLRDHGEELAAAVPPGA +GVTALVTALAELRSRLIAQGERPDADLPDPFRGPAEGYAAMAQTAQPIVELLAWEIARAL +DGDLVEEEPTGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000539.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000539.fa new file mode 100644 index 0000000000000000000000000000000000000000..695766f1237d6646a60be6bfe75e7f650f6f6de4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000539.fa @@ -0,0 +1,55 @@ +>PROKKA_00538 +MPAHPPHDDVAALPEDVLARAERWAAEDPDPAHRDTLRAELDAAAGVGPEAAAARAALAA +RFAGPLVFGTAGLRAEEGPGESRMNRLVVRRTAAGLAAHLWDGVGRDAAPPLAVVGYDAR +RGSAAFAADTAAVLTAAGVQTVLLPDPLPTPVLAFAVRHLSADAGVMVTASHNPPADNGY +KVYLGGRLTDEAGRGAQIVSPADAEIAARIDHAAWAADIPLADDGWTVAGPDLLEAYRAA +ALGVLDDDRHGHRDLRVVYTPLHGVGGAVVPGLLEDAGFGPVHVVAEQAAPDPAFPTVAF +PNPEEPGAMDLALALAAEVDADLVIANDPDADRLALAAPVTDADGARTWRMLSGDAVGTL +LGAHAMPALHAAGRSAANSVVSSPQLAALAEANGVRHHVTLTGFKWISRAPDLGFGYEEA +LGYCVDPDMVRDKDGITAALMAAELAAALTAQGRGLMDALADVDAVTGAMPSAQVSVRVA +DLSLIARTMTALRQQAPATLAGEPVTVRRDLAAGGDGLPPTDALLFATDSGTRVLVRPSG +TEPKLKCYLGTRDADPAAAAERLEALRAEVTALVGG +>PROKKA_00262 +MPAHPPHDDVAALPEDVLARAERWAAEDPDPAHRDTLRAELDAAAGVGPEAAAARAVLAA +RFAGPLAFGTAGLRAEEGPGESRMNRLVVRRTAAGLAAHLWDGVGRDAAPPLAVVGYDAR +RGSAAFAADTAAVLTAAGVQTVLLPDPLPTPVLAFAVRHLSADAGVMVTASHNPPADNGY +KVYLGGRLTDEAGRGAQIVSPADAQIAARIDHAAWAADIPLADDGWTVAGPDLLEAYRAA +ALGVLDDDRHGHRDLRVVYTPLHGVGGAVVPGLLEDAGFGPVHVVAEQAAPDPAFPTVAF +PNPEEPGAMDLALALAAEVDADLVIANDPDADRLALAAPVTDAHGVRTWRMLSGDAVGTL +LGAHAMPALHAAGRSAANSVVSSPQLAALAEANGVRHHVTLTGFKWISRAPDLGFGYEEA +LGYCVDPDMVRDKDGITAALMAAELAAALTAQGRGLMDALADVDAVTGAMPSAQVSVRVA +DLSLIARTMTALRQQAPATLAGEPVTVRRDLAAGGDGLPPTDALLFATDSGTRVLVRPSG +TEPKLKCYLGTRDADPAAAAERLEALRAEVTALVGG +>PROKKA_02411 +MSGPEHLPPTADDDAVPASEARALALAERWSVEDPDPMHREALRAELDAAAGSGPEAEAA +RASLASRFSGPLAFGTAGLRAEEGPGESRMNRLVVRRTAAGLARHLWEDVGEDAAAPLAV +VGYDARRGSLGFAQDTAAVLTAAGVQVVLLPDALPTPVLAFAVRHLSADAGVMVTASHNP +PADNGYKVYLGGRMTDEAGRGAQIVSPADVAIAELIDHEAWTADIPLAEDGWTVAGDELL +EAYREAALAVLDEDRHPDRALRIVYTPLHGVGGAVLPGLLDEAGFGPVHVVPEQAEPDPA +FPTVAFPNPEEPGAMDLALALAAEVDADLVIANDPDADRLALAAPFPGPDGTRVWRMLSG +DAVGTLLGAHLLPALAAAERSVANSVVSSPQLAALAEAQSVAHHVTLTGFKWISRAPRLG +FGYEEALGYCVDPDMVRDKDGITAALVAAELVAGLAARGCTVADALADVDAVTGSMPSGQ +VSVRVADLSVIPRTMAALRAQGPATLAGEPVTVRRDLAEGGAGLPSTDALLFATASGTRV +LVRPSGTEPKLKCYLGARDADPAVAAERLEALRAEVAALVGG +>PROKKA_02293 +MRALDPRVRELAERWSVEDPEPMHRAVLMDELAAADGDDPAAEAARASLASRFSGPLAFG +TAGLRAEEGPGESRMNRLVVRRTAAGLGRHLWNELGPDQPAPLVAVGYDARRGSADFAAD +TAAVLTAAGAQVVLLPRALPTPVLAFAVRHLHADAGVMVTASHNPPADNGYKVYLGGRMT +DEAGRGAQIVSPADVQIAAQIDHDAWTADIPLAAEGWEVAGEDLLEAYRAAALGVLDPGG +HPGRDLRIVYTPLHGVGGAVLPDLLAEAGFADVHVVPEQAAPDPAFPTVAFPNPEEPGAM +DLALALAAEVGADLVIANDPDADRLALAVPAGDGAAPSWRMLSGDAVGTLLGAHLLPRLA +AQGRSAANSVVSAPQLAALAAAAGVEHHVTLTGFKWISRAPRLGYGYEEALGYCVAPDMV +RDKDGMTAALVAAELAASLKAAGRTLDDARADADAVTGSMPSGQVSVRVQDLRIIADTMA +ALRARPPAALAGDPVTVERDLAAGSADLPATDALLFATDAGTRVLVRPSGTEPKLKCYLG +TQDADPTAAAARLDRLREEVAALVAG +>PROKKA_00541 +MPAHPPHDDVAALPEDVLARAERWAAEDPDPAHRDTLRAELDAAAGVGPEAAAARAVLAA +RFAGPLAFGTAGLRAEEGPGESRMNRLVVRRTAAGLAAHLWDGVGRDAAPPLAVVGYDAR +RGSAAFAADTAAVLTAAGVQTVLLPDPLPTPVLAFAVRHLSADAGVMVTASHNPPADNGY +KVYLGGRLTDEAGRGAQIVSPADAEIAARIDHAAWAADIPLADDGWTVAGPDLLEAYRAA +ALGVLDDDRHGHRDLRVVYTPLHGVGGAVVPGLLEDAGFGPVHVVAEQAAPDPAFPTVAF +PNPEEPGAMDLALALAAEVDADLVIANDPDADRLALAAPVTDADGVRTWRMLSGDAVGTL +LGAHAMPALHAAGRSAANSVVSSPQLAALAEANGVRHHVTLTGFKWISRAPDLGFGYEEA +LGYCVDPDMVRDKDGITAALMAAELAAALTAQGRGLMDALADVDAVTGAMPSAQVSVRVA +DLSLIARTMTALRQQAPATLAGEPVTVRRDLAAGGDGLPPTDALLFATDSGTRVLVRPSG +TEPKLKCYLGTRDADPAAAAERLEALRAEVTALVGG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000543.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000543.fa new file mode 100644 index 0000000000000000000000000000000000000000..2bc7a1867390fcbd58cdeae0166d8fd938d0762c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000543.fa @@ -0,0 +1,25 @@ +>PROKKA_00543 +MIPHDDGAAGLGTGLRLVLGSASPGRAEVLTRARVPFRVVVSGVDEAAVGAAAGDPSPAE +LAGLLAEAKGRDVAARVAAAGVDAPTLVLGCDSVFEFDGRAHGKPYEPEVAVERWRAQAS +RQGVLHSGHWLGLVLPESGAGSGMAEEAGVVSAVVRFGAVTEAEIQAYVATGEPLHCAGA +FTVDGAGAALVDGVDGDPNAVIGLSVAWLRRATAALGEDFTRLWEPSNAQR +>PROKKA_00268 +MIPHDDGSAGPGTGLRLVLGSASPGRAEVLTRARVPFRVVVSGVDEAAVGAAAGDPSPAE +LAGLLAEAKGRDVAARVAAAGVEAPTLVLGCDSVFEFDGRAHGKPYEPEVAVERWRAQAG +RQGVLHSGHWLGLVLPEPGVGSGMAAEAGVVSAVVRFGAVTEAEIQAYVATGEPLHCAGA +FTVDGAGAALVDGVDGDPNAVIGLSVAWLRRATAALGQDFTRLWEPSNAQR +>PROKKA_02404 +MRHDDGAAGPGVRPRLVLGSASPGRAEVLTRARVPFRVVVSDVDEAAVGAAAPEADPCEL +AVLLAEAKGRDVAARVAAAGVDGPTLVLGCDSVFEFDGRAHGKPYEPEVAVARWRAQAGR +SGRLHTGQWAGLLLPGEDGAVPDAETSTCVGADVRFAAVDEDTVRAYVATGEPLHCAGAF +TIDGAGAALVESVDGDPNAVIGLSVVVLRAQCEELGLRFADLWEKC +>PROKKA_02287 +MSTLPHGGGAPAALVLGSASPGRAQILRRALLPFRTVVSRVDEEAVGAASPGATPAELAR +LLAEAKAEAVAGVVAAEGVDRPTLVLGCDSVFELDGQALGKPWEPETAIARWRAQSGRSG +TLHTGQHVILLTPGTDAAGAPASGATVSAGVAFTDVDEATIRAYVATGEPLQCAGGFTID +GAGAALVESVEGDPNAVIGLSVSTLRRQCSVLGVDLSALWGSSNCDA +>PROKKA_00546 +MIPHDDGAAGPGTGLRLVLGSASPGRAEVLTRARVPFRVVVSGVDEAAVGAAAGDPSPAE +LAGLLAEAKGRDVAARVAGAGVEAPTLVLGCDSVFEFEGRAHGKPYEPEVAVERWRAQAG +REGVLHSGHWVGLVLPEPGVESGMAAEAGVVSAVVRFGAVTEAEIQAYVATGEPLHCAGA +FTVDGAGAALVDGVDGDPNAVIGLSVAWLRRATAALGQDFTRLWEPSNAQR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000544.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000544.fa new file mode 100644 index 0000000000000000000000000000000000000000..f96356d40d90bbd56d3286b7a44a98b2310fcb4b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000544.fa @@ -0,0 +1,55 @@ +>PROKKA_00544 +MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA +DDELNARLLEDLAALELQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV +FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA +AGGFFPGLVERAEAADVVDDALAARIRSGADAAAQAYRDFADTLEAELRPHAPEADGVGI +EYYRLASRDFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE +RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR +PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG +EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP +EKGYAFLSKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK +AFHTRALRLGGMGLDTLREALA +>PROKKA_00269 +MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA +DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQSIRAV +FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA +AGGFFPGLAERAEAADVVDDALAARIRSGADTAAQAYRDFADMLEAELRPHAPEADGVGI +DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE +RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR +PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG +EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP +EKGYAFLTKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK +AFHTRALRLGGMGLDTLREALA +>PROKKA_02403 +MTQNTPVAADRGARTPSAIDALAERYVADVLALHPDEATTLGFPGHETEYADFSPAGTRA +DDELNARLLADLEALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV +FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVIEQARAHGA +AGGFFPGLVERAEATDVVDAALAERIRAGADAAAQAYRDFADTLQAELRPHAPEADGVGI +ELYRLGSRAFLGAEIDLEETYRWGQEELARIIAAQEADAERIKPGATIEEARALLDADPE +RTLNGTAALQAWMQRLSDEAVQAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR +PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG +EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP +EKGYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRTEHEEREGEGFDLK +AFHTRALRLGGMGLDTLRAALA +>PROKKA_02286 +MTQTTSAPEGARTPSAVDALAERHVAAYLALRPDEATSLGMPGHETEYPDLSPAGAAALD +ELNRTTLEELAGLEPADDVDRVTVAAMRERLGLEREIHATGRTELNNIASEAQGIRAIFD +LMPTDTAEQWGHIAGRLENLPAALRGYAESLLASRDAGHVAAVRQVEIVVEQARAHGAEG +GFFPGLVERAEAADVVDAALAERIRTGAAGAAAAYAEFADTLEAELRPHAPEADAVGIEH +YRLASRVFLGAEIDLEETYRWGQEELDRIIAAQEADAERIKPGATIEEARAILDADPART +LTGTKALQEWMQRLSDEAVEAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSRPG +RMWWSVPAGEEEFTTWAETTTVYHEGVPGHHLQIATAMMNRGTLNLWRRNFAWTSGHGEG +WALYAEKLMEEFGFLDDAGDHLGMLDMQRMRAARVVFDIGYHCGFEMPASEGGGEWTPEK +GYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEAREGADFDLKAF +HTRALRVGGMGLDTLREALA +>PROKKA_00547 +MTQHTSEAAADGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA +DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV +FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGG +AGGFFPGLVERAEAADVVDDALAARIRSGADTAAQAYRDFAATLEAELRPHAPEADGVGI +DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE +RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR +PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG +EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP +EKGYAFLAKHLMISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK +AFHTRALRLGGMGLDTLREALA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000545.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000545.fa new file mode 100644 index 0000000000000000000000000000000000000000..ba481faa01b772774933aae31ebb12d801921816 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000545.fa @@ -0,0 +1,15 @@ +>PROKKA_00545 +MSALLGPGAPDENDESTQATPASADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA +AAAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ +>PROKKA_00270 +MSALLGPGAPDENDASTQATPAPADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA +AEAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ +>PROKKA_02402 +MSAAHEPRTPNAAGTPDDAAAEPTTADPLQLRGVELDPEEMAALTAVLAHARAAEAEAAR +AAAEAADPRPLDRTLRRRGDLGLWARPGRGQWRRGAGLQ +>PROKKA_02285 +MSAALPDDAADREVQDPEPMRLTGSSLEPEEMAALTAVLAQMRAQGGAAVPQAGRSGRLR +RPDRSLVRRGDLGLWARPGEDQWRRAAGRR +>PROKKA_00548 +MSALLGPGAPDENDESTQATPASADPLQLSGPELEPEEMAALAAVLEAAAAARAEAARLA +AAAADPRPLDRTLRRRGDLGLWARPGRGQWRQGAGPQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000547.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000547.fa new file mode 100644 index 0000000000000000000000000000000000000000..6ab50743a681656ff454a9f2f7864b6ddb0a7477 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000547.fa @@ -0,0 +1,20 @@ +>PROKKA_00548 +MRLEPGEQVMVRTRTHPRALLRPAAVLVAVAFLLGLAVGVLARPDLPGLVAANRAVLEAA +AWVVAALVLLPGTVRPLWRWVFRRTVLTDRRILQGAGIGGSGAAMPLVSIADVQRRRRGS +GAGDLHILFQEPARQVHWRLRDVPEAARFEEALAHLTRQARTATWPAPVPTGDLR +>PROKKA_00273 +MRLEPGEQVMVRTRTHPRALLRPAAVLVAVAFLLGLAVGVLARPDLPGIVAANRAVLEAA +AWVVAALVLLPGTVRPLWRWVFRRTVVTDRRILQRAGVGGSGAAMPLVSIADVQRRRRGS +GAGDLHILFQEPARQVHWRLRDVPEAARFEEALAHLTRQARTRTWPAPVPTGDLR +>PROKKA_02398 +MRLEPGEQVMVRTRTHPRALLRPAAVLVTVAFLLGLAMGVLARPDLPGILTQNRALLETA +AWAVAVLALLPGVLLPVLRWATRRTVVTSRRIVQRTGLGGGADVAMSLVSIADVQRRRRG +SGAGDLHILFQERARQVHWRLRDVPEAARFEEALAHLTRQARVASWPAPAPTGGPR +>PROKKA_02282 +MRLEPGEQVVVRTRSHPRVLVGTAARLTGTAFLLGLAMGLLARPGLPSPLRAAVPWLEAV +VWAAAVVAVLVGVVRPLLRWATRATVLTSERLVQRPGLGAGPEAAMPLVSIADVQRRRRG +ASSGDLHILFQDPLRQVYWRLADVPEAERFEQVLAETTRAARDRARPAMPAWGGVL +>PROKKA_00551 +MRLEPGEQVMVRTRTHPRALLRPAAVLVAVAFLLGLAVGVLARPDLPGIVAANRAVLEAA +AWVVAALVLLPGTIRPLWRWVFRRTVLTDRRILQGAGVGGSGAAMPLVSIADVQRRRRGS +GAGDLHILFQEPARQVHWRLRDVPEAARFEEALAHLTRQARTATWPAPVPTGDLR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000548.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000548.fa new file mode 100644 index 0000000000000000000000000000000000000000..bcdbb19a68d62d603e7a0de3c255635ecee869c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000548.fa @@ -0,0 +1,40 @@ +>PROKKA_00549 +MSRPETPDTAPLPIVPPAEDETARDVEERSAEPAGWTSAMRTLDAGLVVGPRAYTSREVA +QRLGVSMASARKIWRALGYPTSPEGHKAFTEADIEAFESVLTLVRSGTLNEDTAISLARS +IGQMTDRMVVWQIEALVEDKIASEGLTDPEARRAVVDMLPDMVGPLEKSMRIVYRRQLNR +AVQRLTVRVEAGLAASAEGRDGSESDAPLPLARAVGFADMVSYTTLSRTMDDRTLARMVL +RFESLAAETISAGGGWLVKTIGDEVMFNAETPEAGAAIALSLAETIAADEELPSARVALT +WGRVLSRMGDIYGPTVNLAARLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPRIVRGF +GEVRPSLLLDGSAQTLLAD +>PROKKA_00274 +MSRPETPDTAPLPIVPPAEDETARDVEERSAQPAGWTSAMRTLDAGLVVGPRAYTSREVA +QRLGVSMASARKIWRALGYPTSPEGHKAFTEADIEAFESVLTLVRSGTLNEDTAISLARS +IGQMTDRMVVWQIEALVEDKIASEDLTDPEARRAVVDMLPDMVGPLEKAMRIVYRRQLNR +AVQRLTVRVEAGLAASAQGRDGSESDAPLPLARAVGFADMVSYTTLSRTMDDRTLARMVL +RFESLAAETISAGGGWLVKTIGDEVMFNAETPEAGAAIALSLAETIAADEELPSARVALT +WGRVLSRMGDIYGPTVNLAARLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPRIVRGF +GEVRPSLLLDGSAQTLLAD +>PROKKA_02397 +MSRAETPETAPLPIIAPDGSGPAEAPRRKDPHDERRADRHEDRRGEAAADRLEEVDAPPP +GAGWTTAMRTLDAGLVVGPRAYTAREVAQRMGVSTASARKIWRALGYPTSPEGHKAFTEA +DVEAFESVLELVRSGALNEDAAISLARSIGQMTDRMVVWQIEALVEDKIVSEGLTDPEAR +RAAVDLLPEIVTPLERAMQIVYRRQLNRAVKRLTVRVEAGLAASEEGRDGSESDSPLPLA +RAVGFADMVSYTTLSRTMDDRTLARMVQRFETLSAEIISAGGGWLVKTIGDEVMFNAETP +ETGAAIALALAEAIAADDELPSARVALTWGRVLSRMGDIYGPTVNLAARLTSLADPGTVL +VDAMTAAALSRDERFVLVPQPPRIVRGVGEVRPSLLLNGSAQTLLAD +>PROKKA_02281 +MTRDTHHDAVPETAPLPVQAPAGAADPAVGRRESDALHHGWTSAIRTLDAGLLDRPRSYS +RREAAQRLGISSVSARKIWRALGYPTVKDEEKVFSAEDIDAFEQVLSLVRDGMLNEDTAI +SLARSVGQMTDRMVVWQIEALVEDQIAAEGKTDPEARRAAVEMLPGLVEPLEKVMRIVYR +RQLTNAVQRLTVRVEAGLAASERGRDGSEDDAPLPLARAVGFADMVSYTTLSRTMGERTL +ARTVQRFESKAAEIIAAGGGWLVKTIGDEVLFNAETPEAGATIALALAEAMADDDQLPAA +RVSLAWGRVLSRLGDIYGPTVNLASRLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPR +IVRGFGEVRPSLLMNGAAQPLIAD +>PROKKA_00552 +MSRPETPDTAPLPIVPSAEDETARDVEERSAQPAGWTSAMRTLDAGLVVGPRAYTSREVA +RRLGVSMGSARKIWRALGYPTSPEGHKAFTEADIEAFESVLTLVRSGTLNEDTAISLARS +IGQMTDRMVVWQIEALVEDKIASEDLTDPEARRAVVDMLPDMVGPLEKAMRIVYRRQLNR +AVQRLTVRVEAGLAASAQGRDGSESDAPLPLARAVGFADMVSYTTLSRTMDDRTLARMVL +RFESLAAETISAGGGWLVKTIGDEVMFNAETPEAGAAIALSLAETIAADEELPSARVALT +WGRVLSRMGDIYGPTVNLAARLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPRIVRGF +GEVRPSLLLDGSAQTLLAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000549.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000549.fa new file mode 100644 index 0000000000000000000000000000000000000000..03db5150b4712b4a415059612c5e17fe714fa62e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000549.fa @@ -0,0 +1,30 @@ +>PROKKA_00550 +MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA +AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW +AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR +EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG +RDNITAVLVRIP +>PROKKA_00275 +MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA +AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW +AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR +EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG +RDNITAVLVRIP +>PROKKA_02396 +MEPSAETPAAAPRPEAAGATHVGAVRELNEDAWTLVGDPLVLAAVADGMGGHEAGEVASA +AAIEVLRRRGPEVLAPGVAHTPEELGHLVHEADAAVVAAGGGRSGTTLTVLACIDTAANR +WAVANVGDSRIYLRPAGAPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGS +SEPLTVDVAEIPVASGDRLLLCSDGLTGELLDEEIRALIDDADELEDALVKLVEAALWRG +GRDNVTAVLVRIP +>PROKKA_02280 +MSEPHAADAAPAEPGAWASVPRPEAVAVTHVGAVRELNEDSWAVVGDPLLLAAVADGMGG +HEAGEVASAAAVAELHRRAPSVLAPGVAHTPQELGALVHEANAAVLAAGGGRAGTTLTVL +ACLDTEVGRWAVANVGDSRIYLRPVGAGVLQQVTVDHSAVQLMVDAGELTPAEARVHPRR +NVITRALGSTQALTVDVMELDVAPGDRFLLCSDGLTGELLDDEILAIMDDAATLDEAAER +LVEAALWRGGRDNITAVLVRIP +>PROKKA_00553 +MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA +AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW +AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR +EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG +RDNITAVLVRIP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000552.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000552.fa new file mode 100644 index 0000000000000000000000000000000000000000..a5d969032955bedc4108b349788ef2943373003a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000552.fa @@ -0,0 +1,15 @@ +>PROKKA_00555 +MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILEHVSAVQAAAGDDVTPTSHPIALE +NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE +>PROKKA_00280 +MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILKHVSAVQAAAGDDVTPTSHPIALE +NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE +>PROKKA_02390 +MPEITRDQVAHLARLAHIQMSDEELATVSGELEQILGHVSAVQAAAGADVAPTSHPIAMS +NVFREDVPAGMLTQEQAVDQAPDAQDGQFKVPAILDGE +>PROKKA_02273 +MAEITRDQVEHLARLAHIRMTDEELDVMSGELESILESVSQVQAVAGEDVVPTSHPIPLE +NVFREDVPTGMLTQEQALDQAPDAEDGQFKVPAILDGE +>PROKKA_00558 +MPEITRDQVEHLARLAHIRMTDEELDTMSGDLEKILEHVSAVQAAAGDDVTPTSHPIALE +NVFREDVPAGMLTQEEALDQAPDSEDGQFKVPAILDGE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000553.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000553.fa new file mode 100644 index 0000000000000000000000000000000000000000..39e6568ef3821f6a03c48233548f7d88aa580f1e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000553.fa @@ -0,0 +1,50 @@ +>PROKKA_00556 +MTETFDVNATIGADELVRLTALQMAERLRAGTTTSVELVQTHLDRIAAHDGDVRADAAGD +RGVRAYLHVNTDEALAVAAEVDAIRAAGGPEADALHPLAGVPVAVKDNIVTRGQPTTAAS +RMLEGWFSPYDATVVARLREARLPILGKTNLDEFAMGGSTEHSAFGITRNPWDGDRVPGG +SGGGSAAAVAAFLAPFALGSDTGGSVREPAAFTGTVGVKPTYGAVSRYGLIAMASSLDQI +GPAARTVADAAALQQVIGGHDPQDSTSLADAPADLTAAARGRDLAGLRIGVVTDLPAEAF +HPGIRAGFDEHVAALREAGAEIVEVSCPSFDAALGAYYLIMPSEASSNLARFDGVRYGHR +VVPDGGGTIEQVMGATRAAGFGAEVKRRIILGTYALSAGYYDAYYGSAQKVRTLVQQDFA +RAFERVDVLLTPTAPTPAFELGAKTDDPMTMYVNDLATIPANLAGVPGMSVPGGVVDGLP +YGLQLMAPAREDARLYEAGAALERLVAERRGGPVWAEAPELEKGAQRATTATTAGGRA +>PROKKA_00281 +MTETFDVNATLGADELVRLTALQMAERLRAGTTTSVELVQAHLDRIAAHDGDVRADADGD +RGVRAYLHVNTDEALAVAAEVDAIRAAGGPEADALHPLAGVPVAVKDNIVTRGQPTTAAS +RMLEGWLSPYDATVVARLREARLPILGKTNLDEFAMGGSTEHSAFGITRNPWDGDRVPGG +SGGGSAAAVAAFLAPFALGSDTGGSVREPAAFTGTVGVKPTYGAVSRYGLIAMASSLDQI +GPAARTVADAAALQQVIGGHDPQDSTSLADAPADLTAAARGRDLAGLRVGVVTDLPAEAF +HPGIRAGFDEHVAALREAGAEIVEVSCPSFDAALGAYYLIMPSEASSNLARFDGVRYGHR +VVPDGGGTIEQVMGATRAAGFGAEVKRRIILGTYALSAGYYDAYYGSAQKVRTLVQQDFA +RAFERVDVLLTPTAPTPAFELGAKTDDPMTMYVNDLATIPANLAGIPGMSVPGGVVDGLP +YGLQLMAPAREDARLYEAGAALERLVAERRGGPVWAEAPELEKGAQRATTATTAGGRA +>PROKKA_02389 +MTQTFDATAELAADQLVRLTALQMAERLRAGTTTSVELVQAHLDRIAEFDGDPRADAAAD +RGVRAYLHVNAEEALAVAAEVDAIRAAGGAEAEALHPLAGVPVAVKDNIVTQGQPTTAAS +RMLDGWMSPYDATVVTRLREARLPILGKTNLDEFAMGGSTEHSAFGITRNPWDLDRVPGG +SGGGSAAAVAAFLAPFALGSDTGGSVREPAAFTGTVGVKPTYGAVSRYGLIAMASSLDQI +GPAARTVADAAALQQVIGGHDPQDSTSLAEEQADLAAAARGRDLAGLRVGVVTDLPADAF +HPGIRAAFDEHVAALREAGAQIVEVSCPSFDAALGAYYLIMPSEASSNLARFDGVRYGHR +VVPDGGGTIEQVMGATRAAGFGDEVKRRIILGTYALSAGYYDAYYGSAQKVRTLVQEDFA +RAFEQVDVLLTPTAPTPAFELGAKTDDPLTMYVNDLATIPANLAGIPGLSLPGGVVEGLP +YGLQLMAPAREDARLYEAGAALERLVEDGRGGPVWAQAPELEKGAQRAATATTAGGRA +>PROKKA_02272 +MTQTFDVNASLSADELVRLTALQMAERLRAGTTTSVELVQAHLDRIAAVDGDPRSDAASD +AGVRAYLHVNTEEALAVAAEVDAIRAAGGAEAEALHPLAGVPVALKDNIVTVGQPTTAAS +KMLDGWMSPYDATVVERIRAAKLPILGKTNMDEFAMGGSTEYSAFGVTRNPWDGQRVPGG +SGGGSAAAVAGFLAPFALGSDTGGSIREPAAFTGTVGVKPTYGAVSRYGVIAMASSLDQV +GPAARTVADAAALQQVIGGHDAHDSTSLPEEQADLVAAAAGRDLAGLKVGVVTDLDAEGF +HPGVKAAFDADVQALRDAGAEIVEVSCPHFAAALGAYYLIMPSEVSSNLARFDGVRYGHR +VVPDGGGTIEQVMAASRAAGFGGEVKRRIILGTYALSAGYYDAYYGSAQKVRTLVQQDFA +AAFEQVDVLLTPTAPIPAFRLGEQTKDPLTMYLNDLFTIPANLAGVPGISVPGGLVDGLP +YGLQFMAPAREDARLYEVGAAVEKLVTEREGGPLWARVPEQHPGAARAAQTPAGGTK +>PROKKA_00559 +MTETFDVNATLGADELVRLTALQMAERLRAGTTTSVELVQAHLDRIAAHDGDVRADADGD +RGVRAYLHVNTDEALAVAAEVDAIRAAGGPEADALHPLAGVPVAVKDNIVTRGQPTTAAS +RMLEGWLSPYDATVVARLREARLPILGKTNLDEFAMGGSTEHSAFGITRNPWDGDRVPGG +SGGGSAAAVAAFLAPFALGSDTGGSVREPAAFTGTVGVKPTYGAVSRYGLIAMASSLDQI +GPAARTVADAAALQQVIAGHDPQDSTSLAEAPADLTGAARGRDLAGLRVGVVTDLPADAF +HPGIRAGFDEHVAALREAGAEIVEVSCPSFDAALGAYYLIMPSEASSNLARFDGVRYGHR +VVPDGGGTIEQVMGATRAAGFGAEVKRRIILGTYALSAGYYDAYYGSAQKVRTLVQEDFA +RAFEQVDVILTPTAPTPAFELGAKTDDPMTMYVNDLATIPANLAGIPGMSVPGGVVDGLP +YGLQLMAPAREDARLYEAGAALERLVAQRRGGPVWAEAPELEKGAQRATTATTAGGRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000554.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000554.fa new file mode 100644 index 0000000000000000000000000000000000000000..0dd439e80c8a0ec1708babadbc198bffeaf98989 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000554.fa @@ -0,0 +1,50 @@ +>PROKKA_00557 +MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG +TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD +VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV +GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN +VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP +DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG +ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEVEELIAAKTINDKIAKQVLGLVA +DGEGAPKEVVAAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA +TRGQADAGRVREIVLERLGVS +>PROKKA_00282 +MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG +TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD +VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV +GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN +VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP +DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG +ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEIEELIAAKTINDKIAKQVLGLVA +DGEGAPKEVVTAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA +TRGQADAGRVREIVLERLGVS +>PROKKA_02388 +MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG +TLPVLNREVVEYAVRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD +VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASNSLVDYNRAGVPLIEIVTKPIV +GAGARAPELARAYVTAIRDIVKAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN +VNSTRAVQHAVTHEIQRQAALLAAGGTVTQETRHWHEDTRTTTSGRPKSDADDYRYFPEP +DLVPVHVDAAWVERVRAEMPELPAVRNKRLKAEWGYTDEEFRDVVNAGVLDEIVATVEAG +ASPAAARKWWMGEIARLANVRETAVAELGVTPAHVVEVEELIAAKTINDKIAKQVLGLVA +DGEGTPKEIVEAKGLAVVSDDGALTEAVDAAIAANPDVAEKIRGGKMAAVGALIGPVMKA +TRGQADAGRVREIVLERLGVS +>PROKKA_02271 +MSTAELMDFQEAMDRFDPVLGFEVHVELNTKSKIFSTGANAFGDEPNTNVTPLDLGLPGT +LPVLNREAVESAIALGLALDAQIAPSCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLDV +ELEDGTVFRVEIERAHLEDDAGKLTHQGGSGRIQGASASLVDYNRAGVPLIEIVTRPIVG +AGDRAPEIARAYVTALRDIVKAIGISDARMEHGNVRCDANVSLMEKGASAFGTRTETKNV +GSTRAVQHAVTHEIQRQAAILAAGGTITQETRHWHEDTRTTTSGRPKSDADDYRYFPEPD +LLPVVVDEAWIERVRAGMPELPAVRNKRLKGEWGFSDEEFRDVVNAGVADQIAQTVEAGA +SPAAARKWWMGEIARLANLREVEAAELGVTPAHVVEIEELIAAKTINDKIAKQVLGLVAD +GEGAPKQIVAAQGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMQAVGALIGPVMKAT +RGQADAGRVREIVLERLGVA +>PROKKA_00560 +MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG +TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD +VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV +GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN +VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP +DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG +ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEVEELIAAKTINDKIAKQVLGLVA +DGEGAPKEVVAAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA +TRGQADAGRVREIVLERLGVS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000556.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000556.fa new file mode 100644 index 0000000000000000000000000000000000000000..307f61a5b7b243f8f1b60b09da24367907a69955 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000556.fa @@ -0,0 +1,31 @@ +>PROKKA_00559 +MPATPRTSRTPAVRPAPALPAPSARTVRWEIAIVLGLSLGKSAVYAIVQLIDKATQAPLG +EQTTVLNPALADRWAFDLTYQLLGIGFALVPVALVLHLMHLRGRNPFRVLGLDLRRPGRD +LAWGLGLFAAIGLGTLGVYAAGRALGITTAIVGSALGESWYQVPVLLLSALRHGLLEEVI +VGAWLVDRLGYLQRLRAAGLARDPAPAVPSSWVSAEGLYLPTRAAVVVLALALLRGAYHL +YQGIGPGVGNALMGVVFALVFLRVRRVMPLVIAHTLLDAVGFVGYPLLARAGLLG +>PROKKA_00284 +MPATPRTSRTPAGPAVRPAPALPAPSARTVRWEIAIVLGLSLGKSAVYAIVQLIDKATQA +PLGEQTTVLNPALADRWAFDLTYQLLGIGFALVPVALVLHLMHLRGRNPFRVLGLDLRRP +GRDLAWGLGLFAAIGLGTLGVYAAGRALGITTAIVGSALGESWYQVPVLLLSALRHGLLE +EVIVGAWLVDRLGYLQRLRAAGLAHDPAPAVPSSWVSAEGLYLPTRAAVVVFALALLRGA +YHLYQGIGPGVGNALMGVVFALVFLRVRRVMPLVIAHTLLDAVGFVGYPLLARAGLLG +>PROKKA_02384 +MSLPVPPALASPVPTALPAPSARTVRWEIAIVLGLSLGRSAVYAVVQLIDKATQAPLGDQ +TTVLNPTVDDRWAFDLTYQLLGIAFALVPVLLVLHLMHLRGRNPFRTLGLDLRRPGRDLA +WGVGLFAVIGLGTLGVYAAGRALGLTTAIVANAMDESWYQIPVLLLSALRHSLLEEVIVG +AWLVDRIGYLQRLKAAGLDRDPVPAVPAAPARRTGAPSSSWTTPEGLFLPTCVATALLAL +ALLRGAYHLYQGVGPGIGNALMGVVFVLVFLRVRRVMPLVVAHFLLNAVGFVGYPLLARA +GLLG +>PROKKA_02268 +MTATARPEHAAGRRGPGAPALPAPSARTVRWEIAIVLGLSLGRSAVYAVVQLIDQATRAP +LGDQTTVLNPTVADRWAFDLTYQLLGIAFSLVPVLLVLHLLWLRGRHPFRVLGLDLRRPG +RDLAWGLGLFTVIGVGTLGVYAAGRALGITTAIVANAMDESWYQVPVLLLSAARHALLEE +VIVGAWLIDRLGYLQRLREAGLGASSSWAGTEGLFLPLRTWPVVLSLALLRGAYHLYQGV +GPGIGNALMGAVFVLVFLRVRRVMPLVLAHFLLDAVGFVGYPLLARAGLLG +>PROKKA_00562 +MPATPRTSRTPAVRPAPALPAPSARTVRWEIAIVLGLSLGKSAVYAIVQLIDKATQAPLG +EQTTVLNPALADRWAFDLTYQLLGIGFSLVPVALVLHLMHLRGRDPFRVLGLDLRRPGRD +VAWGLGLFAAIGLGTLGVYAAGRALGITTAIVGSALGESWYQVPVLLLSALRHGLLEEVI +VGAWLVDRLGYLQRLRAAGLARDPAPAVPSSWVSAEGLYLPTRVAVVVLALALLRGAYHL +YQGIGPGVGNALMGVVFALVFLRVRRVMPLVIAHALLDAVGFVGYPLLARAGLLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000557.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000557.fa new file mode 100644 index 0000000000000000000000000000000000000000..8186b96c46c529fbefdcc89f5afffbbff544f2b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000557.fa @@ -0,0 +1,25 @@ +>PROKKA_00560 +MDHVSYAAGPEGLDATVARIAETLGIERIKGGVHPRFGTQNALFPMAGRQYLEVVEALDH +PASLSAPFGQLVRARTEQGGGWMSWAVATTDIGRFERRLGREAVPGNRRFPDGRELSWRQ +IGVKGTLADPQLPFILRWADGQEDMHPSQAAEPQATIERLNIAGSPERLAEWLGDDEDGQ +VQDVNIEYVAPSGTPGIVSVTFRTPKGEVTL +>PROKKA_00285 +MDHVSYAAGPEGLDATVARIAETLGIERIKGGVHPRFGTQNALFPMTEGQYLEVVEALDH +PASLSAPFGQLVRARTEQGGGWMSWAVATTDIGRFERRLGREAVPGNRRFPDGRELSWRQ +IGVKGTLADPQLPFILRWADGQEDMHPSQAAEPQATIERLNIAGSPERLAEWLGDDEDGQ +VQDVNIEYVAPSGTPGIVSVTFRTPKGEVTL +>PROKKA_02383 +MDHVSYAAGPEGLDATVARIAEALGVERIKGGIHPRFGTQNALFPMAGGQYLEVVEALDH +PASLSAPFGQLVRSRSEQGGGWMSWAVSTTDIGRFERRLGREAVPGNRRFPDGRELSWRQ +IGIKGTIADPQLPFIMRWADGQEDMHPSQAAEAQASIERLSIAGSPDRLAEWLGGEGEDA +HVEDLNVEYVAPSGTPGIVSVTFRTPRGDVTL +>PROKKA_02267 +MNTCRMDHVSYAAGPEGLDATVARIAERLGVERVKGGIHPRFGTQNALFPMTGNQYLEVV +EALDHPASLSAPFGQLVRTRSEQGGGWMSWAVTTNDIGRFERRLGREAVPGNRRFPDGRE +LSWRQIGVKGTLADPQLPFILRWADGQEDMHPSQAAPAQASIARLSIAGSPDRLREWLGG +TEDDEVADVSVDYVAPSGTPGIVSVTFSTPKGEVTL +>PROKKA_00563 +MDHVSYAAGPEGLDATVARIAETLGIERIKGGVHPRFGTQNALFPMTEGQYLEVVEALDH +PASLSAPFGQLVRARTEQGGGWMSWAVATPDIGRFERRLGREAVPGNRRFPDGRELSWRQ +IGIKGTLADPQLPYILRWADGQEDMHPSQAAEPQATIEHLNIAGSPERLAEWLGGEDEDG +QVQDVNIEYVAPSGTPGIVSVTFRTPKGEITL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000558.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000558.fa new file mode 100644 index 0000000000000000000000000000000000000000..9a65389a265c8c3866d6fd63956ebc7bb698c552 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000558.fa @@ -0,0 +1,43 @@ +>PROKKA_00561 +MTDQTTPTPDAWGFSTAQVHAGVAVGQHAFGATALPIFQTTSYDFPSAQVAADRFALKDL +DPLYTRIGNPTQGPVEEKIAALEGGVGALLLASGQAATTFAILNLAGAGDHVVASASLYG +GTQNLFKHTLAKVGVETTFVTDPDDLESWRAAVRPNTTAFFGETLGNPRGDVLDVRAVAD +AAHEAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIVDAGTFDYAQ +HAERYPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSAISPFNAFLV +NLGLETLSLRMERQVANAAAVAGWLEGRDDVEHVVYAGLESSPWHERAQRYLPKGAGAFV +SFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLTDDEQRAAGVTPGLV +RLSLGVEDVEDILADLERGFAAAARRGDDDAGERA +>PROKKA_00286 +MTDQTTPTPDAWGFSTAQVHAGVAVGQHAFGATALPIFQTTSYDFPSAQVAADRFALKDL +DPLYTRIGNPTQGPVEEKIAALEGGVGALLLASGQAATTFAILNLAGAGDHVVASASLYG +GTQNLFKHTLAKVGVETTFVTDPDDLESWRAAVRPNTTAFFGETLGNPRGDVLDVRAVAD +AAHEAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIVDAGTFDYAQ +HAERYPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSAISPFNAFLV +NLGLETLSLRMERQVANAAAVARWLEGRDDVEHVVYAGLESSPWHERAQRYLPKGAGAFV +SFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLADDEQRAAGVTPGLV +RLSLGVEDIEDILADLERGFAAAARRGDDDAGERA +>PROKKA_02382 +MVASASLYGGTQNLFKHTLAKVGIETTFVQDPDDVAAWTAAVRPNTKAFFGETLGNPRGD +VLDVAAVADAAHAAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIV +DAGTFDFAQHAERFPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSA +ISPFNAFLVNLGLETLSLRMERQVANAAAVARWLEGRDDVEHVVYAGLESSPWHERAQRY +LPKGAGAFVSFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLTDDEQR +AAGVTPGLVRLSLGVEDLEDILADLERGFAAAASAGERE +>PROKKA_02266 +MSTQPTPRRGFSTTQIHAGTDAPHAFGATALPIYQTTSYDFPSAQVAADRFALADLGPIY +TRIGNPTQSAVEEKIAALEGGVGALLLASGQSATTFAILNVAGAGDHVVASASLYGGTQN +LFKHTLARVGVEVTFVQDPDDLDAWRAAARPETKAFFAEALGNPRGDVLDVAGVAAAAHD +AGVPLIVDNTLTTPYLLRPFEHGADVVVHSATKYLGGHAAAMAGVIVDSGRFDFARDPER +FPGFNEPDESYHGLVYARDLGVGSPLGANLAFVLKARVQLLRDYGSAISPFNAFLVNLGL +ETLSLRMDRAVASALAVARHLEGHPQVESVSHPGLESSPWHARAQELLPRGAGAFVSFEI +AGGAAAGAAFVDGLELHHHVANIGDVRSLVVHPASTTHAQLAEDEQRAAGVTPGLVRLSL +GLEDVEDILADLDKGFAAAAAALDAADAAEQD +>PROKKA_00564 +MTDQTTPTPDAWGFSTAQVHAGVAVGQHAFGATALPIFQTTSYDFPSAQVAADRFALKDL +DPLYTRIGNPTQGPVEEKIAALEGGVGALLLASGQAATTFAILNLAGAGDHVVASASLYG +GTQNLFKHTLAKVGVETTFVTDPDDLESWRAAVRPNTKAFFGETLGNPRGDVLDVRAVAD +AAHEAGVPLIVDNTLATPYLLRPIEHGADVVTHSATKYLGGHAAAIAGVIVDAGTFDYAQ +HAERYPGFNEPDESYHGLVYARDLGVGSPLGANLAFILKARVQLLRDYGSAISPFNAFLV +NLGLETLSLRMERQVANAAAVARWLEGRDDVERVVYAGLESSPWHERAQRYLPKGAGAFV +SFEIAGGREAGAAFVDGLTLHHHVANIGDVRSLVVHPASTTHSQLTDDEQRAAGVTPGLV +RLSLGVEDIEDILADLERGFAAAARRGDDDAGERA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000559.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000559.fa new file mode 100644 index 0000000000000000000000000000000000000000..b86775a6d71346a501d76a98623d79d13ad54914 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000559.fa @@ -0,0 +1,40 @@ +>PROKKA_00562 +MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELTYETWGTLAADGSNAVLVLHA +LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP +WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA +ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ +RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLADRFDANSYLVVTEALMGHDV +GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTIASPIGHDGFL +TEYGQVADTLKRTLAL +>PROKKA_00287 +MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELAYETWGTLAADGANAVLVLHA +LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP +WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA +ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ +RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLTDRFDANSYLVVTEALMGHDV +GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTITSPIGHDGFL +TEYGQVADTLKRTLAL +>PROKKA_02381 +MTATVSRPPRAALPEGGRHRLRIGELRTETGGVLPDVELAYETWGELDADGSNAVLVLHA +LTGDSHVAAHAADPTPGWWDALVGPGRAVDTDRWFVVAPNMVGGCHGSTGPSSPAADGRP +WGSRFPFLTLRDAVAAERRLADHLGVGAWQAVIGGSMGGARALEWAATHPERVAGVGVLA +ATARSSADQIAWGQAQTAAIRLDPGFLGGDYYEGAGPAAGLGIARRIAHTTYRTAGELER +RFGRSPQGAEDPFGAVVGVPGGRGRYAVESYLDHQATKLTGRFDANSYLLLTEALLGHDV +GRGRGGVEAALAGYRGRAFVAAVDSDRLYLPAEAQALAAVLPARPPVHTIVSPIGHDGFL +TEYGQVADALRDSLAL +>PROKKA_02265 +MTAIDPRILPGHAAHRPHQGPQGEAAPSARSAAPHDARPADRLPAGEFRTLSVGPLELEA +GGRLPGVELAFETWGTLAEDGANAVLVLHALTGDSHVASHRRDESAGWWEELIGPGLAVD +TDRWFVVAPNMLGGCDGSTGPSSPAPDGAPWGGRFPFVTIRDAVAAERRLLDALGVTALQ +AVIGGSMGGARAIEWAVSHPDLVRGVAVLASTASSSAEQIAWAQAQTHAIRLDPEWRGGD +YHPGPGPVTGLGIARRIAHTTYRSAAELQHRFGREPQGAEDPLGTASGERVGRYQVESYL +DHQASKLVGRFDAGSYVALTEALMSHDVGRGRGGVEAALASYPGRAFVAAVDSDRLYFPA +ESERLASLLPGEVPVHTIHSPIGHDGFLTEYGQIADELRRTLEL +>PROKKA_00565 +MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELTYETWGTLAADGSNAVLVLHA +LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP +WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA +ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ +RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLTDRFDANSYLVVTEALMGHDV +GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTIASPIGHDGFL +TEYGQVADTLKRALAL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000560.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000560.fa new file mode 100644 index 0000000000000000000000000000000000000000..67c44631eb455873b62baf6678cdf971857c7ac6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000560.fa @@ -0,0 +1,31 @@ +>PROKKA_00563 +MGNPSSSQPPHASDATPVDDPAAHPWRRYVAIGDSFSEGIGDPDPDRPGYHRGWADRLAE +ELSRLTPPGEDLAYANLAVRGKLLDQIAEDQVEPAIALRPDLISVCAGGNDILRGADPDE +IAARLDAVVERLASAGATVLLFNATDVKGTPVIGRIRGTVAIYNENVRTIALRHDALVPD +MWSLKDLARREMWAEDRLHFSALGHHTIAAMVLDTLGVEHGLEHLRLSPPAPRTWRAARA +SDAAWVRTHLAPWVVRRLRGVSSGDGVTAKRPVPEPLFGAPMPQGSDHTEPLDIVEP +>PROKKA_00288 +MGNPSSSQPPHASDATPVDDPAAHPWRRYVAIGDSFSEGIGDPDPDRPGYHRGWADRLAE +ELSRLTPPGEDLAYANLAVRGKLLDQIAEDQVEPALALRPDLISVCAGGNDILRGADPDE +IAVRLDAVVERLASDGATVLLFNATDVKGTPVIGRIRGTVAIYNENVRTIALRHDALVPD +MWSLKDLARREMWAEDRLHFSALGHHTIAAMVLDTLGVEHGLEHLRLSPPAPRTWREARA +SDAAWVRTHLAPWVARRIRGVSSGDGVTAKRPVPEPLFGAPMPQGSDHTESLNVVEP +>PROKKA_02380 +MRAESPDGDDFPSESTGGGGRGRRGRLTDDGGASRLLLVSNQQESAPQHPAAAEAEPPAD +VVTRAETAAHPWRRYVAIGDSFTEGIGDPDPDRPGYHRGWADRAAEELARRTPDGEDLAY +ANLAVRGKLLDQIAADQVEPALALRPDLISVCAGGNDILRRADPDDVAVRLDAVVERLSA +NGATVLLFNATDTKDTPVLGRIRGTVAIYNENVRTVALRHDALVADMWSLKELARREMWA +EDRLHFSATGHHTIAAMVLDTLAVPHGLEPLRPEPAAPRTWRQARASDAAWARTHLAPWV +VRRIRGVSSGDGVSAKRPVPAPLFGAEMPHGSDPTEPLDVVAR +>PROKKA_02264 +METMSPLTNTADSEPPHAEGHASAEPAHPWRRYVAVGDSFTEGIGDPDPERPGYHRGWAD +HLAEELARLTPAGEEFSYASLAVRGKLMDQIRADQIDPAVELAPDLVSICAGGNDILRRA +DPDETALHLDDAVGRLAETGATVLLFNVPDIKETPVLARIRGRVAIYNENIRTVAARHHA +VVADMWSLKDLARPEMWAPDRLHFSPVGHHTIAAMALDTLGVEHELEPLSPKRAAPRTWR +EARVDDARWARTHLVPWVGRRLRGVSSGDGMQPKRPLPAPLFGADMPHGSDYTEHAAD +>PROKKA_00566 +MGNPSSSQPPHASDATPVDDPAAHPWRRYVAIGDSFSEGIGDPDPERPGYHRGWADRLAE +ELSRLTPPGEDLAYANLAVRGKLLDQIAEDQVEPALALRPDLISVCAGGNDILRGADPDE +IAVRLDAVVERLASDGATVLLFNATDVKGTPVIGRIRGTVAIYNENVRTIALRHDALVPD +MWSLKDLARREMWAEDRLHFSALGHHTIAAMVLDTLGVEHGLEHLRLSPPAPRTWREARA +SDAAWVRTHLAPWVVRRLRGVSSGDGVTAKRPVPEPLFGAPMPQGSDHTEPLDVVEP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000564.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000564.fa new file mode 100644 index 0000000000000000000000000000000000000000..fb48ff40fe3ff3e6632cb3b247d4d9597c58df24 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000564.fa @@ -0,0 +1,38 @@ +>PROKKA_00567 +MDLPAGVTLRPWAEGDDLRLLEVWGDPADVQQHQDRAMLAPDADTPWRHTLVAEDDGVPV +GAGTVVAQALHPRRLWLYLEVAPTARRRGIGSALLGALRDAVEQAHAAGQVTTTHLKTRF +AVASRVAVATGRSADAAEATAPAAGEEAGEAHAAQVAGTEAFLVAAAFSPVQRSRRVAVA +PGSIALPPLRDEDHPEGAVLEDAATGSVELTRAVAAFYDAVHGWDPAQMSVGAAQQLILG +PATGASGAVVLRDAPREEGGAVQAFAVSYTAERQDAPADVFLGWDPELPLDQAQLAAGQL +LAMLVAQHPVQVEVDEAMTALEPILDGLIAQRAAATLVDTRIWATDPA +>PROKKA_00292 +MTGAAGAAGHDDGGALFDSAAVAGGEIVLRPWRPGDDLALLEVWGDPANAQQHQDRAMLA +EDAERPWRRALVAEAAGVPVAAGVVYASSVHPRRLWLYVETAAAERRRGIGRALVAALRG +LAAEAHAAGAIPTTALKARFAKDALVPGVSGADPQTDAEGPAGQPPVDTEAVRSQTAALA +AGTEAFLVAEGFTPVQRSRRVAIAPGAIGLPDVRGEEHPDGVVLEEASTGSVELTQAVTA +FYDAVHAWDPSTLSVGAAQQLLLGPATGAAGAVVLRDAPKAEGGRIRAFAVSYTPERQDA +PADVLVGWDPELGEEDALQAVADLLALLVAQYPVQIEVDEAMAPLERIVDGLIGGNAART +LVDTYVFVDDAPGA +>PROKKA_02376 +MSGAYDDDAGALFDSAAVSGGEVVLRPWRAGDDLALLQVWGDPANVQQHQDRAMLAEDAE +RPWRRALVAEDAGVPVAAGVVYASSLHPQRLWLYVETAAPERRRGIGRALVAALRGLAAE +AHAAGTVPTAALKARFAKDALVPGTAVEEGVDTEAVRAQTAALAAGTEAFLAAEGFTPVQ +RSRRVAVAPGAIGLPDVRDEDRPDGVVLEEASTGSVELTQAVAAFYDAVHAWDPSTMSVG +AAQQLLLGPATGASGAVVLRDAPKAEGGRIRAFAVSYTPERQEAPADVLVGWDPELSEED +ALQSVADLLALLVAQHPVQVEVDEAMAPLERIVDGLIGGNAARTLVDTYVFVDDAA +>PROKKA_02260 +MSPRHDDDAPALTAAVSGGEVVLRPWAEGDDLRLLEVWGDPADVQQHQDRAMLAADADSP +WRRTLVAEEDGVPVGAAVAFAQPLHPGRLWVYGEVARTVRGRGVGRALLEALRGLVAAAH +EAGAVPTTELKARFAVASRVPVGGGEVVEAAPGEAPEAGAAGAEAHAAQVAATERFLVAA +GFTPVQRSRRIAVAPGVIALPALRDEEHPEGRVLEEISTGSVELTRAVAAFYDAAHAWDP +SQMSVGAAQQLILGPQTGAAGAVVLRDAPREEGGTIQAFAVSYTAERQDAPADVLLGWDP +SLGLEEAQLAVGDLLALLVAQHPVQVEADEAMTALEPILDALLAKRAAGTLVDTRVWATD +PS +>PROKKA_00570 +MTGAAGAAGHDDGGALFDSAAVGGGEIVLRPWRPGDDLALLEVWGDPANAQQHQDRAMLA +EDAERPWRRALVAEAAGVPVAAGVVYASSVHPRRLWLYVETAAAERRRGIGRALVAALRG +LAAEAHAAGAIPTTALKARFAKDALVPGVTGADPQTEADGATGRPPVDTDAVRSQTAALA +AGTEAFLVAEGFTPVQRSRRVAIAPGAIGLPDVRGEEHPDGVVLEEASTGSVELTQAVTA +FYDAVHAWDPSTLSVGAAQQLLLGPATGAAGAVVLRDAPKAEGGRIRAFAVSYTPERQDA +PADVLVGWDPELGEKDALQAVADLLALLVAQYPVQIEVDEAMAPLERIVDGLIGGNAART +LVDTYVFVDDATGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000565.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000565.fa new file mode 100644 index 0000000000000000000000000000000000000000..392565d07cf6644cbdbe035c5ede9a88fc529cab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000565.fa @@ -0,0 +1,33 @@ +>PROKKA_00572 +MTRKHLGFLNFGHWIHRPGAEPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQRMFSSP +FPILAAMAARTERISLGTGVIDLRYENPLYMAEAAATTDLISGGRLELGVSRGSPEAALD +GQAQFGYALDEGQTWADVTRERGRRFLSAVRGEGIATPDLTSGWAHSSQPLRIEPHSPGL +ADRIWWGSGSVGSVAGAATDGYNMLSSTLLLQDDGRPFHVQQADQIARYREAFAAAGHAG +PGRTAVTRSAFVIQDREDELYFGRERASRDSSGMLEGGAARSGPTYAGSAEEVAEKLAAD +DAVAAADWVLFANPNQLGVEYNAKIFAGWAEVWRLLGWDA +>PROKKA_00296 +MRYENPLYMAEAAATTDLISGGRLELGVSRGSPEAALDGQAQFGYALDEGQTWADVTRER +GRRFLSAVRGEGIATPDLTSGWAHSSQPLRIGPHSPGLADRIWWGSGSTPSAVEAGRDGY +NMLSSTLLLQDDGRPFHVQQADQIARYREAFAAAGHTGPGRTAVTRSAFVIQDREDELYF +GRERASRDSSGMLEGGAARSGPTYAGSAEEVAEKLAADDAVAAADWVLFANPNQLGVEYN +AKIFAGWAEVWRLLGWDA +>PROKKA_02373 +MNECCNRDIRYENPLYMAEAAATADLLAGGRLELGVSRGSPEAAKDGQAQFGYELADGQT +WAGVTRKRGRRFLAAVRGEGIATPDLASGWAHSSAPLRIEPHSPGLADRIWWGSGSAGSA +VEAAKDGYDMLSSTLLLQDDGRPFHVQQADQIAGYLEAYEAAGHAGTGRTAVTRSAFVIQ +DHEDELYFGRDRNSRESAGMLDGGRARSGPTYAGSAEEVAEKLAADDAVQAADWVLFANP +NQLGPEYNAKIFAGWAEVWRLLGWDR +>PROKKA_02253 +MTTKNLGFLNFGHWIHRPRVGRRPVEPDAKQAIDDVVQMAVDAEAAGLDGAWIRIHHFQR +MFSSPFPILTAMAAHTERIHLGTGVIDLRYENPLYMAEAAATTDLLAGGRLELGVSRGSP +EAARDGQAQFGYELADGQTWSDVARERGRRLLAGVRGEGIATPDLSSGWAHSSAPLRIEP +HSPGLADRIWWGSGTVGSAVEAAKDGYGMLSSTLLLQDDGRPFHVQQADQIARYLEAYEA +GGHTTPARTAVTRSAFVIQDHEDELYFGRDRHSRDSSGHLDGGAARSGPTYAGSAEEVAE +LLAADDAVQAADWVLFANPNQLGAEYNAKLFAGWAEVWRLLGWDS +>PROKKA_00573 +MTRKHLGFLNFGHWIHRPGTAPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQRMFSSP +FPILAAMAARTERISLGTGVIDLRYENPLYMAEAAATTDLLSGGRLELGVSRGSPEAALD +GQAQFGYALAEGQTWADVTRERGRRFLSAVRGEGIATPDLTSGWAHSSQPLRIEPHSPGL +ADRIWWGSGSVGSVAGAAADGYNMLSSTLLLQDDGRPFHVQQADQIARYREAFAAAGHAG +PGRTAVTRSAFVIQDREDELYFGRERASRDSSGMLEGGAARSGPTYAGSAEEVAEKLAAD +DAVAAADWVLFANPNQLGVEYNAKIFAGWAEVWRLLGWDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000566.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000566.fa new file mode 100644 index 0000000000000000000000000000000000000000..c8765b72e89406215bc46e9b8f222da15a6e6dcf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000566.fa @@ -0,0 +1,20 @@ +>PROKKA_00573 +MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHAGDSFLTLAAYHEHPDT +VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG +ADLLAVLDGGGAAPPSEA +>PROKKA_00305 +MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHTGDSFLTLAAYHEHPDT +VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG +ADLLAVLDGGDAAPASEA +>PROKKA_02360 +MTEQPQDPRQDQTAAEPAPEPAEALAAETTDAVAPEAAPGEAGQPSPEMLELAGRMFDAA +RSGDAETLEAYIVAGLNPDLQNGKGDTFLTLAAYHDQPGVVEMLIRVGADVEKANDRGQR +PLTCATFKGDVASMRLLLAAGADPDAGTPSARQTAQMFGGEEITAVLDEPR +>PROKKA_02251 +MTEHQDTQGQHAPATPPAEPAVESAGPSPEMLELAGRMFDAARTGDVDTLEAYIVAGLNP +DLQNGKGDTFLTLAAYHDQPAVVEMLIRVGADVEKANDRGQRPLTCATFKGDVASMCLLL +AAGADPDAGTPSARQTAQMFGGERVAAVLDEAR +>PROKKA_00574 +MSEQWSEKDIELANRLFDMARDGDTAQLKAYLDAGVSTRLRNHAGDSFLTLAAYHERPDT +VAMLIEAGAEIEHANDRGQRALTCATFKRDVASMRHLLAAGADPDAGTPSARQTAQMFAG +ADLLAVLDREDAAPSSEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000567.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000567.fa new file mode 100644 index 0000000000000000000000000000000000000000..f3d5597ecf3b25e3ff3c82a7661923e3e79af456 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000567.fa @@ -0,0 +1,45 @@ +>PROKKA_00574 +MTSSHTLPAAAVTDADDVAHYAKSAGAGRRITDDDQLHEARHPAPTTDRLTLPPLRLGPL +TIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHDPDEVP +RSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKAELFASIV +KAAVTEAAKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTAV +WDDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGDLQAAF +EGRQDRFQPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYLKGYPVGSEIRTA +LSTVPDLATMREILARVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNAEQQAM +IQAAELDVSGG +>PROKKA_00306 +MTSSHTLPAAAMTDADDVADPHAAHYAKSAGAGRRITDDDQLHEGRHPAPTTDRLTLPPL +RLGPLTIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHD +PDEVPRSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSEL +FASIVKAAVTEAAKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFY +SGTAVWDDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGD +LQAAFEGRQDRFQPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYFKGYPVGS +EIRTALSTVPDLATMREILTRVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNA +EQQAMIQAAELDVSGG +>PROKKA_02359 +MTVSSSTTTPERGAATDGLSAADPAAGAPAAVDPHASHYAKSAGAGRRIADDEQLHEGRH +AAPTTDRLSLPALTLGPITVDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALV +ERKPESMRIIKHDPDEVPRSVQLYSVDPVTTGAAVRMLVEEDRADHIDLNFGCPVPKVTR +RGGGSALPWKSELFASIVKAAVTEAGRKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVA +AVALHGRTTRQFYSGTAVWEDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVI +GRGCQGRPWLFGDLQAAFEGRHDRFRPTLGMVADTLYRHAELLVDTFEGDELKALRDIRK +HVAWYFKGYPVGSEIRTALSTVPDLATMAEILSRVDRDQPYPGLDAEGPRGRSGAPKRPH +LPDGWLDSRELNAEQKAMIAAAELDVSGG +>PROKKA_02250 +MTASHTLPDAAVDPHYAKSAGAGRRIADDDQLHEGGHAAPRSDRLNLPPLKLGPITVDVP +VVLAPMAGITNTAFRRLCREYGGGLYVNEMVTSRALVERKPESMRIIQHDPDEVPRSVQL +YSVDPVTTAAAVRMLVEEDRADHIDMNFGCPVPKVTRRGGGSALPWKSELFASIVKAAVT +EASKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTAVWEDIA +RLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWMFGDIQNAFEGRPE +RFHPTLGMVADTLYRHAELLVDTFGGDEVKALRDIRKHVAWYFKGYPVGSEVRTGLSTVP +NLATLRELLDRLDRDMPYPGAPAEGPRGRAGAPKRPHLPDGWLDSRELNEEQRAMIHAAE +LDVSGG +>PROKKA_00575 +MTSSHTLPAAAVTDADDVADPHAAHYAKSAGAGRRIADDDQLHEARHPAPTTDRLTLPPL +RLGPLTIDVPVVLAPMAGITNTAFRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHD +PDEVPRSVQLYSVDPVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSEL +FASIVKAAVTEASKKDIPVTVKMRRGIDEDHLTFLDAGRTARDLGVAAVALHGRTTRQFY +SGTAVWDDIARLREALPDIPVLGNGDIWSAEDAIAMVERTGVDGVVIGRGCQGRPWLFGD +LQAAFEGRQDRFRPTLGMVADTLYRHAELLVDTFGGDETKALRDIRKHVAWYFKGYPVGS +EIRTALSTVPDLATLREILARVDRDQPYPGEAAEGPRGRAGAPKRPHLPDGWLDSRELNA +EQKAMIQAAELDVSGG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000568.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000568.fa new file mode 100644 index 0000000000000000000000000000000000000000..0bfe0872e7d964631394e18e4ab8766dde85a23d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000568.fa @@ -0,0 +1,45 @@ +>PROKKA_00575 +MAEPTTPEPAAGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYPPWDRERWLPE +PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR +SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF +ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT +RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA +EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH +GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATGDRYLEPM +FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI +>PROKKA_00307 +MAEPTTPVPAAGTPAAPSSHWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE +PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR +SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF +ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT +RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA +EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH +GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLEATGDRYLEPM +FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI +>PROKKA_02358 +MAEGWAGPAHQPVLFGPQGRPPYAGRAVQTPGYTPWDRERWLPEPPKSSYRSDFERDRAR +VLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGRSLGCDPDLVDTACLSH +DLGHPPFGHNGEKALDALSADVGGFEGNAQTLRLLARLEQKKLFEDGSSAGLNLTRAALD +AACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFREGVSGSRKSMEAQVMDLADDIS +YSVHDVEDGVVNAAFQLKWLAIPEHRERVVETTRQWYLPLTDPAEVDEALARLEATDVWV +SEMDGSRRALAAMKDMTSQLIGRFCTAAFDATRQVFGNEPLTRHGADVVVPAETETEIAV +MKGIAAAYVMASEQRQPLYARQRELLAELVELLDASGDRYLEPMFAFDWREAADEAARRR +VVLDQVASLTDSTALEWHHTLVQGAEFTRVWI +>PROKKA_02249 +MAEPQPTLFGPADRPPYAGRPVPTPGYTDWDRRRWLAEPPKSSYRSDFERDRARVLHSAA +LRRLGAKTQVVAPDLDDFSRTRLTHSLEVAQIGRELGRSLGCDPDLVDTACLSHDLGHPP +FGHNGEKALDAVAEAAGGFEGNAQTLRLLARLEQKKSFPDGSSAGLNLTRAALDAACKYP +WVREDAPLRPDGKRSRKFGVYADDLPVFEWFRQGVHGARKSMEAQVMDLADDISYSVHDV +EDGVVNSAFQLRWITEPGERRARVLETTRDWYLPGGDLEEIDAALTRLESQDVWMGEMDG +SRRALAGMKDMTSQLIGRFCTAAFDATREVFGNEPLTRHAADVVVPAHTEHEIAVMKGIA +AAFVMTSEQRQPLYARQRDLLTELVDLLMTTGDRYLDPMFAADFQDAADDAARARVVIDQ +VASLTDSTAIEWHRTLVRGETFQRVWL +>PROKKA_00576 +MAERTTPAPADGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE +PPKSSYRSDFERDRARVLHSAGLRRLGDKTQVVAPDADDFARTRLTHSLEVAQVGRELGR +SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF +ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT +RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA +EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH +GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATEDRYLEPM +FAFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000579.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000579.fa new file mode 100644 index 0000000000000000000000000000000000000000..fc8d27799a9f8c202bf584ec10265bd1af9ec52b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000579.fa @@ -0,0 +1,35 @@ +>PROKKA_00642 +MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLRVDKQRQPEPGLDVKTDPVPDIGLDSYR +GMGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA +VALPGDLMDADYRASLVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM +SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI +RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSNPIGRAGQPVEMAPAYVFLASGESSYVNG +ETLNANGGTPTP +>PROKKA_00379 +MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLRIAKQRQPEPGLDVKTDPVPDIGLDSYR +GMGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA +VALPGDLMDADYRASLVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM +SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI +RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPIGRAGQPVEMAPAYVFLASGESSYVNG +ETLNANGGTPTP +>PROKKA_02320 +MTTPEKKDAAAATPVQDSQLAHDDPRTRHPKLDAPEQRQEEPGLDVKTEPVPDIGLDSYR +GLGRLEGRKALITGGDSGIGAAVAVAYAREGADVAIAYLPEEQPDADRVLAAIEAAGRTA +VALPGDLMDAGYREGLVEEAATALGGLDILVNNAGKQIISESLEDLTDQQVLETFQVNIL +SMFTLSRAALTHMGPGSTIINTTSVQAYNPNPMILDYAATKAAINNFTKGLAQQLGERGI +RVNAVAPGPVWSVLQVSYGQPKEKLPVFGHDTPTGRGGQPVEMAPAYVFLASGESSYVNG +ETLNANGGTPTP +>PROKKA_02183 +MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLHITKQRQPEPGLDVKTDPVPDIGLDSYR +GAGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA +VALPGDLMDVDYRASLVDEAAQRLGGLDILVNNAGKQFISDDLVDLTDEQVHETFQINIM +SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI +RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPLGRAGQPVEMAPAYVFLASGESSYVNG +ETLNANGGTPTP +>PROKKA_00612 +MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLHITKQRQPEPGLDVKTDPVPDIGLDAYR +GAGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA +VALPGDLMDADYRAALVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM +SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQVGPKGI +RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPIGRAGQPVEMAPAYVFLASGESSYVNG +ETLNANGGTPTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000582.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000582.fa new file mode 100644 index 0000000000000000000000000000000000000000..9f2f86de8e90bce2bc0dcfc5fc49dece06b2cc67 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000582.fa @@ -0,0 +1,40 @@ +>PROKKA_00647 +MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT +VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKTSFRRIYREVQPDVVHAQCHYMIGEAAI +NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA +AQAMAEHAGLDNVLPVSNGIDASAYELQPGERVDHPGHPVVLFVGRLAVEKNVEVLIRAI +AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGAADRVLLRGHVSEEELRAAYLRADVF +CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERIARIL +DLSDAERAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRALL +>PROKKA_00384 +MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT +VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKTSFRRIYREVQPDVVHAQCHYMIGEAAI +NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA +AQAMAEHAGLDNVLPISNGIDASAYELQPGEKVDHPGHPVVLFVGRLAVEKNVEVLIRAI +AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGAADRVLLRGHVSEEELRAAYLRADVF +CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERIARIL +DLSDAERAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRALL +>PROKKA_02316 +MSDRPGTAADRPLKVLIAADTYPPHVNGAATFCHRLATALHARGHEVHVVMPRGEAGPDT +VEERPEATVHLLRAIPAPTHEYYRLVMPWHAKAAFRRIYREVQPDVVHVQCHYMVGEAAI +NEAERRRIRMVSTNHFMPENLEPFLPFPQWFLDIVSRVSWRDMGRLMGKGAAVTTPTALA +ARAMAEHAGLDNVLPVSNGIDAAAYELQPGETVDHPGHPVVLFVGRLAVEKNVEVLIRAI +AHLARVRPDLDVHAEIVGDGEQRDRIRAAVESEGVADRVLLRGHVSDEELRAAYLRADVF +CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERVARIL +DLPEAERAAMGEASHAKAMHHSAQKTVDVFERLYRGATPAEVRELL +>PROKKA_02175 +MTSSARPAQERPLTVVIAADTYPPDVNGAAVFCFRLASALHERGHRVHVIAARNEPGPDT +VEERPEATVHRLESHRAFTHEYYRLVFPWHASRSIDRILAEVRPDVVHAQCHYMIGEAAI +NVADRRRIRTVSTNHFMPENLEPFLPFPQWFLNIVSKNSWRDMGRLMGKGAAVTTPTALA +AAAMAEHAGLDRVLPISNGIDASAYELAPGEVVERAAHPTVLFVGRLAVEKHVDVLVRAV +AHLARTRPDLDVHAEIVGDGEQRTALDAVIAEEGVADRVRRLGHVSDAELHTAYLRADVF +CQPGTAELQSLVSLEAMSASTPVVLADALALPHLVDDGVNGWLFPPGDHVALAERIARVL +DLPEAGRAAMGEASHAKAVRHSQAKTVDLFERLYRGATPAEIRAAL +>PROKKA_00617 +MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT +VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKISFRRIYREVQPDVVHAQCHYMIGEAAI +NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA +AQAMAEHAGLDNVLPVSNGIDASAYELQPGERVDHPGHPVVLFVGRLAVEKNVEVLIRAI +AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGVADRVLLRGHVSEEELRAAYLRADVF +CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALADRIARIL +DLSDADRAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRAML diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000585.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000585.fa new file mode 100644 index 0000000000000000000000000000000000000000..590b89ef29a877c66fd056a5fb68e1e1bc50eda7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000585.fa @@ -0,0 +1,30 @@ +>PROKKA_00652 +MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET +VAHGGTILFVGTKKQAQEAIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI +DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMAKTPSAVWVVDTKKEHLAVDEAQKL +GIPVVAILDTNCDPDEVAYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQAAAE +PMAEWERELLEQHNAQQAEQAEAPAAEAPAEQAEAPAAEAPAERAEAPAAEAAPQGE +>PROKKA_00389 +MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET +VAHGGTILFVGTKKQAQEAIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI +DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMAKTPSAVWVVDTKKEHLAVDEAQKL +GIPVVAILDTNCDPDEVPYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQAAAE +PMAEWERELLEQHNAQQAEQAEAPAAEAPAEQAEAPAAEAAPQGE +>PROKKA_02311 +MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET +VAHGGTILFVGTKKQGQEVIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI +DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMSKTPSAVWVVDTKKEHLAVDEAKKL +GIPVVAILDTNCDPDEVTYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQSAAE +PMAEWERELLEQHNAQQAEQAEAPAEAQAQAEEASAEAPAQAEEASAGAPAQAE +>PROKKA_02168 +MSVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLTYIDRAYEFVKQT +VAHGGTILFVGTKKQAQEAIAEQATRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEAI +DFEDVAGSTHTKKELLLLNRELEKLQGNLGGIRDMARTPSAVWIVDTKKEHLAVDEAQKL +NIPVVAILDTNCDPDEVAYPIPGNDDAIRSVTLLTRIVADAVAEGLIARQGGKSGDSSAE +PMAEWERELLEQHNAEQAAQAEAPAAEAAESEAPAAE +>PROKKA_00622 +MPVVTMRQLLDSGVHFGHQTRRWNPKMKRFIFTERNGIYIIDLQQSLSYIDRAYEFVKET +VAHGGTILFVGTKKQAQEAIAEQAGRVGMPYVNHRWLGGMLTNFSTVSKRVQRMKELEEI +DFEDVAGSQFTKKELLLLNRELEKLQANLGGIRNMAKTPSAVWVVDTKKEHLAVDEAQKL +GIPVVAILDTNCDPDEVAYPIPGNDDAIRSVNLLTRVVADAVAEGLIARQGGKSGQAAAE +PMAEWERELLEQHNAQQAEQAEAPAAEAPAEQAEAPAAEAPAEQAEAPAAEAAPQGE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000587.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000587.fa new file mode 100644 index 0000000000000000000000000000000000000000..b15b05387bbca1b1d3bff2ac0576bc33d3864874 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000587.fa @@ -0,0 +1,30 @@ +>PROKKA_00654 +METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD +QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA +IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG +VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV +TRALLGEPIGTTVTV +>PROKKA_00391 +METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD +QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA +IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG +VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV +TRALLGEPIGTTVTV +>PROKKA_02309 +METNRAPEDPKTAHVPQTSDDTGRRRVLLKLSGEVFGGGKVGVDPETVRGIAEQIAVAAD +RVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVSTRVQSA +IHMEQVAESYIPLRAIRHMQKGRVVVFGAGTGLPYFSTDTVAAQRALEIGADEVLMAKSG +VDGVYTADPKKDPSAELLTHLTYDEALLRNIRVMDLTAMTMCKDNNLDMRVFGMEGPGNV +TRALLGEPIGTTVTV +>PROKKA_02166 +MSPAQQPENHAVDAEDTGRRRVLLKLSGEVFGGGSVGIDPVTVRGIAEQIAEAAEQVEIS +IVVGGGNFFRGAELSESGMDRRRADYMGMLGTVMNCLALQDFLLQAGVSTRVQSAIHMEQ +VAESYIPLRAVRHMQKGRVVVFGAGTGLPYFSTDTVAAQRALEIGADEVLMAKSGVDGVY +TADPKKDPTAQRLEHLTYDEALRKDIRVMDLTAMTMCKDNGLSMRVFGMEGPGNVTRALL +GEEIGTSVTP +>PROKKA_00624 +METNRAPEDPTTAHAPQTSDDTGRRRVLLKLSGEVFGGGKIGVDPETVRGIAEQIAAAAD +QVEIAIVVGGGNFFRGAELSENGMDRRRADYMGMLGTVMNCLALQDFLIQAGVTTRVQSA +IHMEQVAESYIPLRAIRHMQKGRVVIFGAGTGLPYFSTDTVAAQRALEVGADEVLMAKSG +VDGVYTADPKKDPTAERLTHLTYDEALLRNIRVMDLTAMTMCKDNDLDMRVFGMEGPGNV +TRALLGEPIGTTVTV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000588.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000588.fa new file mode 100644 index 0000000000000000000000000000000000000000..9204f6ec5be965ad1a82afb2aa7bbd961f95288d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000588.fa @@ -0,0 +1,25 @@ +>PROKKA_00655 +MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT +DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRIVMPELTEERRKEYVKLVKSK +AEEHKISVRNARRKAKEAMDKAVKDGEVGEDEGARGEKELDALTKRHVELIDEMAKNKEQ +ELLEV +>PROKKA_00392 +MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT +DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRIVMPELTEERRKEYVKLVKSK +AEEHKISVRNARRKAKEAMDKAVKDGEVGEDEGARGEKELDALTKRHVELIDEMAKNKEQ +ELLEV +>PROKKA_02308 +MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSYTPLQQLASFTTT +DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRVVMPELTEERRKEYVKLVKSK +AEEHKVSVRNARRKAKDALDKAVKDGEVGEDEGARGEKDLDAMTKKHVDLIEEMAKNKEQ +ELLEV +>PROKKA_02165 +MIQETLTSAQEQMERTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT +DARTLLITPFDVSALRNIEKALSDSEVGANPSNDGKVIRVVMPELTAERRKEYVKLVKNK +AEEHKVSVRNARRKAKEAIDKLVKDKEIGEDEGARGEKDLDALTKKHTDLIEEMAKKKEA +ELLEV +>PROKKA_00625 +MIQETLQSAEEQMDRTIEATREDFASVRTGRANPGLYSKVMVDYYGSFTPLQQLASFTTT +DARTLLITPFDQSALRNIEKALSESEVGANPSNDGKVIRIVMPELTEERRKEYVKLVKSK +AEEHKISVRNARRKAKEAMDKAVKDGEVGEDEGARGEKELDALTKRHVELIDEMAKNKEQ +ELLEV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000589.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000589.fa new file mode 100644 index 0000000000000000000000000000000000000000..4fa6c493d2bdb59269a5eb41141f5cfc00034012 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000589.fa @@ -0,0 +1,25 @@ +>PROKKA_00657 +MTPRTTPDAEPVFELVEQDEIGYETTHVDAFMARAREARDGGAPLTAEEVRQARFATVNG +GYATDEVDDELDRLEEELAAAERQAFVAERGDEDWAADLEERVAELVARADRAPAERFRR +PSRADAVSYDVDQVDALVDRLRVTLAGAEDSTDPGAEGGLTADDVRRASFGEAEGAAGYE +EGQVDAYLDAAVDVLLRRA +>PROKKA_00394 +MTPRTTPDAEPVFELVEQDEIGYETTHVDAFMARAREARDGGAPLTAEEVRQARFATVNG +GYATDEVDDELDRLEEELAAAERQAFVAERGDEDWAADLEERVAELVARADRAPAERFRR +PSRADAVSYDVDQVDALVDRLRVTLAGAEDSTDPGAEGGLTADDVRRASFGEAEGAAGYE +EGQVDAYLDAAVDVLLRRA +>PROKKA_02306 +MTTRRPQDAEPPFELVEQDEIGYETSHVDAFLARAREAREGGAPLTADEVRQARFATVNG +GYATDEVDDELDRLEGELAAAEREAFVSERGDEDWSADLEERVAELVARADRAPAERFRR +PSREDATSYDVDAVDALVDRLRVTLAGAEGAAAPDARGGLTADDVRRASFGEAEGDRGYE +EGQVDAYLDAAVDVLLRRA +>PROKKA_02163 +MTPTSPEARADFEHVGPDEIGYEPAHVDAFLERARRAEAGEGDLTAEDVRQARFATVNGG +YAADQVDDELDRLEEVLMGREREDAVGDGAWDRELAERSQELLGRADRAPAERFRRPSAD +DAQSYDVDDVDALVDRLRATLTDGSDELTADDVRRAGFASAQGGDGYDEAQVDAYLDAAV +DVLLRRG +>PROKKA_00627 +MTPRTTPDTEPVFELVEQDEIGYETTHVDAFMARAREARDGGAPLTAEEVRQARFATVNG +GYATDEVDDELDRLEEELAAAERQAFVAERGDEDWAADLEERVAELVARADRAPAERFRR +PSRADAVSYDVDQVDALVDRLRVTLAGAEGSTDPDAEGGLTADDVRRASFGEAEGAAGYE +EGQVDAYLDAAVDVLLRRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000591.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000591.fa new file mode 100644 index 0000000000000000000000000000000000000000..a39cc84529c98f192752c3a9719642a38cc76c3c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000591.fa @@ -0,0 +1,35 @@ +>PROKKA_00659 +MSERMTFGRAINRGLQRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA +ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF +GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD +KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS +PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP +PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEETR +>PROKKA_00396 +MSERMTFSRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA +ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF +GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD +KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS +PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP +PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEETR +>PROKKA_02304 +MSERMTFGRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQDEFGEDRVLDTPLA +ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF +GGGIGSPEHHSESPEAYFLHTPGLRVVSPSSPQEGHDLIRAAIASDDPVVYLEPKRRYHD +KGEVDLDADIPPMSTAKILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS +PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP +PSKLEHLHLPDLDRILDGVDRALGRPNSLDSVDAFAAPETAEQFLAAQTAGEETR +>PROKKA_02160 +MSEQMTFGRALNRGLHRALADDPKVLLMGEDIGRLGGVFRITDGLQEEFGVDRVVDTPLA +EAGIVGTAIGLALRGYRPVVEIQFDGFLYPAFDQIVANLAKLRARTRGRVAVPVTIRIPY +GGGIGSPEHHCESPEAYFLHTPGLRVVSPSSPQAGYEMIRAAIASDDPVVFFEPKRRYHD +KGPVDLDAAPGPLSVGRVLRPGADVTLVAYGPLVKTALQAAEVAEQEGVSVELIDLRSLS +PLDTGLVEASVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLESPPVRVTGLDIPYP +PATLEHLHLPDLDRILEGVDRALGRPNPQDAVDAFAPPQTAEDFLSARADSSEVPA +>PROKKA_00629 +MSERMTFGRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA +ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF +GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD +KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS +PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP +PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEETR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000592.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000592.fa new file mode 100644 index 0000000000000000000000000000000000000000..3a9721360d9ee84250bbe2404bf62c8a2d6ceae9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000592.fa @@ -0,0 +1,46 @@ +>PROKKA_00660 +MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVSVNQVLADVETAKAVVEVSSPFAGVVAAL +HGAEGETLEVGAPLVTFTLEGAEPDVGGPAEGDGRVPTLVGYGAAPDTGKPGRRARRGSA +APATSAAPAGEPARGQAPSTSEAAPAGAGRPQPEAAEPDRADAAHEPAPGERPRCTPPVR +LYARRAGVDLEQVTGTGVGGVITRADVEAFLAGGGQPAAAAAPPQSGAESGSTGGVRTLG +GRPRTEAVPVKGVRKATAAAMVQSAFTAPHVTEFLQVDVTETMELLAELKASREFRDVKL +TPMTLAAKACLVAMERTPDVNARWDEAAGTIVQQNFVNLGFAAATPRGLMVPNVKDAQAM +SLRELADAIRDLTGLAREGRLSPADLAGGTFTLTNVGVFGVDAGTPIINPGEGAIIAIGQ +VRRMPWEHRGEIALRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLTMV +>PROKKA_00397 +MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVTVNQVLADVETAKAVVEVSSPFAGVVAAL +HGAEGETLEVGAPLVTFTLEGAESDVGGPAEGDGRVPTLVGYGAAPDTGKPGRRARRGSA +APATSAAPAGEPARGQAPSTSEAAPAGAGRPQPEAAEPDRADAAHEPAPGERPRCTPPVR +LYARRAGVDLEQVTGTGVGGVITRADVEAFLAGGGQPAAAAAPPQSGAESGSTGGVRTLG +GRPRTEAVPVKGVRKATAAAMVQSAFTAPHVTEFLQVDVTETMELLAELKASREFRDVKL +TPMTLAAKACLVAMERTPDVNARWDEAAGTIVQQNFVNLGFAAATPRGLMVPNVKDAQAM +SLRELADAIRDLTGLAREGRLSPADLAGGTFTLTNVGVFGVDAGTPIINPGEGAIIAIGQ +VRRMPWEHRGEIALRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLAMV +>PROKKA_02303 +MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVTVNQVLADVETAKAVVEVSSPFAGVVAAL +HGSEGETLEVGAPLVTFTVEGAGGDGGDTESGGRVPTLVGYGAAPDTGKPGRRARRGGSA +GSATSAAPAGEPERGRAPSTSEEAPAGAARPQPEAAEPERADEAPEAQPASGTSGERPRC +TPPVRLYARREGVDLTAVSGSGVGGVITRADVEAFLAGGGAPAAEPTASAAAPAEAGTSG +GVRTLGGRPRTESVPVKGVRKATASAMVASAFTAPHVTEFLQVDVTETMELLAELKASRE +YRDVKLTPMTLAAKACLVAMERTPDVNARWDQASGTILQQNFVNLGFAAATPRGLMVPNV +KDAQAMSLTELADAIRELTGRAREGRLSPAELSGGTFTLTNVGVFGVDAGTPIINPGEGA +IIAIGQVRRTPWEHRGEIVLRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLTM +V +>PROKKA_02159 +MTRTVFRLPDLGEGLTESDLVTWRVSAGDDVVLNQVLAEVETAKAVVEVSSPYAGTVAEL +HAQEGQTVDVGSPLVTFDLPGDDAAPSDGPAADGRVPTLVGYGAAPESGAPARRRRRPAS +SAGESTPETGTSAEPAPAPAESAPAERPRSTPPVRLLARRLGVDLESVTGSGDHGVITRA +DVDAAARAASDSAGSEAPAEADAAPGVRTLGGRPRVVVEQVRGVRKATAQAMVSSAFTAP +HVTEFLTVDVTESMELLDELRRDRAFRDVKVTPMTLALRACVLAMERTPEVNARWNGQDG +TIERRHFVNLGMAAATPRGLLVPHVKDAQALDLRGLAVEVAALTERARAGTLTPAELTGG +TFTLTNVGVFGVDSGTPIIHPGEAAILCLGAVRTQPWEHRGQIALRQVVTLSLSFDHRLV +DGEQGSRFLADVGAMLRRPGMTLALV +>PROKKA_00630 +MSQKTFRLPDLGEGLTESEIVTWRVAEGDAVSVNQVLADVETAKAVVEVSSPFAGVVAAL +HGAEGETLEVGAPLVTFTLEGAEPDVGGPAEGDGRVPTLVGYGAAPDTGKPGRRARRGSA +APATSAAPVGEPARGQAPSTSEAAPAGAGRPQPEAAEPARADAAPEAVRGAASGERPRCT +PPVRLYARRAGVDLEQVTGTGVGGVITRADVEAFLAGGGQPAAAATPPQSDAESGSTGGV +RTLGGRPRTEAVPVKGVRRATAAAMVQSAFTAPHVTEFLQVDVTETMELLAELKASREFR +DVKLTPMTLAAKACLVAMERTPDVNARWDEAAGTIVRQNFVNLGFAAATPRGLMVPNVKD +AQAMSLRELADAIRDLTGLAREGRLSPADLAGGTFTLTNVGVFGVDAGTPIINPGEGAII +AIGQVRRMPWEHRGEIALRDVMTLSLSFDHRFVDGEQGSRFLADVGAILRRPGLTLTMV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000596.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000596.fa new file mode 100644 index 0000000000000000000000000000000000000000..146854a01836c24565b8861e28655d34a4a3d35e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000596.fa @@ -0,0 +1,20 @@ +>PROKKA_00668 +MSSSEPTAPVPTAAQFRAAQQSEEFTELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF +MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGAHENP +EATR +>PROKKA_00405 +MSSSEPTAPVPTAAQFRAAQQSEEFIELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF +MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGAHENP +EATR +>PROKKA_02294 +MSSSEPTAPAPTAAQFRAAQQSEEFTELRSTYRSFAFPMTVAFFVWYLVFVIAGAFFPEF +MSIRLGGNITLGLVLGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGGAPET +PEATR +>PROKKA_02156 +MSTGPHTPPAPTPAQFRAAQDSPEFRELRRTQRSFAFPMTVTFFVWYLLFVILGAFFPQV +MAVRLGGNITLGLVLGLLQFVTTFAITFAYVRFSNRVLDPRAAALRERLEREAAGAAPET +PEVAL +>PROKKA_00638 +MSSSEPTAPVPTAAQFRAAQQSEEFIELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF +MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGAPENP +EATR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000597.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000597.fa new file mode 100644 index 0000000000000000000000000000000000000000..2f9987f6645c966d35c907f3f0bc2132598977ea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000597.fa @@ -0,0 +1,50 @@ +>PROKKA_00669 +MSALTPLLQAAPQTVGNPAVNIGIFVAFVVVTLVIVIRASKTNASSADYYAGGRGFSGTQ +NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA +DVLSFRLQQRPVRIAAAFGTMAVCLFYLLAQMAGAGGLVALLLNINDRAGQALVIVIVGV +LMIVYVLIGGMKGTTYVQIIKAVLLIAGAGIMTVWTLALFGFDFNALLGAAVEKNPKGEA +ILEPGLQYGASALTRLDFVSLGLALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG +AFYLFTLVLGYGAGALIGPERILAAPGGQNSAAPLLAFELGGSILLGLISAVAFATILAV +VAGLAITAAASFAHDVYGSVIAKHPLTPQEEVRIGKITVVVIGVLAIVGGIAAQGQNVAF +LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGTPTSMI +PGADFAVFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH +>PROKKA_00406 +MSALTPLLQAAPQTVGNPAVNIGIFVAFVVVTLVIVIRASKTNASSADYYAGGRGFSGTQ +NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA +DVLSFRLQQRPVRIAAAFGTMAVCLFYLLAQMAGAGGLVSLLLNINDRAGQALVIVIVGV +LMIVYVLIGGMKGTTYVQIIKAILLIAGAGIMTVWSLALFGFDFNAMLGAAVEMNPKGEA +ILEPGLQYGASALTRLDFVSLGIALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG +AFYLFTLVLGYGAGALIGPERILAAPGGQNSAAPLLAFELGGSILLGLISAVAFATILAV +VAGLAITAAASFAHDVYGSVIAKHPLTPQEEVRIGKITVVVIGVLAIVGGIAAQGQNVAF +LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGTPTSMI +PGADFAVFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH +>PROKKA_02293 +MSALTPLLQAAPEAVGSPAVNIGIFLAFVVVTLVIVIRASKTSSSSADYYAGGRGFSGTQ +NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA +DVLSFRLRQKPVRIAAAFGTMAVCLFYLLAQMAGAGGLVSLLLNINDRAGQALVIAIVGV +LMIVYVLIGGMKGTTYVQIIKAILLIAGAGVMTVWSLAMFGFDFNAMLGAAVELNPEGEA +ILEPGLQYGASALTRLDFVSLGIALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG +AFYLFTLVLGYGAGALIGPERIMAAPGGQNSAAPLLAFELGGSILLGVISAVAFATILAV +VAGLAITAAASFAHDVYGSVIAKHQLTPNEEVRIGKITVVVIGLLAIVGGIAAQGQNVAF +LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGAPTSMI +PGADFAIFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH +>PROKKA_02155 +MSTFALPLAAAVGDPVVNIGIFVAFVAVTLVIVIRASKKNASAADYYAGGRGFSGTQNGT +AIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMADVL +SFRLRQKPVRIAAAFGTMAVCLFYLLAQMAGAGGLVALLLNITDKGGQALVIVIVGVLMI +VYVLVGGMKGTTYVQIIKAILLITGAGVMTLWSLALFGFDFNAMMGAAVQLNPQGEAILE +PGLQYGKNFTTRLDFLSLGLALVLGTAGLPHVLMRFYTVPTAKEARTSVVWAIVLIGAFY +LFTLVLGYGAGALIGPEKILAAPGGVNSAAPLLAFELGGSILLGLISAVAFATILAVVAG +LALTAAASFAHDVWGSVIAKEPLTPEEEVRIGKITVVVIGVLAIVGGIAAQGQNVAFLVA +LAFAVAASANLPTILYSLFWRGFTTRGAVWSMYGGLIASIVLIVLSPVMSGAETSMIPTA +DFAVFPLKNPGIVSIPLAFVLGWLGSVTSKDVEDPDKQAEMEVRSLTGVGAEKPVAH +>PROKKA_00639 +MSALTPLLQAAPQTVGNPAVNIGIFVAFVVVTLVIVIRASKTNTSSADYYAGGRGFSGTQ +NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA +DVLSFRLQQRPVRIAAAFGTMAVCLFYLLAQMAGAGGLVSLLLNINDRAGQALVIVIVGV +LMIVYVLIGGMKGTTYVQIIKAILLIAGAGIMTVWSLALFGFDFNAMLGAAVEMNPKGEA +ILEPGLQYGASALTRLDFVSLGIALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG +AFYLFTLVLGYGAGALIGPERITAAPGGQNSAAPLLAFELGGSILLGLISAVAFATILAV +VAGLAITAAASFAHDVYGSVIAKHPLTPQEEVRIGKITVVVIGVLAIVGGIAAQGQNVAF +LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGTPTSMI +PGADFAVFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000599.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000599.fa new file mode 100644 index 0000000000000000000000000000000000000000..14d233fb66f699f08a45da55db17067426827560 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000599.fa @@ -0,0 +1,45 @@ +>PROKKA_00671 +MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE +TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE +HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ +QARAASGGTEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTRI +EWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPLD +AGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEEA +TLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGPF +DLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF +>PROKKA_00408 +MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE +TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE +HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ +QARAASGGTEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTRI +EWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPLD +AGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEEA +TLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGPF +DLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF +>PROKKA_02291 +MSAVEVLWYVLGVVAVALGLAVSIALHEVGHLMPAKLFGVRVTQYMIGFGPTIASWRRGE +TEYGFKAVPLGGYVAMVGMLPPPRPGQEPRTASTGFVQQLGRMADDARTQAAAELTAADE +GRQFIQLPVWKRVVIMLGGPFMNLLIALGVTALLVTTVGTSQPSTTAAEVYRCVVTTDEQ +QARAAEGGGQDCRPGDPVAPAHEAGLRPGDTVTSFDGRPVDDWDALSGLIRERAGQPTAI +EWERDGEPHSATITPRLTQRPVTDAVGRPERAPDGTALTEEVGFIGMGSQIETVQQSPLA +AGPVVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALQEA +ELADKAALLLSLVAGVNVALMVFNLIPLLPLDGGHVAGALWEALRRGWARLRGRPDPGPF +DLARMLPLTYAVAGLMLVMGVVLIVADIVEPIRLF +>PROKKA_02153 +MSAVEALWFVGGVVVVALGLALSIALHEVGHLVPAKLFGVRVTQYMVGFGPTVASWRRGE +TEYGIKAFPLGGYVAMVGMLPPPKGGTVARTGSTGFRARAGRMADDARAQAAEEITAADE +GRQFIQLPVWKRVVIMLGGPFVNLLIALALTAVLVSTLGVARPSTTADEVFQCVVSQSEQ +QSRAADGGAAQDCRPGDPAAPAYEAGLRPGDRVVSFDGRDVGSWAELSTAIRARAGQATA +IAWERDGTRTESTLTPLLTERPVTDALGVPERGADGGVKTEPVGFIGLASRQETVTLAPW +EAVPLVGRQAQGVVGVILALPQRLWDTAVAVVTPAPRDPNGPMSVVGVGRIAGEAAALDT +ASPADKAALLLSLVAGVNVALLVFNLIPLLPLDGGHVAGALWEGLRRGWARLRGRPDPGP +FDLAVMMPLTYVVGAAMLAMGVLLIVADIVKPVQLF +>PROKKA_00641 +MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE +TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE +HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ +QARAASGGTEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTRI +EWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPLD +AGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEEA +TLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGPF +DLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000600.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000600.fa new file mode 100644 index 0000000000000000000000000000000000000000..10a6a7a87a3326f22aa795c67a5c41998b76e48f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000600.fa @@ -0,0 +1,40 @@ +>PROKKA_00672 +MPVSLGMPSAPPPVLAPRRTTRQIQVGSVGVGSQHPVSVQSMTTTKTHDIGATLQQIAEL +TAAGCDIVRVACPTDKDAEALKVIAQQSTIPVIADIHFQPKYVFAAIEAGCGAVRVNPGN +IKKFDDKVKEIAQAASDHGTSLRIGVNAGSLDPRLLQKYGKATPEALVESAVWEASLFEE +HGFKDFKISVKHNDPVIIARAYELLAEQGDWPLHLGVTEAGPAFQGTIKSATAFGYLLGQ +GIGDTIRVSLSAPPVEEVKVGLQILQSLNLRERKLEIVSCPSCGRAQVDVYTLAEQVTEG +LQDLEVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIRTVPEDQIVETLIE +EANRIAGEMDLGEDGGDQAAAGAPVVSVH +>PROKKA_00409 +MPVSLGMPSAPPPVLAPRRTTRQIQVGSVGVGSQHPVSVQSMTTTKTHDIGATLQQIAEL +TAAGCDIVRVACPTDKDAEALKVIAQQSTIPVIADIHFQPKYVFAAIEAGCGAVRVNPGN +IKKFDDKVKEIAQAASDHGTSLRIGVNAGSLDPRLLQKYGKATPEALVESAVWEASLFEE +HGFKDFKISVKHNDPVIMARAYELLAEQGDWPLHLGVTEAGPAFQGTIKSATAFGYLLGQ +GIGDTIRVSLSAPPVEEVKVGLQILQSLNLRERKLEIVSCPSCGRAQVDVYTLAEQVTEG +LQDLEVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIRTVPEDQIVETLIE +EANRIAGEMDLGEDGGDQAAAGAPVVSVH +>PROKKA_02290 +MPVSLGMPSAPPPVLAPRRATRQIRVGSVGVGSQHQVSVQSMTTTKTHDIGATLQQIAEL +TAAGCDIVRVACPTDKDAEALKVIAQQSTIPVIADIHFQPKYVFAAIEAGCGAVRVNPGN +IKKFDDKVKEIAQAAAEHGTSIRIGVNAGSLDPRLLKKHGKATPEALVESAVWEASLFEE +HGFKDFKISVKHNDPVIMARAYELLAEQGDWPLHLGVTEAGPAFQGTIKSATAFGYLLGK +GIGDTIRVSLSAPPVEEVKVGLQILQSLNLRERKLEIVSCPSCGRAQVDVYTLAEEVTEG +LKDLEVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIRTVPEDQIVDTLIE +EANRIAAEMGVGEESGDQAAAGAPVVSVH +>PROKKA_02152 +MPVSLGMPSAPPPVLAPRRRTRQIQVGRVGVGSEHPVSVQSMTTTKTHDIGATLQQIAEL +TAAGCDIVRVACPTDKDADALKVIAQQSTIPVIADIHFQPKYVFAAIEAGCGAVRVNPGN +IKKFDDKVKEIAQAATEHGTSLRIGVNAGSLDPRLLQKHGKATPEALVESAVWEASLFEE +HGFKDFKISVKHNDPVIMARAYELLAEQGDWPLHLGVTEAGPAFQGTIKSATAFGYLLGK +GIGDTIRVSLSAPPVEEVKVGLQILQSLNLRERKLEIVSCPSCGRAQVDVYTLAEQVTEG +LKDVTVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIRTVPEDQIVDTLIE +EARRIAAEMGHEDGEGEAAPAGAPSVTVH +>PROKKA_00642 +MPVSLGMPSAPPPVLAPRRTTRQIQVGSVGVGSQHPVSVQSMTTTKTHDIGATLQQIAEL +TAAGCDIVRVACPTDKDAEALKVIAQQSTIPVIADIHFQPKYVFAAIEAGCGAVRVNPGN +IKKFDDKVKEIAQAASDHGTSLRIGVNAGSLDPRLLQKYGKATPEALVESAVWEASLFEE +HGFKDFKISVKHNDPVIMARAYELLAEQGDWPLHLGVTEAGPAFQGTIKSATAFGYLLGQ +GIGDTIRVSLSAPPVEEVKVGLQILQSLNLRERKLEIVSCPSCGRAQVDVYTLAEQVTEG +LQDLEVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIRTVPEDQIVETLIE +EANRIAGEMDLGEDGGDQAAAGAPVVSVH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000602.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000602.fa new file mode 100644 index 0000000000000000000000000000000000000000..7c9868c56545510662f266bcd297cf3adfa6db8f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000602.fa @@ -0,0 +1,60 @@ +>PROKKA_00674 +MPLRMSTLFLRTLRDDPAEAEVASHRLLVRAGYIRRAAPGIYSWLPLGLKVLAKVERIVR +EEMDAIGAQEVHFPALLPREPYEATGRWDEYGDGLFRLQDRRGNDYLLAPTHEEMFTLLV +KDLYSSYKDLPAYLYQIQTKYRDEARPRAGLLRGREFIMKDSYSFTVDDAGLDAAYEAHR +AAYLRIFDRLGLEVVPVRATSGAMGGSRSEEFLHPTEVGEDTFVESDGGYRANVEAVTTV +APAPLDEAAMAVLPAAEVKDTPVSTTIAALVDVANRLAPRDGEPWTAADTLKCVVVTAVV +DGGERRPFVVGVPGDREVDLKRLEASVGPALGVVGEPTLEAATAADLAAHPALVKGYIGP +AAADAVEGTPVLGAEGSVSGLPFFVDPRIAPGTAWITGANADQRHVFGLVAGRDFTWDGV +LEATAVREGDQAPDGSGPLHTRRGMEMGHIFQLGRKYAEALDLKVLDVHGKQVVVTMGSY +GIGITRAVAAIAERYHDDKGLAWPRAVAPADVHVVVATKGEDGLAAAETLAAGLEAEGLT +VLVDDRPKVSPGVKFKDAELIGVPTTVVIGRGLADGELELKDRATGEARPVPVDGAVAAV +LAEVRDGR +>PROKKA_00411 +MPLRMSTLFLRTLRDDPAEAEVASHRLLVRAGYIRRAAPGIYSWLPLGLKVLAKVERIVR +EEMDAIGAQEVHFPALLPREPYEATGRWDEYGDGLFRLQDRRGNDYLLAPTHEEMFTLLV +KDLYSSYKDLPAYLYQIQTKYRDEARPRAGLLRGREFIMKDSYSFTVDDAGLDAAYEAHR +AAYLRIFDRLGLEVVPVRATSGAMGGSRSEEFLHPTEVGEDTFVESDGGYRANVEAVTTV +APAPLDEAAMAVLPAAEVKDTPVSTTIAALVDVANQLAPREGEPWTAADTLKCVVVTAVV +DGGERRPFVVGVPGDREVDLKRLEASVGPALGVVGEPTLEAATAADLAAHPALVKGYIGP +AAADAVEGTPVLGAEGSVSGLPFFVDPRIAPGTAWITGANADQRHVFGLVAGRDFMWDGV +LEATAVREGDEAPDGSGPLHTRRGMEMGHIFQLGRKYAEALDLKVLDVHGKQVVVTMGSY +GIGITRAVAAIAERYHDDKGLAWPRAVAPADVHVVVATKGEDGLAAAETLAAGLEAEGLT +VLVDDRPKVSPGVKFKDAELIGVPTTVVIGRGLADGELELKDRATGEARPVPVDGAVAAV +LAEVRDGR +>PROKKA_02288 +MALRMSTLFLRTLRDDPADAEVASHRLLVRSGMIRRAGFGTFTWLPLGLRVLRRVEQIVR +EEMDAIGGQEVHFPALLPKEPYEATGRWDEYGDGIFRVQDRKGADLLLAPTHEEMFTLLV +KDHYSSYKDLPAYLYQIQTKYRDESRPRAGLLRVRDFVMKDSYSFTVDDAGLDEAYEAHR +AAYERIFARLGLETVPVEATAGAMGGSRSEEFLHPCAIGEDTFVESPGGYRANVEAVTTV +APAPLDEAAMAALPAPEVKETPVSTTIAALVDVANELAPRAEGVWTAADTLKCVVLTAVL +DGDERRQFVVAVPGDREVDLKRLETTVAPALGLSGEPGVEAATEEDLRRHPSLVKGYIGP +GAGPDGGAPVLGAESVSGLPFLVDPRIAAGTAWITGANADQRHVFGLVAGRDFGWDGVVE +ATVVRDGDEAPDGSGPLTARRGIEMGHIFQLGRKYAEALDLKVLDQNGKQVVVTMGSYGI +GVTRAVAAIAESHRDEKGLVWPRAVAPADVHVLATGKGAEVFEAAEQIVAGLEAAGLTVL +FDDRPKVSAGVKFGDVELIGLPTSVVVGRGLADGVVEVKDRATGEARSVPVAEAVDAVVA +EVRDGR +>PROKKA_02150 +MALRMSTLFLRTLRDDPADAEVASHKLMVRAGYIRRAAPGIYTWLPLGLKVLAKVEQIVR +EEMDAIGAQEVHFPALLPREPYEATGRWEEYGDGLFRLQDRRGNDYLLAPTHEEMFTLLV +KDLYSSYKDLPAYLYQIQTKYRDEARPRAGLLRGREFIMKDSYSFTVDDAGLDAAYEAHR +AAYLRIFDRLGLEVVPVRATSGAMGGSRSEEFLHPTEVGEDTFVESDGGYRANVEAVTTV +APAPLDEAAMAALPAAEVKDTPASTTIAALVDVSNELLPREDRPWEAADTLKCVVLTAVV +EGGERRQFVVAVPGDREVDLKRLEASVGPALGLVGEPDLEAATAEDLKRHPSLVKGYIGP +GAGPDGTPVLGAEDSVSGLPFLVDPRIAAGTVWMTGANADQKHAFGLVAGLDFTWDGVVE +ATVVREGDPAPDGSGPLHTRRGMEMGHIFQLGRKYAEALDLKVLDENGRQVVVTMGSYGI +GVTRAVAAIAERYHDEKGLVWPRAVAPADVHVVVATKGEDGVQAALDLAARLEERGLTVI +VDDRPKVSPGVKFKDAELVGVPTAVVVGRGLADGELELKDRATGASRAIALDSAVDEVLA +EVRPQG +>PROKKA_00644 +MPLRMSTLFLRTLRDDPAEAEVASHRLLVRAGYIRRAAPGIYSWLPLGLKVLAKVERIVR +EEMDAIGAQEVHFPALLPREPYEATGRWDEYGDGLFRLQDRRGNDYLLAPTHEEMFTLLV +KDLYSSYKDLPAYLYQIQTKYRDEARPRAGLLRGREFIMKDSYSFTVDDAGLDAAYEAHR +AAYLRIFDRLGLEVVPVRATSGAMGGSRSEEFLHPTEVGEDTFVESDGGYRANVEAVTTV +APAPLDEAAMAALPAAEVKDTPVSTTIAALVDVANRLAPREGEPWTAADTLKCVVVTAVV +DGGERRPFVVGVPGDREVDLKRLEASVGPALGVVGEPTLEAATAADLAAHPALVKGYIGP +AAADAVEGTPVLGAEGSVSGLPFFVDPRIAPGTAWITGANADQRHVFGLVAGRDFTWDGV +LEATAVREGDEAPDGSGPLHTRRGMEMGHIFQLGRKYAEALDLKVLDVHGKQVVVTMGSY +GIGITRAVAAIAERYHDDKGLAWPRAVAPADVHVVVATKGEDGLAAAETLAAGLEAEGLT +VLVDDRPKVSPGVKFKDAELIGVPTTVVIGRGLADGELELKDRATGEARPVPVDGAVAAV +LAEVRDGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000603.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000603.fa new file mode 100644 index 0000000000000000000000000000000000000000..2a6976caf6ba053c2bf6cabccb3112fb4636df2d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000603.fa @@ -0,0 +1,30 @@ +>PROKKA_00675 +MLAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPIQALATNKLGSVFGTATSALTYRRRL +RQDLSTALPMAAVAFAAALGGAVVAAHLPAGVIRPVILAALIAVAVFTAVRPGLGQVAGV +GPRRSTALARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKVVNLATN +LGALAYFVPSGHAVLGLGLLLGAANLMGGYVGARMAIARGTGFIRVVYLMVVTALIVKVG +ADTLAPLLR +>PROKKA_00412 +MLAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPIQALATNKLGSVFGTATSALTYRRRL +RQDLSTALPMAAVAFAAALGGAVVAAHLPAGVIRPVILAALIAVAVFTAVRPGLGQVAGV +GPRRSTALARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKVVNLATN +LGALAYFVPSGHAVLGLGLLLGAANLVGGYVGARMAIARGTGFIRVVYLMVVTALIVKVG +ADTLAPLLR +>PROKKA_02287 +MVAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPVQALATNKMGSVFGTATSAITYRRRL +RQDLSTALPMAAVAFVAALAGAVVAASLPAGVIRPVILVALIAVAVFTAVRPGLGKTAGV +GPERRTAVARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKIVNLATN +LGALAFFIPAGHAVLGLGLLLGAANLVGGYVGARMAIARGTGFIRVVYLVVVAALIVKVG +ADTLAPLLL +>PROKKA_02149 +MELFGPVELSVGIVLLVLAAGFSAGWIDAVVGGGGLLQLPVMLLVPGLSPVQALATNKMG +SVFGTAASAATYARRVRPDLRTALPMAAVALLCSLGGAVVATVLPAAVIRPVILVALVGV +ALVTALRPQWGLTQGLKHAGTAHALRALAVGAVVGFYDGVLGPGTGTFLILGLVGVLGYD +FLQASAKAKIVNLATNVGALAFFLPAGHVVLGLGLLLGAANLTGGYVGARMAISRGTGFI +RTVFLVVVCALILRLAWDVFAPLLG +>PROKKA_00645 +MLAAGFAAGWIDAVVGGGGLLQLPALLLVPGLSPIQALATNKLGSVFGTATSALTYRRRL +RQDLSTALPMAAVAFAAALGGAVVAAHLPAGVIRPVILAALIAVAVFTAVRPGLGQVAGV +GPRRSTALARAVALGAAVGFYDGVLGPGTGTFLILGLVLLLKFDFLHASAQAKVVNLATN +LGALAYFVPSGHAVLGLGLLLGAANLMGGYVGARMAIARGTGFIRVVYLMVVTALIVKVG +ADTLAPLLR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000605.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000605.fa new file mode 100644 index 0000000000000000000000000000000000000000..f9e781c9b1cd0ad3f327cc825929cb04a84ac0d6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000605.fa @@ -0,0 +1,35 @@ +>PROKKA_00677 +MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRATGHVTVWATELDE +DDTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGVIQQGLN +RHMVQVNLGTLEAVLPPPEQVPGEDYAHGRRIRAYVVSATRGAKGPSVTVSRSHPGLVRK +LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN +DEKIDIVDHVDDPAAMIANALSPATTVSVEILDADQHSARAVVPEYQLSLAIGKEGQNAR +LAAKLTGWRIDIVGDGVTTSAPGR +>PROKKA_00414 +MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRATGHVTVWATELDE +DDTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGVIQQGLN +RHMVQVNLGTLEAVLPPPEQVPGEDYAHGRRIRAYVVSATRGAKGPSVTVSRSHPGLVRK +LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN +DEKIDIVDHVDDPAAMIANALSPATTVSVEILDADQHSARAVVPEYQLSLAIGKEGQNAR +LAAKLTGWRIDIVGDGVTTSAPGR +>PROKKA_02285 +MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRVSGHVTVWATELDE +DGTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGLIQQGVN +RHMIQVNLGTLEAVLPPPEQVPGEDYSHGRRLRAYVVSATRGNKGPSVTVSRSHPGLVRK +LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN +DEKIDIVEHAEDPAQMIANALSPAKTVSVEVLDADQHSARAVVPEHQLSLAIGKEGQNAR +LAAKLTGWRIDIVGDGSDASAPAR +>PROKKA_02147 +MSALRMLVAERDIPLDRLVPAIEQALLIAYHRTPGAIKGSRVELDRSTGHVTVWAPEVED +DGTCVGEFDDTPNGFGRIAASTARQVIFQRLRDADDAKVLGEFKDREGELVSGVIQQGSH +RHMVQVDLGSLEAVLPPPEQVPGEDYRHGRRIRAVIVSATRGPKGPSVTLSRSHPNLVRR +LFALEVPEIADGTVEITALAREAGHRTKMAVKATRPGVNPKGAAIGEMGSRVRAVMTELG +GEKIDIVEHADDPAEMIKHALSPAQALSVEILDADQHSARAVVPQHQLSLAIGKEGQNAR +LAARLTGWRIDIVGDAAQQPGADAAQQPGADAASEMAPATEAGAEA +>PROKKA_00647 +MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRATGHVTVWATELDE +DDTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGVIQQGLN +RHMVQVNLGTLEAVLPPPEQVPGEDYAHGRRIRAYVVSATRGAKGPSVTVSRSHPGLVRK +LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN +DEKIDIVDHVDDPAAMIANALSPATTVSVEILDADQHSARAVVPEYQLSLAIGKEGQNAR +LAAKLTGWRIDIVGDGVTTSAPGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000606.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000606.fa new file mode 100644 index 0000000000000000000000000000000000000000..159cc70de5d08fc25583414b7c6009922919c2ff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000606.fa @@ -0,0 +1,81 @@ +>PROKKA_00679 +MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP +GSTPAAPGRSAAPKPAAAPSPRAAAPTSNVGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP +AAPAEPKAPQPPATPGSAAPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR +PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP +GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP +RKGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK +VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE +ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL +TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI +DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA +NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA +ADPSRPVQVLGLSTVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD +QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA +TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG +SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSDHLKIESLRRFKDDATEV +REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV +>PROKKA_00416 +MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP +GSTPAAPGRSAAPKPAAAPSPRAAAPTSNAGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP +AAPAEPKAPQPPATPGSAVPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR +PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP +GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP +RRGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK +VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE +ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL +TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI +DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA +NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA +ADPSRPVQVLGLSAVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD +QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA +TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG +SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSEHLKIESLRRFKDDATEV +REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV +>PROKKA_02284 +MMPKQITPAPAPARGGGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGARKGRKS +KRAKRQEFEQAHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVKVLFTLG +EMASANQSLDEDTFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEEANEDEADLEPR +PAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVQHEGEDRRLTFIDTP +GHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKIDKDTAQ +PDKIRGQLTEYGLVPEEYGGDTMFVDVSARNGINIDQLLEAVLLTADAALELTANPSKDA +RGVAVEANLDKGRGAVVTVLVQTGTLRVGDNMVVGSAHGRVRAMFDENGAPVEEADPSRP +VQVLGLSSVPRAGDSFLVTEDDRTARQIAEKREAADRNAQLAKRRKRITLEDFDQAVAEG +KLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLATVDDAI +IIGFNVRPAERVADLADKEGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVALGSAEVRE +VFRSSKWGSIAGSLVRSGLIRRNAQARLVRDGAVVADNLKIESLRRFKDDATEVREGYEC +GIGLGSFNDIKEGDVIETFEMREKPRA +>PROKKA_02145 +MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRGAYPGAGAKGSAK +PAAAAPAAPKPAGGSAPSPAAAKPAAASAPGASAPKPGSAAPQPGSAAPKPGGSAPKPGA +SAPAPAAQKSAPAAPKAPAAPAPQAPAPKPGASAPKPGASAPKPGGAKPAPRPGNNPFTS +KAGSAGPRPGGGRSGGPRPGNNPFAPSQGMRSGREDRAPRPGGPRPAAGAGGPRPGGPRP +AAAGAGGPRPGGPRPNPGMMPKHITPAATPARGGGRGRPGAGGPGGGPGRPGGGPAGRGG +GRGNAQGAFGRGGGARKGRKSKRAKRQEFEQQHTREIGGVKVLKGDGTTVVRLRRGASLA +DFAEKIHADVADLVKVLFTLGEMASANQSLDEETFQLLGGELGYVVQIVSPEDEDKELLE +AFDIDLEAEAAGEDEADLQPRPAVVTVMGHVDHGKTRLLDAIRSSNVTAGEAGGITQHIG +AYQVPVEHEGSERRLTFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNH +AQSAGVPIVVAVNKIDKDSAQPDKIRGQLTEYGLIPEEYGGDTMFVDVSARNNLHIDDLL +EAILLTADAALELSANPDKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHG +RVRAMFDENGTPVEEATPSRPVQVLGLSSVPRAGDSFLVTDDERTARQIAEKREAADRNA +QLAKRRKRITLEDFDQAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVI +HRGVGAITQNDVNLATVDNAIIIGFNVRPAERVADLADKEGVDMRFYSVIYDAIDDIENA +LKGMLKPEYEEVQLGSAEVREVFRSSKWGAIAGSLVRSGLIRRNAQARLVRDGAVVSENL +KIESLRRFKDDATEVREGYECGIGLGNFNDIKEGDVIETFEMQEKPRV +>PROKKA_00649 +MAKVRVHELAKELGITSKEALSTLKDLGEFVSSASSTIEPPVVKKLRNAYPGAGKSAAKP +GSTPAAPGRSAAPKPAAAPSPRAAAPTSNAGAPAPGPAAGRTAAPKPGAAPTPGPAAPTP +AAPAEPKAPQPPATPGSAAPKPGAAAPKPGASAPKPGAPRPGNNPFSPKGGSAGPRPGAR +PGGRGGAPRPGNNPFAPSQGMRSGREDRAPRPGGPRPPAGAGGPRPGGPRPAAGAGGPRP +GGPRPNPGMMPKQITPAPQPARGRGRPGGGPGGGPGRPGGPGGRGGRGNAQGAFGRGGGP +RKGRKSKRAKRQEFEQQHTREIGGVKVPKGDGTTVLRLRRGASLADFAEKIRADVADLVK +VLFTLGEMASANQSLDEETFQLLGDELGYKVQIVSPEDEDKELLEAFDIDLEAEAANEDE +ADLEPRPAVVTVMGHVDHGKTRLLDAIRSSNVIEGEAGGITQHIGAYQVPVEHEGEQRRL +TFIDTPGHEAFTAMRARGAKVTDIAVLVVAADDGVMPQTVEALNHAQSAGVPIVVAVNKI +DKDTAAPDKIRGQLTEYGLVPEEYGGDTMFVDVSARNNINIDQLLEAILLTADAALELTA +NPHKAARGVAIEANLDKGRGAVVTVLVQTGTLRVGDTMVVGSAHGRVRAMFDENGNAVEA +ADPSRPVQVLGLSAVPRAGDSFLVTDDERTARQIAEKREAADRNAQLAKRRKRITLEDFD +QAVAEGKLDTLNLIIKGDASGAVEALEDSLLKIEVGEDEVQLRVIHRGVGAITQNDVNLA +TVDNAIIIGFNVRPAERVADLADREGVDMRFYSVIYDAIDDIENALKGMLKPEYEEVELG +SAEVREVFRSSKWGNIAGSLVRSGLIRRNAQARLVRDGVVVSDHLKIESLRRFKDDATEV +REGYECGIGLGSFNDIKEGDVIETFEMQEKPRV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000607.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000607.fa new file mode 100644 index 0000000000000000000000000000000000000000..cc157056aa40f8c7db88e32df992e0d6262712d8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000607.fa @@ -0,0 +1,20 @@ +>PROKKA_00680 +MADPARAGRLAQRIKVLVAEALRRGVKDDRVEPVTVTEVRVTNDLQHATVYYTVLGDEAT +VAAAHEGIQDNRGILRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA +KAREGASYAGDADPYRTAEPDADADDAPRA +>PROKKA_00417 +MADPARAGRLAQRIKVLVAEALRRGVKDDRVEPVTVTEVRVTNDLQHATVYYTVLGDEAT +VAAAHEGIQDNRGILRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA +KAREGASYAGDADPYRTAEPDADADDAPRA +>PROKKA_02283 +MADPARAGRLAQRIKVLVAEALRRSVKDDRVEAVTVTEVRVTNDLQHATVYYTVLGDEAT +AAAAHEGIQENRGVLRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA +KAREGATYAGEADPYRTSEPGSEADDAPRA +>PROKKA_02144 +MADPARAGRLAQRIKVLVAEALRRAVKDERVEPVTVTEVRVTNDLQHATVYYTVLGDEAV +VAAAQEAIQENRGVLRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA +KAREGAQYAGDADPYRTSGDDDEQD +>PROKKA_00650 +MADPARAGRLAQRIKVLVAEALRRGVKDDRVEPVTVTEVRVTNDLQHATVYYTVLGDEAT +VAAAHEGIQDNRGILRREVGRGLTIRLVPTLEFVADTVPEAAAHLEDVLRAAKERDAELA +KAREGASYAGDADPYRSAEPDADADDAPRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000608.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000608.fa new file mode 100644 index 0000000000000000000000000000000000000000..7e322408801a0ad3cdd8caaada976ed27275837e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000608.fa @@ -0,0 +1,31 @@ +>PROKKA_00681 +MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY +TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR +AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE +ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSEAAAGLFPVRELTEHEAHEL +AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA +>PROKKA_00418 +MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGADKTY +TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR +AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE +ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSEAAAGLFPVRELTEHEAHEL +AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA +>PROKKA_02282 +MDKPQGWTSHDVVGRLRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY +TATIRLGQSTVTDDAEGDVVQTRLANAVTPERVAEQVAALTGPILQAPSAVSAIKVAGRR +AYDRVRAGEDVALQARPVTVHEFTVHEMRRLDGGRLVDLDVTVRCSSGTYVRALARDLGE +ALETGGHLTALRRTAVGPFDVADALTLEELAEGFVMTGLSEAAAGLFPVRELTEDEAREL +AFGRAVAPTGSGEALVAGRAPDGRVVALISDVRRRGADVAKPQLVFAPAEGPGQGGTA +>PROKKA_02143 +MNARTAHAPTPDAPGTEASGVVLVDKPAGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATG +LLVVGVNKATRLLTAITGTDKEYTATIRLGQSTTTDDAEGEVVQTRLANAVTPERVAEQV +AALTGDILQVPSSVSAVKVAGRRAYDRVRAGEDVQLDARPVTVHAFEVEDFRRLDGGRTV +DLDVTVRCSSGTYVRALARDLGEALDTGGHLTALRRTAVGPFRVEDAVDLDALAERFVMT +ELSAAAAGLFPVRELTAHEAAELSFGRAIDPSGELAAAAGASGKAADGLVAGRTPDGTVV +ALLQDGRRSGRDVARPHLVFAPAEGQGKEEAR +>PROKKA_00651 +MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY +TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR +AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE +ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSKAAAGLFPVRELTEHEAHEL +AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000609.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000609.fa new file mode 100644 index 0000000000000000000000000000000000000000..7329a12e3ab2cda94731881e8e5b99c3cef0804f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000609.fa @@ -0,0 +1,20 @@ +>PROKKA_00682 +MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG +DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG +QW +>PROKKA_00419 +MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG +DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG +QW +>PROKKA_02281 +MILDAWFWAGLVIGAVSLAVCVAMTAIRRHPADSSILSVAAVELFLLVYAVAAAVRQLGG +EGLNGPGWEFWGYVVTALLVPVIAVAWAVTDKTRWSNLVLAVVGPTVVVMLHRMQVIWFG +QW +>PROKKA_02142 +MILDAWFWTGAVVGGLSFVVCLAMTALRRHPADSSIVSVAAVELFLLVYGVVGAFRQLGG +QPLNGPTWEFWGYVLTALLVPVIAVAWAVTDKTRWSNLVMAVAGPTVVVMLHRMQVIWFG +QW +>PROKKA_00652 +MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG +DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG +QW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000611.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000611.fa new file mode 100644 index 0000000000000000000000000000000000000000..708deeabba352146ec286804257dd7c54f8026f7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000611.fa @@ -0,0 +1,35 @@ +>PROKKA_00684 +MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA +VHHPEVPHVDIISPEQRVVLLDEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV +VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG +DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG +VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV +EKLVAQITQDVDEARAILATTPSDR +>PROKKA_00421 +MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA +VHHPEVPHVDIISPEQRVVLLDEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV +VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG +DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG +VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV +EKLVAQITQDVDEARAILATTPSDR +>PROKKA_02279 +MLVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARERDALAVAVTFSPHPRS +VHRPDEPHVDILGPQQRAVLLSETGLDALLMQRYTLEFADQSPEEFVLSMFVRGLNAAVV +VVGHDVRFGRGNVGDFAEMVRLGALHGFEVEAVEEHPAEIGDEPERRCSSTWVREALAAG +DVAQAAAILGRHHTLDGEVVHGFARGRELGFPTANLAPEAEGMIPADGVYAGWVHDVQGE +AWPAAISIGSNPTFEGVSRVVEAHVIDRPEERVEDFDLYGQHIEVEFVQRLRGMVAYEGV +EKLVAQMTQDVEQARAILAATPSDR +>PROKKA_02140 +MLVWNSMAEVPTDLPRTVVALGNFDGVHRGHRAVLERVVEIAHERGQLAVAVTFTPHPRV +VHQPGLEHVEILSPEQRAVRLDETGIDALFLQHYTLEFAAQTPEEFVTSMFVRGLNAAAV +VVGRDVRFGRDNAGDFAEMVRLGGVHGFDVVAVEDLPAEDGDGERRCSSTWIRELLAAGD +VAHAAEVLGRNHVVAGAVVHGFARGRELGFPTANLEADAAGMIPADGVYAGWVHDAHGSV +WPAAVSIGSNPTFEGVSRVVEAHVIDRPEEPVEDFDLYGQQIEVEFVERLRGMVAYEGVE +KLVAQMHQDVDQARAVLAAAPQPAGRV +>PROKKA_00654 +MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA +VHQPEVPHVDIISPEQRVVLLEEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV +VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG +DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG +VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV +EKLVAQITQDVDEARAILATTPSDR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000612.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000612.fa new file mode 100644 index 0000000000000000000000000000000000000000..d2e8375aebfe4e909fa8ba47bfffd52764e63970 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000612.fa @@ -0,0 +1,30 @@ +>PROKKA_00685 +MSAPEPGAPPAVPNLPGRPARARRAGPNPFETGGEHYDAVRPSYPAAAVDRVLAGTADGA +DVVELGAGTGLFTRLLAARPADRVRTVTALEPSASMRAVLEREVAAGTGGRVRAVPGTGE +ATGLPAASADVVVAAQAWHWMDPAAASAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTRI +MHAGDVHAARPEQRRFAAPFGAEEHARWAWTQPMTAAGLHGLMASRSYWLRADERIRSRM +TANLDWYLHEHLGHAADAVLQVPYVTVAWWAAPVRGGRPR +>PROKKA_00422 +MSAPEPGAPPAVPNLPGRPARVRRAGPNPFETGGEHYDAVRPSYPAAAVDRVLAGTADGA +DVVELGAGTGLFTRLLAARPADRVRTVTALEPSASMRAVLEREVAAGTGGRVRAVPGTGE +ATGLPAASADVVVAAQAWHWMDPAAASAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTRI +MHAGDVHAARPEQRRFAAPFGAEEHARWAWTQPMTAAGLHGLMASRSYWLRADERIRSRM +TANLDWYLHEHLGHAADAVLQVPYVTVAWWAAPVRGGRPR +>PROKKA_02278 +MTGPGPGVPRLPGRPARARREAGNPFADAGGEHYDAVRPSYPAEAVAWVLEGLGQGLDRG +LDVVEVGAGTGLFTRSLTALPVERVRSVAAVEPAASMRAVLERDVAAGSDGRVRAVPGTA +EATGLPEASADVVVAAQAWHWVDPAAGSAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTR +IMHAGDVHAARPELRRFAAPFGAEEHARWTWTLPQTAADLHGIMASRAYWLRASETTRAK +MSANLDWYLHEHLGHGPDEAIVVPYVSVAWQASST +>PROKKA_02139 +MSERGLPDSGAAPRPAGGYVPALPSRPAITRTGGVNPFEVSPEQGEQYDAVRPSYPAAAV +DWVLDGLGAGLDVVETGAGTGLFTRRLAERPAERVRSVAAVEPSEAMRAVLERDVAAGSA +GRVRAVDGTGEATGLADGCADVVVAAQAWHWMDAERASAEAARVLRPGGRLAAVWNQLDV +TVPWVHRLTRIMHAGDVHAAAPERRRFAAPFGPEEHARWSWSLTTTPAGLHALMASRSYW +LRAREGTRARMTANLDWYLHEHLGHAAGEELTLPYVTVAWRAPAPAR +>PROKKA_00655 +MSAPEPGASPAVPNLPGRPARARRAGPNPFETGGEHYDAVRPSYPAAVVDRVLAGIADGA +EVVELGAGTGLFTRLLAARPADRVRTVTALEPSASMRAVLEREVAAGTGGRVRAVPGTGE +ATGLPAASADAVVAAQAWHWMDPAAASAEAARVLRPGGRLAAVWNQLDTAVPWVHRLTRI +MHAGDVHAARPEQRRFAAPFGAEEHARWAWTQPMTAAGLHGLMASRSYWLRADERIRSRM +TANLDWYLHEHLGHAADAVLQVPYVTVAWWAAPVRGGRPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000613.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000613.fa new file mode 100644 index 0000000000000000000000000000000000000000..220bd0867cbd4a90fa68cc8eccdcce42fc7efb06 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000613.fa @@ -0,0 +1,34 @@ +>PROKKA_00686 +MSTPPVPHSPAPSSFPLRPPAPPLDLPLIGHGYPALLRTPRARWWNPLASFGLVLAGLVG +LLVLGGVLGALALIATSGPALLGAADPTDVTDLDLYSAPMVLLNNLLLAALIGVALLAVA +LGHPVAARFVHSVEGRVRWRWLARCVVVLTPLFLAYVLGAWALDGAPTAPRAQDWVWLLV +MAFVLTPFQAAGEEYLFRGWLLLAVGTWIRRPVVAAAVTAVLSAATFSLAHGSLDPWILL +DLAAFAVAAVLLTWRTGGLEAAVALHVVNNVVIIAVGTLVGTVEDSYVGAETAGSPAATL +LSVAVVAVATALLLWQARRAGIARTVPVTVGARP +>PROKKA_00423 +MSTPPVPHSPAPSSFPLRPPAPPLDLPLIGHGYPALLRTPRARWWNPLASFGLVLAGLVG +LLVLGGVLGALALIATSGPALLGAADPTDVTDLDLYSAPMVLLNNLLLAALIGVALLAVA +LGHPVAARFVHSVEGRVRWRWLARCVVVLTPLFLAYVLGTWALDGAPTAPRAQDWVWLLV +MAFVLTPFQAAGEEYLFRGWLLLAVGTWVRRPVVAVAVTAMLSAAAFSLAHGSLDPWILL +DLAAFAVAAVLLTWRTGGLEAAVALHVVNNVVIIAVGTLVGTVEDSYVGAETAGSPAATL +LSVAVVAVATALLLWQARRAGIARTVPVTVGARP +>PROKKA_02271 +MTTASPPPPPPRGRLAPAAAPTPPGRRLDLPIIGAEYPQLLRTPRSRWWHPLLSAGLVLG +SVLVLLAVLTLPMMLALVSEVGWDVFASADPADLARVEEALFSAPMMLLNNLMLAAFIGI +AVLAVAVCHPVAARFVHSVQGRIRWRWLLRAHLVLLPLFLVYVLGTWALDGAPTAPRAED +WVWLVVMAFLLTPLQAAGEEYLFRGWLLLAIGSWFRRPLPAIVLAAAVSAVTFSLAHGSF +DPWILLDLSVFAVAAVLLTWRTGGLEAAVALHVVNNVVVIVFGTLAGTVNESFVDVETTG +SPLATLVSAAVIALSTALLLWQARRAGIARTVPVSVGARP +>PROKKA_02138 +MRTPRARWWNPLASFGMVLLGVGVLTVLLTVPMALVLFQQLDPGELWSAEGPSEASLELA +LFSAPMVLLNNLLLAALTGVALLAVLVAHPVKARFLHSVEGRVRWRWLLRAHLVLLPLFL +VYVLGTWALDGARVAPRPEDWGWLLAMALLVTPFQAAGEEYLFRGWTMLALGTWIRRPGV +AVAVTAAVSAVAFALAHGSLNPWILLDLGVFAVAAVLLTWRTGGLEAAVALHVVNNVVIL +AFGTVTGLATESYVTASTQGDPLATLVSAAVTALATVLLLWQAKRAGVARTVPSAVGARP +>PROKKA_00656 +MSTPPVPHSPAPSSFPLRPPAPPLDLPLIGHGYPALLRTPRARWWNPLASFGLVLAGLVG +LLVLGGVLGALALIATSGPALLGAADPTDVTDLDLYSAPMVLLNNLLLAALIGVALLAVA +LGHPVAARFVHSVEGRVRWRWLARCVVVLTPLFLAYVLGAWALDGAPTAPRAQDWVWLLV +MAFVLTPFQAAGEEYLFRGWLLLAVGTWIRRPVVAAAVTAVLSAATFSLAHGSLDPWILL +DLAAFAVAAVLLTWRTGGLEAAVALHVVNNVVIIAVGTLVGTVEDSYVGAETAGSPAATL +LSVAVVAVATALLLWQARRAGIARTVPVTVGARP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000614.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000614.fa new file mode 100644 index 0000000000000000000000000000000000000000..d162c8ef39ed1a2cd583678409c64f4e82110b35 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000614.fa @@ -0,0 +1,15 @@ +>PROKKA_00687 +MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV +GRRRRMLGYLQKVDIERYRALIERLGLRK +>PROKKA_00424 +MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV +GRRRRMLGYLQKVDIERYRALIERLGLRK +>PROKKA_02270 +MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV +GRRRRMLGYLQKVDIERYRALIERLGLRK +>PROKKA_02137 +MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV +GRRRRMLGYLQKVDIERYRALIERLGLRK +>PROKKA_00657 +MALDPAVKQQIIKEYATHEGDTGSPEVQIAVLSRRIKDLTEHLKEHKHDHHTRRGLMALV +GRRRRMLGYLQKVDIERYRALIERLGLRK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000615.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000615.fa new file mode 100644 index 0000000000000000000000000000000000000000..44f200bf82062f82d22c4722d259964e890f5a8d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000615.fa @@ -0,0 +1,70 @@ +>PROKKA_00688 +MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE +GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ +VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH +SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP +FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA +SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL +TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST +GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST +LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT +AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK +IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG +ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK +IDDRGKLSLSPVVAESDALAETADAIESSQIEA +>PROKKA_00425 +MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE +GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ +VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH +SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP +FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA +SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL +TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST +GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST +LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT +AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK +IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGGSAEAARSAVNAIANPQVPEVG +ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK +IDDRGKLSLSPVVAESDALAETADAIESSQIEA +>PROKKA_02269 +MEGPEITFAEAVIDNGAYGKRTIRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE +GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ +VVVTVTSIAPDEIYDTVAINAASVSTQLSGLPFSGPIGGVRMALVDDGAGKRQWVAFPKH +SQLQDAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGASAPTEEVVAEGLEAAKP +FIRALCEAQADLVKRAGKDPVDVPVFKDYEDDAFEAVEKLATDRLTEIFSIGDKQTRESA +SDAYHVEVMDELAGEDKPFAERRGEIAKAYGSVTKQVVRQRILKDQVRIDGRGLTDIRKL +TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYLHHYNFPPYST +GETGRVGSPKRREIGHGALAERAMVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST +LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT +AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK +IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG +ERYLGTVVKLTTFGAFVSLTPGKDGLLHVSELRKLNEGKRVDDVEDVLGVGQKVQVEITK +IDDRGKLSLSPVVAESDADAETADAIESSQTEA +>PROKKA_02136 +MEGPEITFAEAVIDNGRHGTRTVRFETGRLAQQAAGSAMVYIDEETSMLSATTVGKHPRE +GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFTKGIRNEVQ +VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALLDDGSGQRQWVAFPKH +SQLEDAVFNMAVAGRVAGDDVAIMMVEAEAGENAWTLVKERGAQAPTEEIVAEGLEAAKP +FIRALCEAQADLAARAGKAPVEVPVFKDYEQDAYDAVEKIATDRLTEIFSIADKQEREAA +SDAYHLEVIEELAGEGKDFAERKGEVAKAYGSLTKQIVRRRILKDQVRIDGRGLTDIRKL +TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYMHHYNFPPYST +GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST +LSLLNAGVPLRAHVAGIAMGLVSAEVEGQTQYAALTDILGAEDAFGDMDFKVAGTSEFVT +AIQLDTKLDGIPASVLAGALTQAREARLHILSVLEAAIDQPDELAPTAPRIISVRIPVDK +IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG +ERYLGTVVKLTTFGAFVSLTPGKDGLLHISELRKLNEGKRVEDVEDVLGVGQKVQVEITK +IDDRGKLSLAPVVADEDAAAGESREEDEEA +>PROKKA_00658 +MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE +GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ +VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH +SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP +FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA +SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL +TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST +GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST +LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT +AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK +IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG +ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK +IDDRGKLSLSPVVAESDALAETADAIESSQIEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000617.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000617.fa new file mode 100644 index 0000000000000000000000000000000000000000..0c03895bba732a0d0daa8c4e8372aec1261d0eed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000617.fa @@ -0,0 +1,30 @@ +>PROKKA_00690 +MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA +GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN +FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP +DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV +LGLRTVASRPGLTYGLDGYLDLG +>PROKKA_00427 +MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA +GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN +FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP +DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV +LGLRTVASRPGLTYGLDGYLDLG +>PROKKA_02265 +MTDAPAPSAVPADDAVPRVAILGAGGKMGRHAVPAVREAAALELVAELGSADPLEAILDA +GATHVLDLTVPDVSPRNAAFAVEHGLHTVIGTSGWGPERREALAAQLAEHPGVGVLIAPN +FSVGSVLASAFAAKAARFFESVELIEMHHPAKLDAPSGTAVRTAELIGQARREAGVPPSP +DATERDPDGSRGAVVDGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGIV +LGLRTVASRPGLTYGLDGYLDLG +>PROKKA_02133 +MTETTPRTPVPGDATPRVAILGASGKMGRHAVPAVRAAQGLELVAELGSGDPLQAVLDAG +ATHVLDLTVPDASPENVAFAVEHGLHVVVGTSGWGAERRAALEERLAARPGVGVLIAPNF +SVGSVLASAFAARAARWFESVEVVELHHPAKLDAPSGTAVRTAEMIAASRAEAGVGPSPD +ATERDPDGARGAVVDGVHVHAVRLRGLEAHQEVLLGGPGEQLTVRHDAFDRQAYMPGVVL +ALREVAGRPGLTYGLDAVLGLD +>PROKKA_00660 +MTETRTPSAVSAPDDVPRVAILGARGRMGRHAVPAVRAAEGLELVAELGSQDRLDAVLDA +GATHVLDLTVPDASPENVAFAVEHGLHTVVGTSGWVPERRERLEAQLAEHPGVGVLIAPN +FSVGSVLASAFAAQAARYFESVELVELHHPDKVDAPSGTAVRTAELIGAARDAAGVPVSP +DATEHDPDGARGAVVHGVHVHAVRLRGLEAHQEVLLGGPGEQLVVRHDAFDRGAYMPGVV +LGLRTVASRPGLTYGLDGYLDLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000619.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000619.fa new file mode 100644 index 0000000000000000000000000000000000000000..1593b538e13d8284a5fbe5e2a27139cf78752bfb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000619.fa @@ -0,0 +1,35 @@ +>PROKKA_00693 +MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDRGADGLVVTGTTGE +TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY +NKPNQAGIRAHFETVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL +QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGA +RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATRDELSVIRADLAE +AGITF +>PROKKA_00430 +MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDRGADGLVVTGTTGE +TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY +NKPNQAGIRAHFETVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL +QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGS +RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATPDELSVIRADLAE +AGITF +>PROKKA_02261 +MSAVRSASAPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDGGADGLVVTGTTGE +TSTLTDEENLAMFRTVVEAVGDRAKVVAGTGTNDTAHTLELSRRAKETGVDGLLLVTPYY +NKPNQAGIRAHFEAVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL +QSTTTVLAHSDLDLYSGDDGATLPLMALGAVGVVSVAAHVAPGLYRKLVDAVHAGDLAAA +REHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQASADELSDIRADLAE +AGITF +>PROKKA_02131 +MTDARRTVNPSELPFGTVVPAMVTPMDQDGAVDLQAAAVLATHLVDQGADALVITGTTGE +TSTLTDEENLAMFRTVVEAVGERARVIAGTGTNDTHHSLELSRRAAEIGVHGLLLVTPYY +NKPNQAGIRRHFETIADGVDLPIMLYDIPGRSVMPIQPETLVALAAHPNITALKDAKGDL +QSTTTVLAHTDLHVYSGDDGATLPLMAMGAVGVVSVAAHVAVPGYRALVDAVHAGDLRAA +RDAHFALDPVQRGIMSHVQGAVAAKTVLAGQGIIPTAAVRLPLVAADDAELAAIRADLAE +AGISF +>PROKKA_00663 +MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAVLAEHLVDRGADGLVVTGTTGE +TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY +NKPNQAGIRAHFEAVADGVDLPIMLYDIPGRSVMPIEPETIIALAQHPNIRALKDAKGDL +QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGA +RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATPDELSVIRADLAE +AGITF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000620.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000620.fa new file mode 100644 index 0000000000000000000000000000000000000000..86b4ddf669d7dff563023998e46a9c0987450168 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000620.fa @@ -0,0 +1,55 @@ +>PROKKA_00694 +MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD +LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE +HRIKPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL +DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF +SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD +EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG +ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN +VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFLSIITV +VNRQTGAIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTV +GTWVNRKLRRRPMIIPVVLEA +>PROKKA_00431 +MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD +LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE +HRIKPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL +DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF +SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD +EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG +ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN +VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFISIITV +VNRQTGAIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTV +GTWVNRKLRRRPMIIPVVLEA +>PROKKA_02260 +MTPGTRLSTPPKLKKGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD +LILPDFDYIRDRMDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE +HRIKPRTRVVKEDEIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL +DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF +SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYKDD +EVVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG +ANVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN +VILAGNGTVVDMTDGLVKVVGEVDCGYVYVDGSSVGEISDSDLKDRRVLGEEGFISIITV +VNRQTGSIVSGPDIHARGVAEDEKVFEDIKPKIARALEEAVQSSKDHTAHQLQQVVRRTV +GTWVNRKLRRRPMIIPVVLEA +>PROKKA_00464 +MTRSSRNSSSRRRGGGQSRRPRSSGAPGQLAKGGLRITPLGGLGEIGRNMTVFEHQGKLL +IVDCGVLFPEDHQPGIDVILPDFTSIRDRLQDVVGVVLTHGHEDHIGGVPYLLKERPDIP +LIGSELTLAFIEAKLKEHKIVPKTHMVVAEDKRHMGPFELEFVAVNHSIPDALAVAIRTE +AGLILHTGDFKMDQFPLDRRITDLRHFARLGEEGVDVFLTDSTNAEVPGFTISERELTPA +IDHVFRTAPKRIIVSSFASHVHRIQQVLDAAHASGRKVAFVGRSMVRNMGIAGDLGYLKI +PKGLVVDFKKLQDMPDEKIALISTGSQGEPMAALGRMANQTHQIKLNKGDTVLLASSVVP +GNETSITGIINKFTDMGVNVVHKGNAKVHVSGHASAGELVYCYNIVQPRNVMPVHGEAAH +LHANAELAKKTGLPEDRVFITKDGDVLDLVDGRVSVAGKVEAGLVYVDGDTIGKVTEGTL +EERRTMQEAGVVTVVAIVDPDTNQLAEPLEFMTKGFIQDASVFKGAAEKVKSALSRSNVQ +DIDDIEKLERVIGDAVTRHLERAYRRAPLVTVVVVDA +>PROKKA_00664 +MTAGTRLSTPPKLKRGTCRIVQLGGLEEVGRNMVTFEIDGKILIVDCGVLFPEEHQPGVD +LILPDFDYIRDRVDDVVGIVLTHGHEDHIGAVPYLLRLRDDIPVIGSKLTLALIEAKLEE +HRITPRTRVVKEDDIVEFGPFECEFVAVNHSIPDALAVAIHTDAGTILHTGDFKMDQLPL +DGRITDLRAFARLGEEGVDLFMTDSTNAEVPGFTTTEAEIGPTLERYFATAKRRIVVASF +SSHVHRVQQVLDAAHKHGRKVAFGGRSMIRNMTIAAKLGYLNVPNGILVDIRKVDKYRDD +EIVLMVTGSQGEPMAALSRMANGDHQVQLEEGDLVVLASSLIPGNENSVFRVINGLMKLG +ATVVHKGMAKVHVSGHASEGELLYCYNIVEPEFVMPVHGETRHLIANGRIAEKTGVPAEN +VILAGNGTVVDMTDGLVKVVGEVECGYVYVDGSSVGEISDSDLKDRRVLGEEGFLSIITV +VNRQTGTIVSGPDVHARGVAEDEKVFEEIKPKIVRALEEAVQSSKDHTAHQLQQVVRRTA +GTWVNRKLRRRPMIIPVVLEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000621.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000621.fa new file mode 100644 index 0000000000000000000000000000000000000000..32ce610a1bcba7820d536b8adc12f30ff859db44 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000621.fa @@ -0,0 +1,89 @@ +>PROKKA_00695 +MPAVSAVRGSLVGMATRTSPTRSSSSSATSRSGSAGRRGSGRKGSTATVPEADRPAAPLR +ALHTLWMGLATPVGAGFRKLGPDVRIDREERRDGTGLVLLLLAALIAAVEWWGLRGTAVG +RVVHGVVGGTVGWFALLVPIALLVVAVRCFRHATDHRANGRIIIGLLMATVAGSGIAHLV +GGVPSAADAFEDMLGAGGMVGYLATAPLASLLTPVPVWVLMILLAFFSVLVLTATPVGSI +PQRIAGGYDWLTGQDPEGASEQRAARRAERRRAREERREAEDLAAPLSVDAETGRTHPDH +DQSYLDGPAAGAHAAGASRPGLFARLFGGRRAREEQAADAAPEHTASTAYDSPVIHEAEV +GSHAAPEAETTQVLPRPAPRRAARGEQGVFDSEQAAADARDAGRDASDDFDPWVDEDDAP +EDADAEPQPPAGVRRPTAADRALEQVREHARAQREAAAPAAAAPEEDAGEDTPFALDDAP +RQGSGAAAPSSSSAVPASTPAPVPPVTAEPARGTQSELGGDVSYTLPQSALLPAGPQPKE +RSEANDRVVAALTTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYA +VASSDVRILSPIPGKRAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGY +VVANLAKMPHMLVAGATGAGKSSFVNSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVP +HLVTPIITSPKKAAEALQWVVKEMDTRYDDLAAFGYKHVDDFNKAVRAGQVKLPPDSKRV +LRPYPYLLVIVDELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIK +ANVPSRMAFATSSVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHA +VVEHVKSQMQVQYRADVIPEKTEKVIDEDIGDDLDLLLQAVELVVTTQFGSTSMLQRKLR +VGFAKAGRLMDLMESRGVVGPSEGSKARDVLVKPDDLADVLATISGDTPPSATSGDGDAS +AGTGDGDASASAAPRDLVQEDLDSRPAAVDWNDEDDDEGSEDAWQLTGR +>PROKKA_00432 +MATRTSPTRSSSSSATSRSGSAGRRGSGRKGSTATVPEADLPAAPLRALHTLWMGLATPV +GAGFRKLGPDVRIDREERRDGTGLLLLLLAALIAAVEWWGLRGTAIGRVVHGVVGGTVGW +FALLVPIALLVVAVRCFRHATDHRANGRIIIGLLMATVAGSGIAHLVGGVPSAAEAFEDM +LGAGGMVGYLATAPLASLLTPVPVWVLMILLAFFSVLVLTATPVGSIPQRLAGGYDWLTG +QDPEGASERRAARRDERRRAREVRREAEDLATPLSVDAETGRTHPDHDQSYLDGPAAGAH +AAGASRPGLLARLFGGRRAREDQAADAAPEHTAGTAYDSPVIHEAEAGSHAAPEAETTQV +LPRPAPRRAARGEQDVFDAERAAANARDADQDASDDFDPWVDEDDAPEDADAEPQPPAGV +RRPTAADRALEQVREHARAQREAAAPAAASLEEDAGEDTPFALDDAPGQGSGTAASSSAV +PASTPAPVPPVTAEPARGTQSPLGGDVSYTLPQSALLPAGPQPKERSEANDRVVAALTTT +FTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYAVASSDVRILSPIPGK +RAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGYVVANLAKMPHMLVAG +ATGAGKSSFVNSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVPHLVTPIITSPKKAAE +ALQWVVKEMDTRYDDLAAFGYKHVDDFNKAVRAGQVKLPPDSKRVLRPYPYLLVIVDELA +DLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIKANVPSRMAFATSSVT +DSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHAVVEHVKSQMQVQYRA +DVIPEKTEKVIDEDIGDDLDLLLQAVELVVTTQFGSTSMLQRKLRVGFAKAGRLMDLMES +RGVVGPSEGSKARDVLVKPDDLADVLATISGDTPPSATSGDGDASASAGPRDLVQEDLDS +RPAAVDWNDEDDDEGSEDAWQLTGR +>PROKKA_02259 +MVLPRPTRRRPARGAQGVFDAERADDPAGSRDADRDASDDFDPWVDEEDAPEDADAEPTP +PAGVRRPTAADRALEQVREHARAQREAAAAAEEPAEDADVDLEVEEPGRAAGPAAPSSPA +AAVPSSTPEPVPPVTAEPARGTQSELGGDVSYTLPQSALLPAGPQPKERSEANDRVVAAL +TTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYAVASSDVRILSPI +PGKRAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGYVVANLAKMPHML +VAGATGAGKSSFVNSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVPHLVTPIITSPKK +AAEALQWVVKEMDTRYDDLAAFGYKHVDDFNKAVRAGQVKLPPDSKRVLRPYPYLLVIVD +ELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIKANVPSRMAFATS +SVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHAVVEHVKSQMQVQ +YREDVVPEKTEKVIDEDIGEDLDLLLQAVELVVTTQFGSTSMLQRKLRVGFAKAGRLMDL +MESRGVVGPSEGSKARDVLVKPDDLADVLATISGDAPPSGGSGEGGAPAAAPAAPASAGP +RDLVQEDLDARPAAQSWDDEDDDEGSEDAWQLTGR +>PROKKA_02130 +MATRTSPARSSSSSAKSRSGSSRPAKGSSGKGASAASPDLDRQPAFARAVRTGWMALATP +VGAAVRKAGPDVRIARDDRRDGTGLLLVLVALLVAAVEWWGLRETAVGGVVHDVVGGTVG +WFAFLLPVVLGVVAVRCFRHPLDHRANGRIVIGLLLATVAGSGIAHLVGGLPSAAESFAD +VLHAGGIVGYLATVPLASLLTAVPVWALMVALAVFSLLVITATPLGSIGSRLRGAYAWLT +GQDAEDAEARREQRRAERADRREAGEHRGEQTTADLFGDDRPGGRTHPDHDQSYLDAHGS +SAAPAPARRPGLLARLFGRGHEEPAPAGRVSAPRAYESAVVEEAPAASRAASGSHAADEA +PAAAVEPARPARRRNAAPRRAAATEVFDAEAPRGRRSAPPADDDFDPWVDEDSADDLDRA +DDADTGALEVVPPAGVKRPTAADRALEQVREHARSQREATVEEAEKAEEHDDEAWDEHET +LVLPTAAASAPAPAPAAVVPSVSRPEPVPEVTPEPARPSRPPQDGGHPYELPQSALLPAG +PQPKERTESNDRVVQALTTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEK +NIAYAVASSEVRILSPIPGKRAIGIEIPNTDKEVVALGDVLRSQAAQRNDHPMIMGVGKD +VEGGYVVANLAKMPHMLVAGATGAGKSSFVNSMIVSILMRSTPDEVRMVMVDPKRVELTA +YEGVPHLVTPIITSPKKAAEALQWVVKEMDTRYDDLAAFGFKHVDDFNRAVRAGEVKLPP +DSKRVLRPYPYLLVIVDELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVV +TGLIKANVPSRMAFATSSVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNE +SEIHAVVEHVKAQMQVQYREDVVPEKSEKVIDEDIGDDLDLLLQAVELVVTTQFGSTSML +QRKLRVGFAKAGRLMDLMESRGVVGPSEGSKARDVLVKPDDLADVLATINGDTPPSRPAA +PASAAAPAPAPAAATEAAPDRWASADLVGDDLDSRPAATSWDGEDDDEGSEDAWQLTGR +>PROKKA_00665 +MATRTSPTRSSSSSSATSRSGSAGRRGSGRKGSTATVPEADRPAAPLRALHTLWMGLATP +VGAGFRKLGPDVRIDREERRDGTGLVLLLLAALIAAVEWWGLRGTAVGRVVHGVVGGTVG +WFALLVPIALLVVAVRCFRHATDHRANGRIIIGLLMATVAGSGIAHLVGGVPSAADAFED +MLSAGGMVGYLATAPLASLLTPVPVWVLMILLAFFSVLVLTATPVGSIPQRIAGGYDWLT +GQDPEGASEQRAARRAERRRAREERREAEDLATPLSVDAETGRTHPDHDQSYLDGPAAGA +HAAGASRPGLFARLFGGRRAREEQAADAAPEHTASTAYDSPVIHEAEAGSHAAPEAETTQ +VLPRPAPRRAARGEQGVFDAEQAAADARDAGRDASDDFDPWVDEDDAPEDADAEPQPPAG +VRRPTAADRALEQVREHARAQRESAAPAAARQEGDAGEDTPFALDDAPGQGSGAAAPSSS +SAVPASTPAPVPPVTAEPARGTQSELGGDVSYTLPQSALLPAGPQPKERSEANDRVVAAL +TTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYAVASSDVRILSPI +PGKRAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGYVVANLAKMPHML +VAGATGAGKSSFVNSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVPHLVTPIITSPKK +AAEALQWVVKEMDTRYDDLAAFGYKHVDDFNKAVRAGQVKLPPDSKRVLRPYPYLLVIVD +ELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIKANVPSRMAFATS +SVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHAVVEHVKSQMQVQ +YREDVIPEKTEKVIDEDIGDDLDLLLQAVELVVTTQFGSTSMLQRKLRVGFAKAGRLMDL +MESRGVVGPSEGSKARDVLVKPDDLADVLATISGDTPPSAASGDGDASASAAPRDLVQED +LDSCPAAVDWNDEDDDEGSEDAWQLTGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000625.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000625.fa new file mode 100644 index 0000000000000000000000000000000000000000..1453eca86938b3a6748be01f47b42f8a28ff5305 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000625.fa @@ -0,0 +1,15 @@ +>PROKKA_00700 +MRESEFRRLMDEEFGPARAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCDLHEIPQ +ERRLGRDVPPKR +>PROKKA_00437 +MRESEFRRLMDEEFGPARAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCDLHEIPQ +ERRLGRDVPPKR +>PROKKA_02254 +MRVSEFQRLMDEEFGPGRAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCELHDIPE +ERRLGRDVPPKR +>PROKKA_02126 +MTEFQRLMEDEFGPARAGLVADSLHLPGFDATASEALAAGADPKDVWRAVCDLHEIPAER +RLGRDVPPTR +>PROKKA_00670 +MRESEFRRLMDEEFGPARAGLVADSLHLPGLDTTATAALAAGVDPRRVWLAVCDLHEIPQ +ERRLGRDVPPKR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000626.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000626.fa new file mode 100644 index 0000000000000000000000000000000000000000..b17557058e3bf1217f09d3fb7561e93737c22b47 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000626.fa @@ -0,0 +1,36 @@ +>PROKKA_00704 +MSKVTDREKALEAALAQIDKQFGKGSVMRLGDQTQAPVEVIPTGSVAMDVALGIGGLPRG +RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARQLGVDTDALLVSQP +DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKVT +GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG +NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG +QGKENARRFLKDNPDLANEIEERILTKLGIGVAPEAEDDEAPALTAVPGDTAAG +>PROKKA_00438 +MSKVTDREKALEAALAQIDKQFGKGSVMRLGDQTQAPVEVIPTGSVAMDVALGIGGLPRG +RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARQLGVDTDALLVSQP +DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKVT +GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG +NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG +QGKENARRFLKDNPDLANEIEERILTKLGIGVAPEAEDDEAPALTAVPGDTAAG +>PROKKA_02253 +MSKTPDREKALEAALAQIDKQFGKGSVMRLGDQTQTPVEVIPTGSVAMDVALGIGGLPRG +RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARKLGVDTDALLVSQP +DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKIT +GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG +NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG +QGKENARRFLKDNPDLAQEIEERILTKLGIGVDPEAEADEAPALTAVPGDTAAG +>PROKKA_02125 +MSKASATEKVATEREKALEAALAQIDKQFGKGSVMRLGERSQAPVEVIPTGSVAMDVALG +IGGLPRGRVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARKLGVDTD +ALLVSQPDTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMS +QALRKVTGRLHQTNTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLK +EAGSPVGNRTRVKIVKNKMAPPFKQAEFDILYGEGISKEGSLIDMGVEEGIVKKSGAWFT +YDGDQLGQGKENARRFLKDNPDLADEIEHRIFTKLGIGADPQAEDDAEGETPALQAVAGD +VAAG +>PROKKA_00671 +MSKVTDREKALEAALAQIDKQFGKGSVMRLGDQTQAPVEVIPTGSVAMDVALGIGGLPRG +RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARQLGVDTDALLVSQP +DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKVT +GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG +NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG +QGKENARRFLRDNPDLANEIEERILTKLGIGVAPEAEDDEAPALTAVPGDTAAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000627.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000627.fa new file mode 100644 index 0000000000000000000000000000000000000000..4e82a409264d93962e19f94a055e718c368de260 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000627.fa @@ -0,0 +1,33 @@ +>PROKKA_00705 +MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAS +DAARDAAPARDAGAPAEDVPDPAPGAAPDLGALLTRASDLPSPAPGAGPRSLPWSGREDT +RADTERRGRRRAPAKRSGRTRPREDGRAPAEPAPQTDRPRRRPGPAPLPTAPREREEAAR +EVVLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRS +KGLARRALGHELQQKGVDREIAAEALEAIDGEDERAAALDLVRRRLRGRTVPGGASPEAR +AERDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE +>PROKKA_00439 +MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAA +RDAVPARDAGTPAGDGSDPAPGAAPDLGALLTRASDLPSPAPGAGPRALPWSGREDTRAD +TERRGRKRATTPPRRGRPRDEGRPAVDPRPAVETDRPRRRPGPAPLPTAPREREEAAREV +VLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRSKG +LARRALGHELQQKGVDREIAAEALEAIDGEDERTAALDLVRRRLRGRTVPGGASPEARAE +RDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE +>PROKKA_02252 +MTRARRDAGGGAARRSERNGRSGAASGASAFDDARDTDAARMWLELAGVPEADAPAAARS +VDEPPAAPTDGPDDPPLATAENGSSAAPSGPAAAPDEAGPPDLGSLLGRASDLPSPAPGA +AARVLPWSADARPERGGRGARGTSSEARRARRRTARLAAADVASAPEAASTPEEANARED +ARPRRRPGPAPLPAEPREREEAAREVVLRQLALGPRSRGQLEAKLADREAEPELIARVLD +RFEEVRLVDDAAFAEVWVRSRHRSKGLARRAIGHELRQKGVDRDVAAEALEAIDGEDERA +AALELVRRRLRGRRVPAGNGPHARAERDKVTRRLVGMLGRKGYGGGLAFAVVKEVLGELE +E +>PROKKA_02124 +MPEDPREREEAARQVVLRQLAMGPRSRRQLERKLADREAEPELVERVLDRFEEVSLVDDA +AFAEVWVRSRARGKRLSRRAISRELHDKGVDRDVAEEALAAIEPEDERQAALELVRSKMR +GRPAPAADGPEGRAERDKVTRRLVGMLGRKGYGPGLAFGVVKEVLAELDEA +>PROKKA_00672 +MTRSRRNVGGGAAHRSETTGRSGSASGASAFDDARDSDVGRMWLDLAGAPEPTSSDADAA +RDAVPARDAGTPAGDVPDPAPGVAPDLGALLTRASDLPSPAPGAGPRTLPWSGREDTRAD +IERRGRKRATTPPRRGRPRDEGRPAVDPRPAVETDRPRRRPGPAPLPTAPREREEAAREV +VLRQLALGPRSRGQLERKLAERQAEPELIERVLDRFEEVRLVDDAAFAEVWVRSRHRSKG +LARRALGHELQQKGVDREIAAEALEAIDGEDERAAALDLVRRRLRGRTVPGGASPEARAE +RDKVTRRLVGMLGRKGYGGGLAFAVVKEVLAEHEE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000629.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000629.fa new file mode 100644 index 0000000000000000000000000000000000000000..13c69894ec6d04e0d3a3dd7ab5dab98937640f15 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000629.fa @@ -0,0 +1,35 @@ +>PROKKA_00707 +MPAAASRPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTQAER +EGVPHHLLDVLDVGQEASVAAFQSAVRDLFAQIRARGRTPILVGGSGLYVRAALDVLEFP +PTDPALRAELEARAQREGLAGLRAELASLDPVSAERLQDARRIVRALEVCRLTGRPFSAF +MPERTYAPEVAPVVQLGLRLDRAELHRRIAARVERMLAEGLLDEVRRLDVPGPDGLRQGP +TASRAIGYAQMLAVLDGELTEAEAADQTVVATRRFARRQETWFRADPRVVWLDAQDEDVV +AEALAVVAGDAT +>PROKKA_00441 +MPAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTPAER +EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLDFP +PTDPALRTELEARAQREGLAGLRAELAALDPVSAERLQDARRIVRALEVCRLTGRPFSAF +MPERTYAPEVAPVVQLGLRLDRSELHQRIAARVERMLAEGLLDEVRRLDVPGPGGLRQGP +TASRAIGYAQMLAVLDGELTEAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDVV +AEALAVVAGGAA +>PROKKA_02250 +MRAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDIGTAKVTEAEREG +VPHHLLDVLDVGQEASVAAFQSAARGVFEDVRSRGRTPILVGGSGLYVRAALDVLEFPPT +DPEVRAAVEAELAERGEAALRAELAAVDPESAAKVADARRLVRALEVHRITGRPFSAFMP +RREHDPSVAPVVQIGLSLERAVLHERIEARVERMLAAGLLDEVRALDVPGPDGLRQGPTS +ARAIGYAQMLAVLDGTLTPEQAAEQTVVATRRFARRQETWFRADPRVHWVDALAPDVVAQ +ALAVVAGS +>PROKKA_02122 +MSAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTQAER +EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLEFP +PTDPALRAELEARAQREGLTGLRAELAALDPASAERLRDARRIVRALEVCRLTGRPFSAF +MPERTYAPEVAPVVQLGLRLDRAELHQRIAARVERMLAGGLLDEVRRLDVPGPDGLRQGP +TASRAIGYAQMLAVLDGELTAAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDVV +AAALAVVAGDAT +>PROKKA_00674 +MPAAAARPPVVAVVGATATGKSALAVALAHALDGEVVNGDALQFYRGMDVGTAKVTPAER +EGVPHHLLDVLDVGQEASVAAFQSAARDLFDQIRARGRTPILVGGSGLYVRAALDVLDFP +PTDPALRTELEARAQREGLAGLRAELAALDPVSAERLQDARRIVRALEVCRLTGRPFSAF +MPERTYAPEVAPVVQLGLRLDRAELHRRIAARVERMLAGGLLDEVRRLDVPGSEGLRQGP +TASRAIGYAQMLAVLDGELTEAEAAEQTVVATRRFARRQETWFRADPRVVWLDAQGEDIV +AEALAVVAGDAT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000630.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000630.fa new file mode 100644 index 0000000000000000000000000000000000000000..f9655d95ec2b184698684500df8b16d298eb94c5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000630.fa @@ -0,0 +1,35 @@ +>PROKKA_00708 +MTEQPAAPAAQDPLHASAPRVPFTKGHGTGNDFVLIADPDGNTQLDAQRVARLADRHRGI +GADGVIRAVRSARLPEGEALLAEHPEAEWFMDYRNGDGSIAEMCGNGVRVFVHFLVEKGL +VDLAPGRAITIGTRAGVKAVTRLEHGYAIDMGPWSYLNPELAEEAASDSMVLAHGLTDPR +PALSVSMGNPHTVVPLASFADLQGLDLGRAPEVDPAPPHGTNVEFVAAHEPLVREGVGRV +RMRVHERGVGETQSCGTGACAVAVAMRAWSGDQGTDSWLVEVPGGVLAVDVVPGPEGAEH +VVLSGPAELVFDGELTA +>PROKKA_00442 +MTEQPAAPAAQDPLHASAPRVPFTKGHGTGNDFVLIADPDGNTQLDAERVARLADRHRGI +GADGVIRAVRSARLPEGEALLAEHPEAEWFMDYRNGDGSIAEMCGNGVRVFVHFLVEKGL +VDLAPGQAITIGTRAGVKAVTRLEHGYAIDMGPWSYLDPELAEEAASDSMVLAHGLTDPR +PALSVSMGNPHTVVPLASFADLEGLDLGRAPEVDPAPPHGTNVEFVAAHEPLVREGVGRV +RMRVHERGVGETQSCGTGACAVAVAMRAWSGDQGSDSWLVEVPGGVLAVDVVPGPEGAEH +VVLSGPAELVFDGELTA +>PROKKA_02249 +MTEKTAAAAAPTSDAAPRVPFTKGHGTGNDFVLLADPDGNVHLEAAQVAVLADRHRGIGG +DGVIRAVPSRHVEEGRALLAAHPEAEWFMDYRNGDGSIAEMCGNGVRVFVHFLSEKGLVD +LAPGESITIGTRAGVKTVSRLAHGYAIDMGPWSYLDPELAEEAASDAMVLAAGLADPRPA +LSVSMGNPHTVVPLASFEDLEGLDLTRAPEVDPAPSHGSNVEFVAAHEPLVREGVGRARM +RVHERGVGETQSCGTGACAVAVAMRAWSGEGGSDSWLVEVPGGVLGVDFVAHPDGTEHVV +LAGPAELVFDGELTV +>PROKKA_02121 +MTEQPAAPAAQDPLHASAPRVPFTKGHGTGNDFVLIADPDGNTQLDAQHVARLADRHRGI +GADGVIRAVRSARLPEGEALLAEHPEAEWFMDYRNGDGSIAEMCGNGVRVFVHFLVEKGL +VDLAPGQAITIGTRAGVKAVTRLEHGYAIDMGPWSYLDPELAEEAASDSMVLAHGLPDPR +PALSVSLGNPHTVVPLASFADLQGLDLGRAPEVDPAPPHGTNVEFVAAHEPLVREGVGRV +RMRVHERGVGETQSCGTGACAVAVAMRAWAGDQGTDSWLIEVPGGVLAVDVVPGPEGAEH +VVLSGPAELVFDGELTV +>PROKKA_00675 +MTEQPAAPAAQDPLHASAPRVPFTKGHGTGNDFVLIADPDGNTQLDAQRVARLADRHRGI +GADGVIRAVRSARLPEGEALLAEHPEAEWFMDYRNGDGSIAEMCGNGVRVFVHFLVEKGL +VDLAPGRAITIGTRAGVKAVTRLEHGYAIDMGPWSYLDPELAEEAASDSMVLAHGLTDPR +PALSISMGNPHTVVPLASFADLQGLDLGRAPEVDPAPPHGTNVEFVAAHEPLVREGVGRV +RMRVHERGVGETQSCGTGACAAAVAMRAWSGDQGSDSWLVEVPGGVLAVDVVPGPEGTEH +VVLSGPAELVFDGELTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000633.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000633.fa new file mode 100644 index 0000000000000000000000000000000000000000..0ac4352271c962615b451df6d28f687aed26f367 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000633.fa @@ -0,0 +1,54 @@ +>PROKKA_00714 +MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADSVVADHEDAPD +AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ +LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA +QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ +VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR +DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV +RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHIVDGSHPDPEGQIA +AVRSVFAEVHAHRIPEIIVLNKADAADPAVIARIRAKEPHAVVVSARTGEGIDELERAIA +ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV +VEADAL +>PROKKA_00445 +MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADGAAAEHRDAPD +AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ +LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA +QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ +VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR +DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV +RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQIA +AVRSVFAEVDAHRIPEIIVLNKADAADPAVVARIRSKEPHAVVVSARTGEGIDELERAIA +ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV +VEADAS +>PROKKA_02244 +MTEEKNPTPAGGSEDEIQAVIDRILAADDARRSAAQGRADTPGRADAETAGDADAGTPDR +TSALAGRALALAEGGDGHTAADGDQDELAARHSLRRVQGLSTELEDMTEVEYRQLRLERV +VLAGVWTEGTAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATYLGKGKAQELAEI +VALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQVELAQL +EYLLPRLRGWGESMSRQAGGRAAGGEGIGSRGPGETKIELDRRRIRTRMAKLRKDIAGMK +PAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTVRKAMTP +DGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQISAVRSVF +AEVDAHRIPEIIVLNKADAADPAVVARIRAKEPHTVVVSARTGEGIEELERAIAATIPRP +DVRLELLIPFTRGELVSRLHSEDAEILAEGYEEGGTRLSVLVRQDLAPEYEDYVVDPAAS +>PROKKA_02116 +MTEEKNPTPAGGSEDEIQAVIDRILAADDARRATEREAAGRGSADSAAADHEGAPDRSGA +LAGRALALAEGGDGHTAADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQLRLERVVLA +GVWTEGTAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKARELADVVAL +TGADTVIVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHATSREGRAQVELAQLEYL +LPRLRGWGESMSRQAGGRAAGGEGIGSRGPGETKIELDRRRIRTRMAKLKKDIAGMKPAR +EAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVQNALFATLDPTVRKAVTPDGI +GYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDASHPDPEGQIAAVRSVLREV +DAQSVPEIIVLNKADAAEPDVIARIRAKEPHTVVVSARTGEGIPELESAISATIPRPDVR +LELLVPFTDGQVVSRLHSVDAEILSETYEETGTRLTVLVRRDIAADLEGYRVDAAAGDDA +QEAASA +>PROKKA_00678 +MTEKNQHTPGPQGAHGSEDEIQAVIDRILAADDARRASEREATGRGSADSVVADHEDAPD +AGTPDRSGALAGRALALDEGEDGHTDADGDQDELAARHSLKRVQGLSTELEDMTEVEYRQ +LRLERVVLAGVWTEGSAEDAENSLRELAALAETAGSEVLDGVIQRRATPDPATFLGKGKA +QELAEIVALSGADTVVVDSELAPSQRRALEDVVRVKVIDRTALILDIFAQHASSREGRAQ +VELAQLEYLLPRLRGWGESMSRQAGGRAAAGEGIGSRGPGETKIELDRRRIRTRMAKLRR +DIAGMKPAREAKRANRRRNRVPSVAIAGYTNAGKSSLLNRLTHAGVLVENALFATLDPTV +RKAMTPDGIGYTLSDTVGFVRNLPTQLVEAFRSTLEEVADADVILHVVDGSHPDPEGQIA +AVRSVFAEVDAHRIPEIIVLNKADAADPAVVARIRSKEPHAVVVSARTGEGIDELERAIA +ATIPRPDVRLELLIPFTRGELVSRLHSADAEILAEGYEEGGTRLSVLVREDIAPDFAEFV +VEADAS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000634.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000634.fa new file mode 100644 index 0000000000000000000000000000000000000000..02e29ec789dd6dae9a3777eab941ee765e6e38b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000634.fa @@ -0,0 +1,65 @@ +>PROKKA_00715 +MSGGAEEVGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL +VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE +PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGMIGSATDGAAGPSSLLGKEVM +YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA +DVVVTNHAMLAISAFEGLAVLPAYSAVVVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR +RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD +KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD +PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA +LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASRGGALGLFSSRRAAEDA +AAEMRRRLGPKTTILCQGDATLSALVRQFSEEPDTSLFGTMSLWQGVDVPGNSLRLVVID +RIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD +PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD +>PROKKA_00446 +MSEEEQEAGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL +VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE +PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGVIGSATDGAAGPSSLLGKEVM +YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA +DVVVTNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR +RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD +KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD +PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA +LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASRGGALGLFSSRRAAEDA +AAEMRRRLGPKTTILCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLVVID +RIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD +PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD +>PROKKA_02243 +MSGAGTEGTTPAGEGAQPRTDHEREALRLLDAAVEATGGQQRAGQREMVLQVARALESRR +HLLVQAGTGTGKSLAYLIPALQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDEL +PREPVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGLLGSAADGTGGPSSLLGK +EVMYLRAWADQTETGDRDDLDVPVTDRAWRQVSVSAIDCLGASRCPMAEECFSERARADA +ADADVVVTNHAMLAISAFEGLAVLPAYSAVVVDEAHELQDRVTGAVTGQLSGSIVHGAAT +SLRKHTTVAVEDLMEAGAGLDRAFTDAPSGLLAAGPDEVQEQALNAVLAAARQCLSDLGQ +DKDKEADADGGRQMARSRVLEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGD +ESDPPQLFVAPISVAGKLREGLFGKATTVLTSATLTVGAGERRFDSVAGDVGLAGPDAPR +FEALDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASGGGALGLFSSRRAA +EDAAAEMRRRLGPKATVLCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLV +AIDRIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVHDRGVVA +VLDSRLATERYGGYITSALPDFWRTTDRAVVLGVLGRLAETGS +>PROKKA_02115 +MTDSTTGPAGAVPTTDREEEALRLLDVVVEATGGQQRAGQREMVLQVARALESRRHLLVQ +AGTGTGKSLAYLIPALQHAMDQEDPVVVATATLALQAQIMKRDAPRLVQALAGELPREPV +VALVKGRSNYLCRHKVDGGYPGDEGEETLFEVADDGGLIGSGEDGEPSSPLGKEVMYLRA +WADVTETGDRDDLEVPVTDRAWRQVSVNAVDCLGATRCPLAEECFSERARADAADADVVV +TNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLRRHTS +VAVEDLAQAAAGLDRAFTDTPSGLIQGGPDDVQEQALTAVLSAARQCFSDLGKDKEGEAD +AGRQMARSRLLEVVEVAERMLAAHPEADFPEVLWATRPGRFEPGSGWQPGDEADPPQLYV +APISVAGRLREGLFGKATTVLTSATLTVGQGERRFDSVAGDVGLAGPDAPRFTALDVGSP +FDYPRQGVLYVARHLPKPGRTASPESLDELEALLRASNGGALGLFSSRRAAEDAAEHMRR +RLGRGHTVLCQGDATLSALVRQFADEPDTSLFGTMSLWQGVDVPGPSLRLVVIDRIPFPR +PDDPLSQARTRDVARHGGNGFMRVSATHAAVRMAQGAGRLVRSVEDRGVVAVLDSRLATE +RYGGYITSALPDFWRTTDRAVVRGVLERLAREAH +>PROKKA_00679 +MSEEEQEAGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL +VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE +PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGVIGSATDGAAGPSSLLGKEVM +YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA +DVVVTNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR +RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD +KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD +PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA +LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLSASRGGALGLFSSRRAAEDA +AAEMRRRLGPKTTILCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLVVID +RIPFPRPDDPLSQARTRDVARNGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD +PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000635.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000635.fa new file mode 100644 index 0000000000000000000000000000000000000000..8d814279ad4638ab89f4001d45ee6e18f0dff2f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000635.fa @@ -0,0 +1,25 @@ +>PROKKA_00716 +MSTTDDQPAARAPLTDRQRRIVQTIRDAIADHGYPPSMREIGDAAGLASLSSVTHQLGRL +ERHGYIRRDPGRPRALEVLLDVDGTPLGEAASPAAAPSSRVTAIPAWHTGADEADSVPVP +WVGRIAAGGPVLAEQQVEDVMAIPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQE +TAENGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRSL +>PROKKA_00447 +MSTTDDQPAARAPLTDRQRRIVQTIRDAIADHGYPPSMREIGDAAGLASLSSVTHQLGRL +ERHGYIRRDPGRPRALEVLLDVDGTPLGEAASPAAAPSSRISAIPAWHTGADEADSVPVP +WVGRIAAGGPVLAEQQVEDVMAIPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQE +TAENGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRSL +>PROKKA_02242 +MATTDEQPAPLTDRQRRIVQTIRDAIAEHGYPPSMREIGDAAGLASLSSVTHQLGRLEQH +GYIRRDPGRPRALEVLLDVDGTPLGEAAPPAAAAPSGLPAIPAWHTGAEDADTVPVPWVG +RIAAGGPVLAEQQVEDVMAVPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQETAE +NGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRAL +>PROKKA_02114 +MATSPTPPPGGAQPLTDRQRRIVRTIRQAIAERGYPPSMREIGDAAGLASLSSVTHQLGQ +LERFGYLRRDPGRPRALEVLRDEDGAAAVADAAPGAPEIPSWHTGASEDATVEVPWVGRI +AAGGPILADQQVEDVMAVPRRLTGEGDLFMLRVVGDSMVDAAICDGDWVVVRRQETAENG +DIVAALLDDEATVKTLRRRDGHTWLLPQNTAYEPILGDHATLMGRVVTVLRAL +>PROKKA_00680 +MSTTDDQPAARAPLTDRQRRIVQTIRDAIADHGYPPSMREIGDAAGLASLSSVTHQLGRL +ERHGYIRRDPGRPRALEVLLDVDGTPLGEAASPTAAPSSRVSAIPAWHTGADEADSVPVP +WVGRIAAGGPVLAEQQVEDVMAIPRRLTGEGELFMLRVTGDSMVDAAICDGDWVVVRRQD +TAENGDIVAALLDDEATVKTFRRRDGHTWLLPQNTAYEPILGDHATVMGRVVTVLRSL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000636.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000636.fa new file mode 100644 index 0000000000000000000000000000000000000000..1a5ffc88314f6a4a5be9e8269761d1172fb03b0a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000636.fa @@ -0,0 +1,20 @@ +>PROKKA_00717 +MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA +VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV +PATR +>PROKKA_00448 +MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA +VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV +PATR +>PROKKA_02241 +MTLMTAQFAGSPAAARRRPAAIRLTRRGRLLLRGIPVMAAAAAATLAVAFLLGVLLSPAA +VSADTAAPATQTVTVMPGDSLWTIATTIAPEEDVYEVIAAIDELNGLEGRAPALGEELFI +PATR +>PROKKA_02113 +MTAVTAVLSRTHQLTSVRARPTRAVAASTRAAARTSGVRLTRRGRLLFRGLPVILSVAAA +TVAAAFFAGVLFSPPAVSADTPAEELQTVTVMPGDSLWTIARDVAPEADRRDTMRRIDEL +NGLEGRDPELGQELYVPPTR +>PROKKA_00681 +MTLTTAQFAGSPATARPRPATIRLTRRGRLVLRGIPVIAAAVAATLAAAFFLGVLLSPAA +VSADTAGPATQSVTVMPGDSLWTIATTVAPEADVYEVIATIDELNGLEGRAPAPGEELFV +PATR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000637.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000637.fa new file mode 100644 index 0000000000000000000000000000000000000000..3235cc4afce39dd071b347de7dba5457f27b14c2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000637.fa @@ -0,0 +1,40 @@ +>PROKKA_00718 +MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR +YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY +PLLAGGTDTVFVDGGRAEDHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV +YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR +LGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR +GLGLRPSVSDSNFVFFGHLEDASDVWRRLLDRGVLVRDVGIPHHLRVTAGTEAETTAFLT +ALAEVLGETGDRS +>PROKKA_00449 +MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR +YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY +PLLAGGTDTVFVDGGRAADHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV +YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR +LGYLAADPAVTDALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR +GLGLRPSVSDSNFVFFGHLEDASDVWGRLLDRGVLVRDVGIPHHLRVTAGTEPETTAFLT +ALEEVLGETGHRS +>PROKKA_02240 +MTDLSSLPLRENLRGLSPYGAPQLDVPHMLNTNENTHPVPQEVATAIAERVAAVAGGLNR +YPDREFTALRRALARYLGHGLTEGHVWAANGSNEILQQILQAFGGPGRTLLSFLPSYSMY +PLLAGGTDTAFVDGGRAADHTLSAERAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV +YAAQAENESAGGPGAMIVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR +VGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLETVEDIKGQRDRIVATLR +ELGLEPSVSDSNFVFFGRLEDAADVWRRLLERGVLVRDVGIPHHLRVTAGTEEETTAFLE +ALEAVLAEIGHRR +>PROKKA_02112 +MTDLSSLPLRDSLRGQSPYGAPQLDVPYMLNTNENTHPVPQAVAEAITARVAKVAGGLNR +YPDREFTELREHLAAYLGHGITPEQVWAANGSNEVLQQILQAFGGPGRTLLSFLPSYSMY +PLLANGTDTAFVDGGRAADHTLSAEHAAALVREHRPNVVFLASPNNPTGTALGLDVIEAI +YAAQAQNEAEGGHGAMVVVDEAYAEFALAGTDSALTLLRGRERLIVTRTMSKAFALAGAR +LGYLAADAAVADALRLVRLPYHLSAVTQATAIAALERVDELLETVEDIKGQRDRIVAELT +GMGLVPAVSDSNFVFFGRLADAHAVWEALLERGVLVRDVGIPHHLRVTAGTEEETTAFLD +ALREIVEQDPAVVSAVDAD +>PROKKA_00682 +MTDLSSLPLRENLRGLSPYGAPQLDVPYMLNTNENTHPVPEEVATAIAERVAAVAGGLNR +YPDREFTGLRRALAGYLGHGLTADHVWAGNGSNEILQQILQAFGGPGRTLLSFLPSYSMY +PLLAGGTDTVFVDGGRAEDHTLSAEHAAAMVREHRPHVVFLASPNNPTGTALDLATIEAV +YAAQAQNEAAGGPGAMVVVDEAYAEFALAGTRSALTLLPGRERLIVTRTMSKAFALAGAR +LGYLAADPAVADALRLVRLPYHLSAVTQATAEAALDHVDALLRTVEDIKAQRDRIVSTLR +GLGLRPSVSDSNFVFFGHLEDASDVWRRLLDRGVLVRDVGIPHHLRVTAGTEAETTAFLT +ALAEVLGETGDRS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000638.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000638.fa new file mode 100644 index 0000000000000000000000000000000000000000..1b6cd43b0275b91bcc2684205ab867a69211ee71 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000638.fa @@ -0,0 +1,25 @@ +>PROKKA_00719 +MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV +RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP +YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA +FARALRAAVEDDPRMTGVPSTKGAL +>PROKKA_00450 +MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV +RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP +YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA +FARALRAAVEDDPRMTGVPSTKGAL +>PROKKA_02239 +MAAELISGRRARMTRTTSESDVHVEMDLDGTGRAEISTSVPFYDHMLTALARHSQIDLTV +RATGDTHIDVHHTVEDVAITLGEVLKTALGDKSGIRRFGEASVPLDEALARAVVDVSGRP +YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA +FARALRAAVEDDPRMSGVPSTKGAL +>PROKKA_02111 +MAAELMSGRRARMQRTTSESDVYVEMDLDGTGTSEISTTVPFYDHMLTALSRHSQIDLTV +RATGDTHIDVHHTVEDVAITLGEVLKTALGDKRGIRRFGEASVPLDEALARAVVDVSGRP +YLVHEGEPEGQQYHLIGGHFTGSMTRHVFEAITYHASICLHMDVVRGRDPHHIVEAQFKA +FARALRAAVEDDPRVHDVPSTKGAL +>PROKKA_00683 +MAAELISGRRARMTRTTSESDVYVEMDLDGTGRAEISTTVPFYDHMLTALSRHSQIDLTV +RATGDTHIDVHHTVEDVAITLGEVLKAALGDKSGIRRFGEASVPLDEALARAVVDVSGRP +YLVHEGEPEGQQYHLIGGHFTGSMTRHVFESITYHAAICLHMDVVRGRDPHHIVEAQFKA +FARALRAAVEDDPRMTGVPSTKGAL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000642.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000642.fa new file mode 100644 index 0000000000000000000000000000000000000000..931f71898946265944cc58889301a211cb0623c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000642.fa @@ -0,0 +1,35 @@ +>PROKKA_00723 +MTGSHDDGGLARDDGLGPIDETVAVPHPAARELPGHIRAALDRMREKTAGENTADTAGVP +WQGRDLSGPGVDGSANPLHVFDEDDGTSPAEWTAVMSALTDGSAGEREVTEVLARIRVFA +AVVPTLAGDEDDVHDHADHTGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTNVPALT +AWNPVARPVAVWLPRACLSAVDEGCELVVIDAGAEHTYVVRRPAVWSLAQQREWTPAYRD +QEIADEIAEVADLVPNLLNLGLAPGSGVATHTGSGAVMNGGGAGPELQIVAMPTRDADAA +GVRLMTATLKTLLADLPLLAERADSVEITVRRP +>PROKKA_00454 +MTGSHDDGGLARDEGLGPIDETVAVPHPAARELPGHIRAALDRMREKTAGENTADTAGVP +WQGRDLSGPGVDGSANPLHVFDEDDGTSPAEWTAVMAALTDGSAGEREVTEVLARIRVFA +AVVPTLAVDEDDVHDHTGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTNVPALTAWN +PVARPVAVWLPRACLSAVDEGCELVVIDAGAEHTYVVRRPAVWSLAQQKEWTPAYRDQEI +ADEIAQVADLVPNLLNLGLAPGSGVATHTGSGAVMNGGGAGPELQIVAMPTRDADATGVR +LMTATLKTLLADLPVLAERADSVEITVRRP +>PROKKA_02235 +MTHGHDDGAPAGVAGAGPIEETVAVPRPDSRELPGHIRAALDRMREKTAGPNTADTAGVP +WEGRDLSGPGVDGSANPLHVFDEDDGTSPEEWTRVMAALTTGAAGEAEVTDVLSRIRVFA +AVVPTLAVDEDDVHDHADHSGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTSVPALT +AWNPIARPVAVWMPRACLSAVDEGCELVVVDAGAEHTYAVRRPAVWALAQQKPWTPSYRD +QEIADEIAQVADLVPHLLNLGLAPGSGVATHTGSGAVMSGGGAGPELQIVAMPARDADAA +GVRLMAATLKTLLADLPLLAERADSVEVTVRRP +>PROKKA_02107 +MSSASSSEPAHDAEATVPVPAPGGRELPGHIRAAMERMRQKTARENTADTAGVPWAGRDL +SGPGLEGSANPLHIFDEDDGTAPAEWARVMDALTEGTAGEAEVVDVLGRIRVFAAVVPTL +AVDEADVHDHAAHSVHEHAQHEDAAHGDKAADVALVTMRAPDGRQALPVFTSVPALTAWN +PLARPVAVWAPRACLSAVDEGCELVVVDAGAEHTYAVRRPAVWALAQQKPWTPSYLDQEI +AEEIAGVADLVPNLLNLGLAPGPGVATETASGEVMNGGGSGTELTVLAMPARDADAAGIR +LMTTTLAMLLGDLPLLAERADSVEITVRRP +>PROKKA_00687 +MTGSHDDGGLARDDGLGPIDETVAVPHPAARELPGHIRAALDRMREKTAGENTADTAGVP +WQGRDLSGPGVDGSANPLHVFDEDDGTSPAEWTAVMSALTDGSADEREVTEVLARIRVFA +AVVPTLAVDEDDVHDHADHTGHEHDVAAHGDKAADVALVTMRAPDGRQALPVFTNVPALT +AWNPVARPVAVWLPRACLSAVDEGCELVVIDAGAEHTYVVRRPAVWSLAQQREWTPAYRD +QEIADEIAEVADLVPNLLNLGLAPGSGVATHTGSGAVMNGGGAGPELQIVAMPTRDADAA +GVRLMTATLKTLLADLPLLAERADSVEITVRRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000643.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000643.fa new file mode 100644 index 0000000000000000000000000000000000000000..83be803ecd03d2bc4be79c1673b79522aac5bcb9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000643.fa @@ -0,0 +1,40 @@ +>PROKKA_00724 +MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC +GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE +TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV +VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDALDASAAPAAETAAAAETAPAAE +TAPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKARAEAAAEEEAAEA +APAAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADGTVLGQD +GLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG +>PROKKA_00455 +MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC +GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE +TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV +VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDALDASAAPAAETAAAAETAPAAE +TAPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKARAEAAAEEEAAEA +APAAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADGTVLGQD +GLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG +>PROKKA_02234 +MRTRTLTGVATAALGAVVVAGAGPALAQTVITQGSALSAPAGACSLTIVDDATAYTAAHC +GAGQWEVGSPVLDAEGVQIGTVSGLPGTSGVDVVRVALAEDVEVVGEWSTRPAASVEVGE +TVFTHGSSVPLGAPNSLSHTQTFDAATVCDDAYSDQMALDVASTYPGDSGGAVYDAQQRV +VGVISGVAPVTFDEEGNVVGCDAQSLSSIMVPVESLDAVGQETAAPAAVEPAAAEAPATE +VTETPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIRAELIERAEAEAAAEAP +AEQPAAEAPVAEAVVAGTEDVVAAPAEGVAYGTQVMAETSQGGFASVTVTAYDADGTVLG +VDGLDLTGEYRAWMPVPAEVPAGGSVVVTVVDAAGDATDTQVTLGGQLIG +>PROKKA_02106 +MKKTTLTGATTAALGAVVVAGAGSALAATPLTQGAALSVPAGECSITLVSDTTAFTAAHC +GAGQWTVGSAVHAADGARIGSVSALPGSTGVDVVKIALDEDVDVVGDWSTRPAASVKPGE +TVYTQGSSVPLGSPNSISDPETYDIAETCGDVYTDQVSLDAATTRPGDSGGAVYDAKQRV +VGVVSGLAPVSFDEEGRAVGCDAASLSTIMVPAESLKAVAAAPAKATAPAPTVGKHGVIL +KAPTAPAAKAPAAEKKAPAAKAPAAEKKAAPAPTLGKHGVSAETATAGTTTLKVAPEDGI +DFRTRVQATTKTGGFSYMAVTAYDAAGKQIGHLHLHSDGQPMTWINTPAQVPAGGHIEVQ +LKDAAGQPTDATVTLGGVPVN +>PROKKA_00688 +MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC +GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE +TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV +VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDALDASAAPAAETAAAAETAPAAE +TAPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKARAEAAAEEEAAEA +APAAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADGTVLGQD +GLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000644.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000644.fa new file mode 100644 index 0000000000000000000000000000000000000000..ad8cb1e9e499a619d581a60b03c812b7e84c376f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000644.fa @@ -0,0 +1,23 @@ +>PROKKA_00725 +MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR +LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV +ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL +C +>PROKKA_00456 +MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR +LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV +ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL +C +>PROKKA_02233 +MNSSSTPTPEPSETARHAWRAYFEATQMLSEMLERGLKKDSGMSLADYNLLLLLYEAPEG +RLRMGELASGMVFSPSRITYQVKTLVARGLIERRAAECDRRGFEAVLTDEGRTAFRRAAA +GHARQVDELFLSHLEPGEAETLERIFTRLGGRLEGLC +>PROKKA_02105 +MTSSSTPAAEPTGPRAARHAWRAYFESTQMLQDQLERGLKAECGITLADYNLLLLLVESD +GGRLRLGELASRMVFSPSRVTYQVKSLVARGLIERRRVECDRRGFEAVLTDAGRTAFRRA +AVVHARQVDELFLDLLQPGEAEVLGRVFTRVGTALESRCAGRAAPSEPCGAQASNSADA +>PROKKA_00689 +MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVLERR +LKQDCGMSLADYNLLLLLYESPEDRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV +ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLVDLAPGEAESLTRIFSRLGRRLEGL +C diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000645.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000645.fa new file mode 100644 index 0000000000000000000000000000000000000000..ba579062ffcb736eec4cc8b0ee9dedf76ffd9cdf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000645.fa @@ -0,0 +1,25 @@ +>PROKKA_00726 +MTTPGAPDASAPFTPQARHLAVVSGGSGDPSQTRMLAERMAESASAALSEHGVVPQIHLI +TLRELAVDIAQALVTFAISPALRAALDEVAQADAVIAVSPTYKASYSGLFKSFWDLAEPT +SVVGVPVLLGATGGTARHSLMIDTAMRPLFAYLKARIVPTAVFAASDDWGEAAGVQASMR +TDPLQSRIRAAGRDLAEITLSRPPRARAAAPADIDLEVTPFEQLLNPGP +>PROKKA_00457 +MTTPGAPDASAPFTPQARHLAVVSGGSGDPSQTRMLAERMAESASAALSEHGVVPQIHLI +TLRELAVDIAQALVTFAISPALRAALDEVAQADAVIAVSPTYKASYSGLFKSFWDLAEPT +SVVGVPVLLGATGGTARHSLMIDTAMRPLFAYLKARIVPTAVFAASDDWGEAAGVQASMR +TDPLQSRIRAAGRDLAEITLSRPPRARAAAPADIDLEVTPFEQLLNPGP +>PROKKA_02232 +MIGQGAFEATDPLMPQARHVAVVSGGSGDPSQTRMLAERMAEAASAALSEHGVVPEIHLI +TLRELATDIAQAMVTFAVSPALRAALDEVQQADAVIAVSPTFKASYSGLFKSFWDLVDDE +SLIGVPVLLGATGGTVRHSLMIDTALRPLFAYLKSRIVPTAVFAASDDWGEADGAQASTR +TDPLRSRIRSAGRDLAEILLNRPPRARAAAPETLDLEVTPFEQLLNPDA +>PROKKA_02104 +MSTSAFESTDPFTPGARHIAVVSGGIGDPSQTRKLADRLARASADALSAAGVVPEIHVVS +LRELATDLGAGMVTTARSPALLDAVAQVEHADAVIAVSPTFKASYSGLFKSFVDLIDDEA +LVGVPVLLGATGGTARHSLMIDQAMRPLFAYLKARIVPTAVFAASDDWGRADGQNDSTRT +TPLDARIRAAGEDLAEVLRHRPARVRPAADATDDDLEVIPFDQLLHPGR +>PROKKA_00690 +MTTPGAPDASAPFTPQARHLAVVSGGSGDPSQTRMLAERMAESASAALSEHGVVPQIHLI +TLRELAVDIAQALVTFAISPALRAALDEVAQADAVIAVSPTYKASYSGLFKSFWDLAEPT +SVVGVPVLLGATGGTARHSLMIDTAMRPLFAYLKARIVPTAVFAASDDWGEAAGVQASMR +TDPLQSRIRAAGRDLAEITLSRPPRARAAAPADIDLEVTPFEQLLNPGP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000646.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000646.fa new file mode 100644 index 0000000000000000000000000000000000000000..478be67ca1ffa24b42d5d542890fd68c25c4080c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000646.fa @@ -0,0 +1,40 @@ +>PROKKA_00727 +MQFGVFTIGDITADPTNGTAPTEHQRIKDTVKIARHAEQAGFEVFATGQHHNPPFVAPGN +PPTLLAYLAAQTETLQLSTATTLITTMDPVRLAEDYAYLQHLADGRVDLTMGRGNTGPVY +PWFGKDIRQGIQLAVENYNLLYRLWHEETVDWSGNHRTPLQDFTLTPQPLDGVAPFVWHG +SIRSPEIAEQAAYYGDGYFHNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA +YMAKNSQDAVAEFRPYFDNAPVYGHGPSLEDFSRMTPLTVGSPQQVIERTLTFRDWVGDY +QRQMFLIDHAGLPTDTVLRQIDLFGEEVLPVLRKEFDALKPDDVPAAPTHEFLVARARRG +EAPVPGGKEGSQAQLDRAAAAEQRATADAAKGGAAQ +>PROKKA_00458 +MQFGVFTIGDITADPTNGTAPTEHQRIKDTVKIARHAEQAGFEVFATGQHHNPPFVAPGN +PPTLLAYLAAQTETLQLSTATTLITTMDPVRLAEDYAYLQHLADGRVDLTMGRGNTGPVY +PWFGKDIRQGIQLAVENYNLLYRLWHEETVDWSGNHRTPLQDFTLTPQPLDGVAPFVWHG +SIRSPEIAEQAAYYGDGYFHNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA +YMAKNSQDAVAEFRPYFDNAPVYGHGPSLEDFSRMTPLTVGSPQQVIERTLTFRDWVGDY +QRQMFLIDHAGLPTDTVLRQIDLFGEEVLPVLRKEFDALKPDDVPAAPTHEFLVARARRG +EAPVPGGKEGSQAQLDRAAAAEQRATADAAKGGAAQ +>PROKKA_02231 +MQFGVFTIGDVTQDPTTGTTPTEHQRIKDTVRIAQHAAQAGFEVFATGQHHNPPFVAPGN +PPTLLAYLAAMTTDLQLSTATTLITTMDPVRLAEDYSYLQHLADGRVDLTMGRGNTGPVY +PWFGKDIRQGIPLAVENYNLLYRLWHEETVDWSGKFRSPLQNFTLTPQPLDGVAPFVWHG +SIRSAEIAEQAAYYGDGFFYNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA +YMAKNSQDAVKEFRPYFDNAPVYGHGPSLEQFSSMTPLTVGSPQQVIERTLGFRDWVGDY +QRQMFLIDHAGLPTDTVLKQIDIFGEEVLPVLRKEFAALKPDDVPEAPTHEFLVERARRG +EAPVPGGKEGSQAQIDRAAAAEKRAAAKAGEGA +>PROKKA_02103 +MQLGIFTIGDITADPTTGTTPTEHQRIKDTVTIARHAEQAGFDVFATGQHHNPPFVAPGN +PPTLLSHLAAVTETMTLSTATTLITTMDPVRLAEDYSYLQHLADGRVDLTLGRGNTGPVY +PWFGKDIRQGVNLAVENYNLLYRLWHEETVDWSGQFRTPLQDFTLTPQPLDGVAPFVWHG +SIRSPEIAEQAAYYGDGFFHNNIFWNKEHIIRMVRLYRQRFEHYGHGKAHQAYVGLGGQA +YMAKNSQDAVKEFRPYFDNAPVYGHGPSLEDFTSMTPLTVGSPQQVIERTLSFRDWVGDY +QRQMFLIDHAGLPTDTVLKQIDLFGEEVLPVLREEFAALKPDDVPEAPTHEFLVERARRG +EAPVPGGREGSPAHAAREAARAKQAEQQKKKEDAR +>PROKKA_00691 +MQFGVFTIGDITADPTNGTAPTEHQRIKDTVKIARHAEQAGFEVFATGQHHNPPFVAPGN +PPTLLAYLAAQTETLQLSTATTLITTMDPVRLAEDYAYLQHLADGRVDLTMGRGNTGPVY +PWFGKDIRQGIQLAVENYNLLYRLWHEETVDWSGNHRTPLQDFTLTPQPLDGVAPFVWHG +SIRSPEIAEQAAYYGDGYFHNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA +YMAKNSQDAVAEFRPYFDNAPVYGHGPSLEDFSRMTPLTVGSPQQVIERTLTFRDWVGDY +QRQMFLIDHAGLPTDTVLRQIDLFGEEVLPVLRKEFDALKPDDVPAAPTHEFLVARARRG +EAPVPGGKEGSQAQLDRAAAAEQRATADAAKGGAAQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000651.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000651.fa new file mode 100644 index 0000000000000000000000000000000000000000..e9da354970ea8f787a75b40633ee00158405b6d4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000651.fa @@ -0,0 +1,30 @@ +>PROKKA_00733 +MAALLGLALGCGLFLLWWSLWSPPTERPGAARPDSRLRVLIAQSGIQRLSPAGVVSAMAV +GGLVVGLLVLSLTSTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI +RAGLTLPEALIQLGETGPEGLREPFQQFARDYRAGARFVDALDRLKARMADPVADRLVVS +LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT +QPAAVAAYRSAAGGAVLLAGMVASVVCYRVMLRIGALPREKRVFA +>PROKKA_00464 +MAALLGLALGCGLFLLWWSLWSPPTEKPGAARTDARLRVLIAQSGIQRLSPAGVVSAMAV +GGLVVGLLVLSLTSTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI +RAGLTLPEALIQLGETGPEGLREPFQQFARDYRAGARFVDALDRLKARMADPVADRLVVS +LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT +QPAAVAAYRSAAGGAVLLAGMVASVVCYRVMLRIGALPREKRVFA +>PROKKA_02220 +MAVLLGLLLGGGLFLLWWSLWSPPVQRPQTARPDSRLRVLIAQSGIRRLSPAGVVSAMAV +GGVVTGLLILAVTRTWTIAACFALFGAAVPWLLLSWQARRRTTALRELWPDAVDHARSAI +RAGLTLPEALIQLGESGPEGLREPFRQFARDYRSGARFVDALDRLKARMADPVADRLVVS +LRLTREVGGADIGRLLQTLSEFLRQDARTRAELEARQSWTVNAARLAVCAPWIVLLLLGT +QPSAVAAYQSAAGGAVLLGGLVASVVCYRVMLRIGALPEEKRVFA +>PROKKA_02096 +MGAVLGLGLGAGLFLMWWSLWSEPVVSAEEPRGPGRLAELIARSGIERLTPAGVVGAMAA +GCVVAALIVLAVTRTWTIAACFGLFGAALPWALLTWQATRRTRALRDLWPDAVDHVRSAV +RAGLTLPEALTQLGETGPEGLRAPFREFARDYRSGARFLDALERLKTRMADPVADRLVAS +LRLTREVGGADIGLLLQSLSEFLRQDARTRAELEARQSWTVNAARLAVCAPWIVLLLLGT +QPLAVTAYQSVAGGALLLAGLVVSALCYRIMLRIGALPQEKRVFA +>PROKKA_00697 +MAALLGLALGCGLFLLWWSLWSPPTEKPEAARPDSRLRVLIAQSGIQRLSPAGVLSAMAV +GGLVVGLLVLSLTGTWTIAACFAVFGAAVPWLLLSWQARRRSTALRELWPDAIDHARSAI +RAGLTLPEALIQLGETGPEGLREPFQHFARDYRAGARFVDALDRLKARMADPVADRLVVS +LRLTREVGGADIGRLLQTLSEFLRQDARIRAELEARQSWTVNAARLAVCAPWLVLLLLGT +QPAAVAAYRSAAGGAVLLAGMVASIVCYRVMLRIGALPREKRVFA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000652.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000652.fa new file mode 100644 index 0000000000000000000000000000000000000000..e3444661865cdad346717387b365c159fe55672d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000652.fa @@ -0,0 +1,34 @@ +>PROKKA_00734 +MTSALIWAALLGLTLGAGLLLILVTQPVGWRPSLEQRVEPQLRHHIPASRLLEEERAGAS +PWGTWGRILDPVVQAGVGWVQRISPGGAALDRKLAAAGLAVTSTDFRAQQVLSGAAGAAV +AAVLALSLTVTGRVPVITGVALVIAGGMAGFLLREQLLSLRVRRRREAILSEFPSVAELF +ALSVGAGESAAGALERIAGTARGELAGEFRTTLADMRAGASLSAALKAMGRRVQLAPVER +FIGGVLIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPLVFGILPLTVIF +AVFPGISLMRLGF +>PROKKA_00465 +MTSALIWAALLGLTLGAGLLLILVTQPVGWRPSLEQRVEPQLRHHIPASRLLEEERAGAS +PWGTWGRILDPVVQAGVGWVQRISPGGAALDRKLAAAGLAVTSTDFRAQQVLSAAAGAAV +AAVLALSLTVTGRVPVITGVALVIAGGMAGFLLREQLLSLRVRRRREAILSEFPSVAELF +ALSVGAGESAAGALERIAGTARGELAGEFRTTLADMRAGASLSAALKAMGRRVQLAPVER +FIGGVLIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPLVFGILPLTVIF +AVFPGISLMRLGF +>PROKKA_02219 +MSASLLWAALLGLTLGAGLLLIAVAQPLGWRPTLEQRVEPQLRHHTPASRLLEDEEAGAS +PWGAWGRILDPVLRAGVGWLHRLSPAGETLERKLAAAGMTVSAADFRAQQVLSAAAGAGI +ATAFSVALALAGRIPVVTGVGFVIVGGMAGYLLRDQLLSLRVQRRRAAILTEFPSVAELF +ALSVGAGESAAGALERIATTARGELAGEFRATLAEMRAGSSLSAALKSMGRRVQLAPVER +FIGGILIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPIVTR +>PROKKA_02095 +MSGGLLWGIALGLVMAAGVWLIVTAQPWGWRPSLEERIEPQLRHHVPASRLLADGRATST +PWGTWGRLLGPSLAGATRGLQRLSPAGESLTLKLQAAGSELSVMDFRAQQVLCAVIATAA +GTVLSVLLTLAGAVPVVSGVALVVAAGLSGYVLRDQMLTWAVARRRTAILTEFPSVAELF +ALSVGAGESATGAMERIVRSARGEMAGEFDRTLADVRAGASLSSALKAMGRRVQLEPVER +FIGGILIALDRGTPLADVLRAQAQDVRELGRRELMESAGRKEIQMMVPLVFGILPLTVVF +AIFPGLALLRLSF +>PROKKA_00698 +MTSALIWAALLGLTLGAGLLLILVTQPVGWRPSLEQRVEPQLRHHIPASRLLEEERAGAS +PWGAWGRILDPVVQAGVGWVQRISPGGVALDRKLAAAGLAVTSADFRAQQVLSAAAGAAV +AAVLALSLTVTGRVPVITGVALVIAGGMAGFLLRDQLLSLRARRRREAILSEFPSVAELF +ALSVGAGESAAGALERIAGTARGELAGEFRVTLADMRAGASLSAALKAMGRRVQLAPVER +FIGGVLIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPLVFGILPLTVIF +AVFPGISLMRLGF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000654.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000654.fa new file mode 100644 index 0000000000000000000000000000000000000000..1e11202facdc1dbfff8989bcb49788a0de05a382 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000654.fa @@ -0,0 +1,20 @@ +>PROKKA_00736 +MPRGAAHGAQAPRGGHTGVRWRDDRGAAVAESTMVMTLVVLLFAALLQAGVVIHTRNVMI +DAASAGARYGALADRSPEDGVQRARELLSAGVPGQSGADVAAELTSQDGVPVLRVTVSSS +LPGLGFLPGPIPVEVSGHAFRQ +>PROKKA_00467 +MPRGAVHAVPVPRGVHMGVRWRDDRGAAVAESTMVMTLVVLLFAALLQAGVVIHTRNVMI +DAASAGARYGALADRSPEDGVQRARELLSAGVPGQSGADVAAELTSQDGVPVLRVTVSSS +LPGLGFLPGPIPVEVSGHAFRQ +>PROKKA_02194 +MTAGSGAAAAAPRRRRPRWRDDRGAAVAESTMVMTLVVLLFAALLQAGLVIHTRNVMIDA +ASAGARYGALADRVPEDGVQRARELLAAGVPGQSGARIVAEPTSQDGVPVLRVTISSSLP +GVGFLPGPIPVEVSGHAHRL +>PROKKA_02093 +MEPAARPAVQGRPGPDRRAGDRGSVVAENAMVTALLVLLFAAVLQVGIIVHVRNVMIDAA +SAGARYGALADRDPAEGAARARDVLSASVPGQSGAQVRSEPTTVGGVPVVRVTITSSLPG +LGFLPGPVPIEVHGHAFRY +>PROKKA_00700 +MPRGAAHDAPAPRGGHTGVRWRDDRGAAVAESTMVMTLVVLLFAALLQAGVVIHTRNVMI +DAASAGARYGALADRNPEDGVQRARELLSTGVPGQSGADVAAELTSQDGVPVLRVTVSSS +LPGLGFLPGPIPVEVSGHAFRQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000655.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000655.fa new file mode 100644 index 0000000000000000000000000000000000000000..12b2f572dde71d3315eeda3c0880bfc60269ed2f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000655.fa @@ -0,0 +1,20 @@ +>PROKKA_00737 +MRSVNDVRDERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAVKAVVAE +ADHPSAGAAHATVELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEVVAVRVDVGVPVPLT +PAAWSLTPVTVGSDARQTVPRF +>PROKKA_00468 +MRSVNDVRDERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAVKAVVAE +ADHPSAGAAHATVELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEVVAVRVDVGVPVPLT +PAAWSLTPVTVGSDARQTVPRF +>PROKKA_02193 +MPIASDVRDERGSATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAAKVVVSG +TEGRSAAQAHAAVRLTLADFGIDYGAYELDLGCSAGDCVSLDPGEVVQARVDVEVPIPLT +PADWSLAPVTVGSDARQAVPRF +>PROKKA_02092 +MPSATDARHGPTHAPWRGTDLADDVGSATVEFLGLSLILLIPLAYLMLFVSQVQAAAFGA +LASADQAARVMVSGEGGNPGQAEGTIPLTLADYGFDAADAEWSVACDVGGCGTLEPGEVV +DVTVAISLDPPLLPDGWVSVDIATVDSHSRARMPRF +>PROKKA_00701 +MRSVNDVRDERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAVKAVVAE +ADHPSAGAAHATLELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEVVAVRVDVAVPVPLT +PAAWSMTPVTVGSDARQTVPRF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000656.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000656.fa new file mode 100644 index 0000000000000000000000000000000000000000..48dbca2f866af8bd70529858465b14c8d6acc164 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000656.fa @@ -0,0 +1,20 @@ +>PROKKA_00738 +MRRRLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAIAGAE +ELGFRLGEDPGVVLSDDDVAASASAHLAAVGAQEAVPGLGGMNARVADDGTTVVVTLDAR +ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR +>PROKKA_00469 +MSRRLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAIAGAE +ELGFRLGEDPGVVLSDDDVAASASAHLAAVGAQEAVPGLGGMNARVADDGTTVVVTLDAR +ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR +>PROKKA_02192 +MRALSALRRDDGQTTVLTVGLCALLIGLMLVMLAATTVQLQHRRLQSLADGAALAGAEEL +GFRLGEDPGVVLDDGDVAASAAAHLDAVDAASSVHGLGGMAAGVADDGATVTVRLDAEVD +LLAAAGPFAGMLPLSVPIQATGDSRTSLSR +>PROKKA_02091 +MTRRHRSRPQRRPDRRHGAHERGEITVLTLGLSAIVVGLLLVVLSATLVLIQARKVQSLA +DGAALAGAEQLAFQLDADPRVVLEPGSVQASVNEHLDAVGARESVPGLESVSAQVAGDGA +TVVVRARAKVTLVPSGAGWLADLIPASVPVSAEGSSRTVLTR +>PROKKA_00702 +MRRPLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAVAGAE +ELGFRLGEDPGVVLSDGDVAASASAHLAAVGAREAVPGLGGMSARVAEDGTTVVVTLDAR +ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000657.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000657.fa new file mode 100644 index 0000000000000000000000000000000000000000..1f23e8e285c36987e54a8c44e1efce74b2b6d0e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000657.fa @@ -0,0 +1,40 @@ +>PROKKA_00740 +MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS +HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG +EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF +EVNAPYAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV +DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA +EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI +RWRAEQVKAAQED +>PROKKA_00471 +MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS +HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG +EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF +EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV +DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA +EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI +RWRAEQVKAAQED +>PROKKA_02189 +MADTDFSAEIDSLRHTLASIEQVSDIDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS +HRQADLKRITSLESRIEDLETMVELAAEEDEPSLLDDANDELASIRKSLEELEVVTLLSG +EYDPRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF +EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV +DVFRSSGPGGQSVNTTDSAVRMTHIPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLQRKA +EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGAIDAFVDAGI +RWRAEQAKAAQED +>PROKKA_02087 +MADTDFSAEIDALRHTLASIEQVSDVEKMTAEVAELEKEAAAPDLWDDPEAAQKVTSKLS +HRQADLKRIKSLADRIDDLETMVELAAEEDEPSLLDDANVELTSIRKALEELEVVTLLNG +EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQKGWSTKVMDTSYAEEAGLKSATF +EVNAPFAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV +DVFRSSGPGGQSVNTTDSAVRMTHIPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLVRKA +EEDAKKKEMAGDIKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGAIDDFIDAGI +RWRAEQVKAAQED +>PROKKA_00705 +MADTDFSAEIDSLRHTLASIEQVSDLDRIKADIAELEQQASAPDLWDDPEEAQKVTSKLS +HRQTDLKRITSLESRIEDLETMVELAAEEDEPSLLDDANQELTSIRKALEELEVVTLLSG +EYDQRDAVVTIRAGAGGVDAADFAETLMRMYLRWAEQRGWSTKVMDTSYAEEAGLKSVTF +EVNAPYAFGTLSVEAGTHRLVRISPFDNQGRRQTSFAAVEVVPLIESDDSIEIPESEIKV +DVFRSSGPGGQSVNTTDSAVRMTHLPTGIVVSMQNEKSQIQNRAAALRVLQSRLLLLRKA +EEDAKKKEMAGDVKASWGDQMRSYVLNPYQMVKDLRTGHEEGNPSSVFDGHIDDFVDAGI +RWRAEQVKAAQED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000658.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000658.fa new file mode 100644 index 0000000000000000000000000000000000000000..2c598f301ccf7fe90f3be5081233f848dd5d5f5d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000658.fa @@ -0,0 +1,35 @@ +>PROKKA_00741 +MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH +PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF +IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG +GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG +QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA +NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDRGFETLIHHNETAVKILVSPTGQGL +>PROKKA_00472 +MTMRAARWHGKKDIRIEEIDSPSAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH +PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF +IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG +GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG +QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA +NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL +>PROKKA_02188 +MTMRAARWHGKKDIRIEEIASPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH +PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDQDRPDYNLAPDMNF +IGLGGDGGGLAEQIAVRRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG +GAGPIGALTAAVLKGKGLTVYVSELSELRRQKVLEAGVVDEAFDPREVDVPAKIRELHDG +QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVLKEIDLRGTIAYA +NDHADTIRMVEDGTVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL +>PROKKA_02086 +MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH +PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF +IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVALIG +GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG +QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA +NDHADTIRMVEDGAVDLTPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL +>PROKKA_00706 +MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH +PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF +IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG +GAGPIGALTAAVLKGKGLTVYVSELSELRRQKVLEAGVVDEAFDPREVDVPAKIRELHDG +QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA +NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000659.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000659.fa new file mode 100644 index 0000000000000000000000000000000000000000..7866fa0786f88ff9997c77b5cfe71fd08b89d5fd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000659.fa @@ -0,0 +1,40 @@ +>PROKKA_00742 +MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV +YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV +AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA +RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA +LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH +SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP +IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR +>PROKKA_00473 +MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV +YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV +AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA +RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA +LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH +SQPSDAINAAMRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP +IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR +>PROKKA_02187 +MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALECAGVAPEDVDMV +YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLVRLGEADVVV +AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA +RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA +LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAYAEEKGLTILATVGALGQTAGPDSSQLH +SQPSDAINAAMRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP +IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR +>PROKKA_02085 +MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV +YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV +AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA +RAEQDEVAAASHQRAARAQSQGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGS +LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTVLATVGAPGQTAGPDSSQLH +SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLGYPHEKTNIHGGAIALGHP +IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR +>PROKKA_00707 +MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV +YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV +AGGQESMTNAPHLLPGARTGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA +RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEIPQRKGDPLVVSQDEGVRPDTTAESLGA +LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH +SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLGYPHEKTNIHGGAIALGHP +IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000660.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000660.fa new file mode 100644 index 0000000000000000000000000000000000000000..071129ff0f8d4a3c3f7d9ee48e317e3b48438b6b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000660.fa @@ -0,0 +1,30 @@ +>PROKKA_00743 +MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGATDLSVVSNNCGVDG +WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY +TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQAPDEPETYVLERSIV +TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV +FVHRIVEVGTDIEKRIEKRTVRASGEGRA +>PROKKA_00474 +MALDKTVATPAEAVADVPDGASLAVGGFGLTGNPVQLIEALLEQGATDLSVVSNNCGVDG +WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY +TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQTPDEPETYVLERSIV +TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGI +FVHRIVEVGTDIEKRIEKRTVRASGEEQA +>PROKKA_02186 +MALDKTVATAAEAVADVPDGASLAVGGFGLSGNPIQLIEALLEQGAADLSVVSNNCGVDG +WGLGILLGAGRIRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY +TRSGVGTQVAEGGLPMRYDAEGNVVKSSAAKPTDTFVLGEGYVSQDPAEEQTYVLEQSIV +TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDEVHLPGV +FVHRIVEVGTDIEKRIEKRTVRAAGEES +>PROKKA_02084 +MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGAMDLSVVSNNCGVDG +WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY +TRSGVGIQVAEGGLPMHYDADGTVVKSSQAKPTDTFVLGEGYLNQAPGEPETYVLERSIV +TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV +FVHRIVEVGTDIEKRIEKRTVRASGEEQA +>PROKKA_00708 +MALDKTVATPAEAVADVPDGASLAVGGFGLSGNPVQLIEALLEQGATDLSVVSNNCGVDG +WGLGILLGARRLRKMTSSYVGENKEFARQYLEGELEVELVPQGTLAEKLRAGGAGIPAFY +TRSGVGTQVAEGGLPMRYDADGTVVKSSQAKPTDTFVLGEGYLSQTPDEPETYVLERSIV +TDFSLVHAWKGDRHGNLVFRKATRQFGPPAAMAGRVCIAQVEELVEPGEIDPDDVHLPGV +FVHRIVEVGTDIEKRIEKRTVRASGEEQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000661.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000661.fa new file mode 100644 index 0000000000000000000000000000000000000000..0f52bdfbf0aa9067be4163ac07d3974dfaaed6ec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000661.fa @@ -0,0 +1,25 @@ +>PROKKA_00744 +MSEQTTGRPRGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL +GTGPYPTEEAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG +DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVFKDGTPKIVDQCTLPLTGRAVVDRI +ITDLAVIDVVGTPEQPRLALVETAPGVTEEQARALTGAPLD +>PROKKA_00475 +MSEQTTERPQGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL +GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG +DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI +ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGAPLD +>PROKKA_02185 +MSEQSTERPEGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNYIPAGRSVVLQSENGIL +GTGPYPVEDEVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSSAG +DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI +ITDLAVIDVVGTPEQPRLRLVETAPGVSEEQVRDLTGAELD +>PROKKA_02083 +MSEQTTGRPRGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL +GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEISAAG +DLANWMVPGKMIKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI +ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGAPLD +>PROKKA_00709 +MSEQTTGRPQGLSRDQMAARAAQELPDGAYVNLGIGMPTLIPNHIPAGRSVVLQSENGIL +GTGPYPTEDAVDPDLINAGKETVTVNPGASFFDSALSFGMIRGGKIDVAVLGGMEVSAAG +DLANWMVPGKMVKGMGGAMDLVHGAGRVIVMMDHVSKDGTPKIVDQCTLPLTGRAVVDRI +ITDLAVIDVVGTPEQPRLALVETAPGVTEEQVRALTGASLD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000663.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000663.fa new file mode 100644 index 0000000000000000000000000000000000000000..40cba5650fcb7925f318609cfb14b5f1daf89e26 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000663.fa @@ -0,0 +1,30 @@ +>PROKKA_00750 +MERPENPATRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE +ESIRSTLSRARARDGVVGEEFGGSLSRSGRQWVVDPIDGTKNFVRGVPVWATLIALLIDG +EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRITVSGVDRVEDASLSFSSIEGWRER +GSIRAFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF +TSLDGEDGPFGGHALATNGLLHDDVLARLRAGDETEDSA +>PROKKA_00480 +MERPENPATRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE +ESIRSTLSRARARDGIVGEEFGGSLSRSGRQWVVDPIDGTKNFMRGVPVWATLIALLIDG +EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRITVSGVDRVEDASLSFSSIEGWRER +GSIRAFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF +TSLDGEDGPFGGHALATNGLLHDDVLARLRAGEEAEGGA +>PROKKA_02180 +MERPENPANRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE +ESIRSTLSRARARDGIVGEEFGGSLSRSGRQWVVDPIDGTKNFVRGVPVWATLIALLVDG +EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRISVSGVDDVADASLSFSSIEGWRER +GAIREFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF +TSLDGEDGPFGGHALATNGLLHEDVLARLRPSGGGED +>PROKKA_02075 +MDQTWNAARDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVSDADRAAEESI +RSTLSRARARDLILGEEFGGNLSRTGRQWVVDPIDGTKNFVRGVPVWATLIALLIDGEPV +VGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRIQVSDVDRVEDASLSFSSIEGWRERGAV +REFLQLTSDVWRVRGFGDFWSYMLLAEGAVDVATEPELALHDMAALVPIVREAGGRFTSL +DGEEGPFGGHALATNGLLHDEVLRRLTPGQD +>PROKKA_00714 +MERPENPATRGRDLTEDLRLAHMLADNVDSITMSRFKAQDLEVSTKPDLTPVTDADRAAE +ESIRSTLSRARARDGIVGEEFGGSLSRSGRQWVVDPIDGTKNFVRGVPVWATLIALLIDG +EPVVGVVSAPALHRRWWAAAGQGAFAGTSLTRAQRITVSGVDRVEDASLSFSSIEGWRER +GSIRAFLQLTSDVWRVRGFGDFWSYMLVAEGAVDIAAEPELELHDMAALVPIVREAGGRF +TSLDGEDGPFGGHALATNGLLHDDVLARLRAGDETEGGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000665.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000665.fa new file mode 100644 index 0000000000000000000000000000000000000000..2f6543e8dacb9792586613e6d904b1c1fcb2369f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000665.fa @@ -0,0 +1,47 @@ +>PROKKA_00752 +MTRPTRAAAHSPAPRPDAAETWPAPVARGPVRGEVRLPGSKSLTNRHLVLAALADGPCVL +HGVLESRDTALMRTALTALGARFEPLSDGGLRVHPMPVGEPLAGDVAVDCGLAGTVMRFV +PFVAALRPGRVRFDGDAGARLRPMAPVLDALRQLGVAVNEEGEPGRLPFTMTTRADAATV +APDGDVPEVAVDASGSSQFLSAALLAAAGMPRGLRLRHTGQTVPSPEHVAMTVGVLRALE +VDVAETGPGAWTVAPGRIPAHEATVEPDLSNAGPFLAAAVATGGSVTVPDWPTRTTQIGD +RWRRILPQFGASVALTVDRTDRSRGRLTVTGVVQDDGAPRITGAGEIADTAELAPTAAAL +ALLASGPTRLTGIGHLRGHETDRLAALTAEAARLGITVDEEETSLGFPGTDASGPLSPAA +LETYHDHRMATFAAVVGLRVPGTGIVDVATTAKTMPDFPALWTALVAPGDAAEEAR +>PROKKA_00482 +MTRPTRAATHSPAPRPDAAETWPAPMARGPVRGDVRLPGSKSLTNRHLVLAALADGPCIL +HGVLESRDAALMRTALTALGARFEPLSDGGLRVHPMPVGEPLAGDVAVDCGLAGTVMRFV +PFVAALRPGRVRFDGDAGARLRPMAPVLDALRQLGVAVVEEGEPGRLPFTTTTRADAATV +APDGDVPEVAVDAAGSSQFLSAALLAAAGMPRGLRLRHTGEAVPSPEHVAMTVGVLRALE +VDVAETGPGAWTVAPGRIPAHEATVEPDLSNAGPFLAAAVATGGSVTVPDWPTRTTQIGD +RWRRILPQFGASVALTVDRTDRSRGRLTVTGAVHDDGAPRITGAGEIADTAELAPTAAAL +ALLASGPTRLTGIGHLRGHETDRLAALTAEAARLGITVDEDETSLGFPGTDASGPLSPAA +LETYHDHRMATFAAVVGLRVPGTGIVDVATTAKTMPDFPALWTALVAPGDAAEEAR +>PROKKA_02178 +MTRPTPAPEDPSEHPSERPVEPLAGDVVAWPAPAARGPVRGTVRLPGSKSLTNRHLVLAA +VADGPVTLRGALVSRDSALMRAALESLGARFEDLPDGGLRVHPLPLGKPLEGEVEVDCGL +AGTVMRFVPFVAALRPGRVRFDGDAGARVRPMAPVIDALRRLGVAVHEEGEPGLLPFTVH +TPPDAATVAGGPRATEDGAPVPEAAVDAGASSQFLSGALLAAAAMPRGLRLRHTGATVPS +PEHVGMTVAVLRSLGVRVEQPDATSWTVAPGGIAAHEAAIEPDLSNAGPFLAAAAVTGGS +VTVPDWPTRTTQIGDRWRRILPAFGASVALTVDRTDRSRAALTVTGGTRPDGTPLVTGAR +DVADTAELAPTVAALALLAEGPTRLTGIGHLRGHETDRLAALAAESARFGVEVDEQADAL +GFPGTDASGPLTPAAAQTYHDHRMATFAAVVGLRVPGTAVVDVATTAKTMPDFPAMWASL +VAPAAGADEAGAL +>PROKKA_02073 +MTAPGPAAPSPTTPPCASAASRTPASAWPDPWPAPAAAGPVRGTVRVPGSKSLTNRCLVL +AAISAGPSVLHGVLRSRDTDLMRTALTALGARFEDRADGAVVVQPLPVGVPLEEPVAVDC +GLAGTVMRFVPAVAALRPGTVVLDGDAGARVRPMAPLLDGLAQTGTRVEFLGAEGFLPVR +LTTGEELGAEAAIDSSASSQFLSGLLLSAARRPAGLTLRHTGAQVPSPEHVAMTVQFLRE +HGVHVDTLEEGAWRVHPGAPAGVESAVEPDLSNAGPFLAAAAVTGGEVSVPDWPAATTQI +GDRWRSILPAFGAEVSFTPDPTDDARGTLTVRGGVDEAGRPRIAGAGELAGTAELAPTAA +ALALLASGPTHLTGIGHLRGHETDRLAAIAAEAGRFGVRVEESADALAFPGSDSSGPLRP +AEARTYHDHRMATFAAVVGLAVPGTAVQDVATTAKTLPDFPALWTALVGGEPAHDRPERD +EVR +>PROKKA_00716 +MTRPTRAAAHSPAPRPDAAETWPAPVAHGPVRGEVRLPGSKSLTNRHLVLAALADGPCVL +HGVLDSRDAALMRTALTALGARFEALSDGGLRVHPMPVGEPVAGDVAVDCGLAGTVMRFV +PFVAALRPGRVRFDGDAGARLRPMAPVLDALRQLGVAVNEEGEPGRLPFTMTTRADATTV +APDGDVPEVAVDASGSSQFLSAALLAAAGMPRGLRLRHTGQTVPSPEHVAMTVGVLRALE +VDVAETSPGAWTVAPGRVPAHEATVEPDLSNAGPFLAAAVATGGSVTVPDWPTRTTQIGD +RWRRILPQFGASVALTVDRTDRSRGRLTVTGAVHDDGTPRITGAGEIADTAELAPTAAAL +ALLASGPTRLTGIGHLRGHETDRLAALTAEAARLGVTVDEGETTLGFPGTDASGPLSPAA +LETYHDHRMATFAAVVGLRVPGTGIVDVATTSKTMPDFPALWTALVAPGDAAEEAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000666.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000666.fa new file mode 100644 index 0000000000000000000000000000000000000000..666a858a9c0fea3395f5d0544146e7f798f33d73 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000666.fa @@ -0,0 +1,30 @@ +>PROKKA_00753 +MSAALLTHPSRTVDWPAMSTDNSRPEFARPEDAPEHDRADIDVAAESEQQRRARFERDAL +EFVDQLYSAALRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY +RKRQRQPLEADNPEVEDWQMARAAEHTSGGLRSAETEALDRLPDSQVKDALQAIPEEFRL +AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAARGIKAQPKKKTGR +GGTKQTETSTKEATR +>PROKKA_00483 +MSAALLTHASRTVDWPAMSTDNSRPEFARPEDAPEHDRADIDVAAESEQQRRARFERDAL +EFVDQLYSAALRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY +RKRQRQPLEADNPEVEDWQMARAAEHTSGGLRSAETEALDRLPDSQVKDALQAIPEEFRL +AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAARGIKAQPKKKTGR +GGTKQTETSTKEATR +>PROKKA_02177 +MTTALMARPDRDVDWRVMSTDNNLPEIARPADAPEHDRADIDVAAEDEQQRRARFERDAL +EFVDQLYSAAMRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY +RKRQRQPLEADSPEVEDWQMARAAEHTSSGLRSAETEALDHLPDSEVKDALQAIPEEFRL +AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAERGIKAQPKKTGRG +AAKKTETSTKEATR +>PROKKA_02072 +MAATLLERPVLTGSRGAAVDWPAMSTQNSTPEIARPADAPALDLPGIDVDAESEAQRRAR +FERDALEFVDQLYSAAMRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTN +TYINLYRKKQRQPLEADTDTVEDWQMARAAEHTSSGLRSAETEALDHLPDSEVKDALQAI +PEEFRLAVYFADVEGYAYKEIAEILDIPIGTVMSRLHRGRKQLRERLTDYAGERGMGPKG +RTAQETSTQEEKR +>PROKKA_00717 +MSAALLTHPSRTVDWPAMSTDNSRPEFARPEDAPEHDRADIDVAAESEQQRRARFERDAL +EFVDQLYSAALRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTNTYINLY +RKRQRQPLEADNPEVEDWQMARAAEHTSGGLRSAETEALDRLPDSQVKDALQAIPEEFRL +AVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAARGIKAQPKKKTGR +GGTKQTETSTKEATR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000667.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000667.fa new file mode 100644 index 0000000000000000000000000000000000000000..4785237f1a4da4a12be36a7339089587b5b2fda6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000667.fa @@ -0,0 +1,15 @@ +>PROKKA_00754 +MTADQHGHECRVAQDASLERLYQYLDGALTPEDIEQVRAHVAECPDCRHQKELEELIRSA +VRRCCQEKAPAQLRATIMTRITQISTTTVTWG +>PROKKA_00484 +MTVDQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA +VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG +>PROKKA_02176 +MTADQHGRECRDAQEDTLERLYQYLDGALTPEEIDQVRAHVEDCEDCRHQQELEQFIRTA +VRRSCQEKAPEQLRTTILTRITQLSTTRVTWR +>PROKKA_02071 +MSQDGDCRGCNDGEDRLEQLYQYLDGALTPEDIDQVRAHVDQCPDCHHQQELELIIRSAL +RRSCQEKAPAQLRATIMTRITQVSTTTVRRAG +>PROKKA_00718 +MTADQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA +VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000670.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000670.fa new file mode 100644 index 0000000000000000000000000000000000000000..3e3ddd95f9f09f64ca48108d1b30bba7c30b88eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000670.fa @@ -0,0 +1,50 @@ +>PROKKA_00757 +MRFLTDPAVDLTYNDVFLVPSHSDVASRMDVDIAPDDGTGATIPLVSANMTAVTGRRMVE +TMARRGGLGILPQDIPADVIRDVVRRVKAAHPVADTALTVGPQDTVLDLLHLVDRRNHGA +VCVVDAHGGLLGVVRPQDCEDVDRFTSAASVMHPPAVTLTLAELGGTDGAPDKDALRAAF +ERLHAAHQEMAPVVDPAVGTAAPVLRGVVTAAGLLRSSLFTPGLDDDGRLRVGAAVGING +AVGEKAAVLVEAGVDVLVVDTAHGHQQTMLDALAAVRALDPGVPVVAGNVVSGDGVRDLV +AAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAARELGARVWADGGVKHPRDVA +LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA +RKAMFEEGISSSRMYVDPRRPSVEDLLDTITSGVRSSLTYAGAHDLAEFRERAVVGLQSA +AGYEEGRPVASSW +>PROKKA_00487 +MRFLTDPAVDLTYNDVFLVPSHSDVASRMDVDIAPDDGTGATIPLVSANMTAVTGRRMVE +TMARRGGLGILPQDIPADVIRDVVRRVKAAHPVADTALTVGPQDTVLDLLHLVDRRNHGA +VCVVDAHGGLLGVVRPQDCEDVDRFTSAASVMHPPVVTLTLAELGGTDGAPSKDALRAAF +ERLHAAHQEMAPVVDPAVGTAAPVLRGVVTAAGLLRSSLFTPGLDDDGRLRVGAAVGING +AVGEKAAVLVEAGVDVLVVDTAHGHQRTMLDALAAVRALDPGVPVVAGNVVSGDGVRDLV +AAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAARELGARVWADGGVKHPRDVA +LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA +RKAMFEEGISSSRMYVDPRRPSVEDLLDTITSGVRSSLTYAGAHDLAEFRERAVVGLQSA +AGYEEGRPVASSW +>PROKKA_02173 +MRFLTSPTVDLTYNDVFLVPSHSEVTSRLDVDIAPDDGTGATIPLVSANMTAVTGRRMVE +TMARRGGLGILPQDIPVEVIAEVVRRVKSAHPVADTALTVGPQDTVLDLLHLVDRRNHGA +VCVVDADGGLLGVVRPRDCEDVDRFASAASVMQPASVTLTPAELGEAGGADGGQALRAAF +DRLNAAGQDMAPVVEPAAGSAAPALRGVVTAAGLLRSSLFTPSLDDAGRLRVGAALGVNG +AVGDKAAALVEAGVDVLVVDTAHGHQQSMLDALAAVRALDAPVPVVAGNVVSADGVRDLV +EAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECSAAARDLGARVWADGGVKHPRDVA +LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA +RKAMFEEGISSSRMYVDPRRPSVEDLIDTITSGVRSSLTYAGAQDLAQFRERAVVGVQSA +AGYEEGRPVASSW +>PROKKA_02068 +MRLMHEPAVDLTYNDVFLVPSHSEVGSRTAVDIAPDDGTVGSVPLVSANMTAVTGRRMAE +TLARRGGLGVLPQDVPVDVVAKTVAAVKAAHAVADTALTVDAHATVLDVLHLVDRRAHGA +VCVVDDDGRLLGVAGAEDCGDVDRFASVVSVMRTPSVLLSPADLEGPDAPRAAFEVLHAA +GRPLAPVVEDPVADRPVLRGVVTGQGLVRSSLAAPALDASGRLQVGAALGVNGDVGSRAA +ALLAAGADVLVVDTAHGHQRVMRDALAAVRALDPEVPVVAGNVVTAEGVRDLVAAGADVV +KVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAAREVGARVWADGGVKHPRDVALALAAGA +SQVMIGSWFAGTLESPGDLVQGSDGRRYKESFGMASARAVEHRTRDEDAFSRARKAMFEE +GISSSRMYVDPRRPSVEDLVDGITAGLRSSLTYAGAANLAQFRERAVVGVQSAAGYEEGR +PVPASW +>PROKKA_00721 +MRFLTDPAVDLTYNDVFLVPSHSDVASRMDVDIAPDDGTGATIPLVSANMTAVTGRRMVE +TMARRGGLGILPQDIPADVIRDVVRRVKAAHPVADTALTVGPQDTVLDLLHLVDRRNHGA +VCVVDAHGGLLGVVRPQDCVGVDRFASATSVMHPPAVTLTLAELGGTDGAPSKDALRAAF +ERLHAAHQEMAPVVDPAVGTAAPVLRGVVTAAGLLRSSLFTPGLDDDGRLRVGAAVGING +AVGEKAAVLVEAGVDVLVVDTAHGHQRTMLDALAAVRALDPGVPVVAGNVVSGDGVRDLV +AAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAARELGARVWADGGVKHPRDVA +LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA +RKAMFEEGISSSRMYVDPRRPSVEDLLDTITSGVRSSLTYAGAHDLAEFRERAVVGLQSA +AGYEEGRPVASSW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000671.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000671.fa new file mode 100644 index 0000000000000000000000000000000000000000..e132a95fde3088d7b8e54522f6f30f2d73031e30 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000671.fa @@ -0,0 +1,45 @@ +>PROKKA_00758 +MEWLLLILGLALIVGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS +ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE +LIPKNMSIAEPMAIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS +PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVREDQALPEVLD +LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ +LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF +PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR +RIERVRFDPAAEDEETRA +>PROKKA_00488 +MEWLLLILGLALIVGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS +ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE +LIPKNMSIAEPMAIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS +PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVREDQALPEVLD +LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ +LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF +PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR +RIERVRFDPAAEDEETRA +>PROKKA_02172 +MEWLLLILGFALVLGTGFFVAVEFSMIAIDVPTVQRMVDEGDKGAEPLLRCLKSLSTQLS +ACQLGITLTTLLTGYVMDPAISRLIDPVLLDVGVPESVVGTVSLVVAMVVATLLSMLIGE +LIPKNMAIAEPMTIGRALARPQLLFSTVFKPAILVLNGFSNGVLARFGIEAKEEISGARS +PEELSSLVRRSAQLGTLDEQTATFLDRTLRFADRTAADVMTPRIRVETVGEDQPLPEVVD +LARRTGFSRFPVIGESSDDIRGVVHVKKVVAVPRERRADLEAGSLMTEVIRVPETVHLDQ +LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDKVTPGVLQTAAGRWYF +PAELRPDEAQAQITSLSVPEDGAYETIGGFIMARLGRLAAVGDVVSVDGGTLSVERMDGR +RVERVRFDPAAAADKEARA +>PROKKA_02067 +MEWILLILGLLLVLGTGFFVMVEFSLIAIDAPTVQRMVDDGDRSWEPLLTCLKSLSTQLS +ACQLGITLTTLLTGYVMDPAISRLVDPLILAVGLPQSVAGPVSLVVAMAAATLLSMLLGE +LVPKNMAIAEPLRLGRALARPQLVFAAVFKPAILVLNGFSNGVLHRMGLEAKEEISGARS +PEELSSLVRRSAQLGTLDEQTATFLDRTLRFAERTAADVMTPRIRMETVGEDDGLLDVVE +LARRSGYSRFPVIGESPDDVLGVVHVKKAVAVPMDRRADLTAGALMTDVIRVPETVHLDQ +LLAELREASLQLAIVVDEYGGTAGVVTLEDVVEEIVGEVSDEHDRVTPGVLQTASGRWYL +PAELRPDEAHAQIKALDVPEDGAYETIGGFVMARLGRIPAVGDVVPLDVGTLTVERMDGR +RVDRVRFDPRPVTEEARA +>PROKKA_00722 +MEWLLLILGLLLIAGTGFFVAVEFAMIAIDVPTVQRMVDAGDRGAEPLLRCLKSLSTQLS +ACQLGITLTTLLTGYVMDPAISRLIDPLLLQVGLPAGVVGTVSLVVAMVVATLLSMLLGE +LIPKNMSIAEPMTIGRALARPQLVFSTVFKPAILVLNGFSNGVLARVGIEAKEEISGARS +PEELSSLVRRSAQLGTLDAQTATFLDRTLRFADRTAADVMTPRIRVETVGEDQALPEVLD +LARSTGYSRFPVIGDSSDDIRGVVHVKKVVAVPRERRADLEAGALMTEVIRVPETVHLDQ +LLAELRDANLQMAVVVDEYGGTAGVVTLEDVVEEIVGEVADEHDRVTPGVLQTASGRWYF +PAELRPDEVRTQIPALVVPEDGAYETVGGYILARLGRLAEVGDVVDVDGGTLTVERMDGR +RIERVRFDPAAEDEETRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000675.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000675.fa new file mode 100644 index 0000000000000000000000000000000000000000..b8dde0d0451f09a5f9602dd4eedd9666220e6df3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000675.fa @@ -0,0 +1,20 @@ +>PROKKA_00763 +MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT +LQQQLDDGLVDVLRRDDGESVYRRCEDEGHHHHLVCRSCWTTVEVTAPHVEAWATAVAAE +HGFTDADHTVEITGVCARCRTEGRTRGA +>PROKKA_00493 +MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT +LQQQLDDGLVDMLRRDDGETVYRRCEDEGHHHHLVCRICWTTVEVTAPHVEAWATAVAAE +HGFTDADHTVEITGVCARCRTEGRTRGA +>PROKKA_02167 +MSAPDPGPRVVRPRATRQKAAVDRALETIPDFVSAQELHARLQEEGERISLATVYRTLQQ +QLEDGQVDVLRREDGESVYRRCEARGHHHHLVCRLCWSTVEVTAPPVEAWAARIAAEHGF +TEAEHTVEITGVCADCAATRAADAG +>PROKKA_02062 +MSETPGRPSEAPAPRGRSTRQKAAVDGALDAAEDFVSAQELHARLRDAGERVSLATVYRA +LQQRLDEGTVDMLRREDGESVYRRCAAEGHHHHLVCRVCWTTVEVTAPGVEEWAARMAAE +HGFSDPDHTVEITGVCAECRAAGRG +>PROKKA_00727 +MSTVSAPEPSPRAARPRATRQKAAVDRALDRIPDFVSAQELHARLQDQGERVSLATVYRT +LQQQLDDGLVDMLRRDDGESVYRRCEDEGHHHHLVCRICWTTVEVTAPHVEAWATAVAAE +HGFTDADHTVEITGVCARCRAEGRTRAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000679.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000679.fa new file mode 100644 index 0000000000000000000000000000000000000000..c98d3e5adbe90d8dfebb8c82b3d3d2fe9989bcd1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000679.fa @@ -0,0 +1,53 @@ +>PROKKA_00767 +MDTNTVFLLAAIGLYFLAMIAIGLYASRKNTDLDDYMLAGRDMKPSVAALSAGASDMSGW +LLMGLPGAIYAAGLVEGWMAVGLTVGAWVNWRVVAPRLRSYTEVAGNSITIPSFLENRFK +DRTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPESFYAQGISINYLTGMLVVAG +ITVLYTLFGGFLGASLTDVAQGVLMFLSLLAVPIVVILTMGGWDAVVEGIRAADAAGGGV +NHFSMFENATLIGVLSSLAWGLGYFGQPHIIVRFMALRTPHDAAVARRVGIGWMALSVFG +AVMVALVGIAYFQANPGTTLEDPETVFLVLASIMFHPFVAGLVLAAVLAAIMSTLSSQLI +VCSSALVEDLYMLRGRTGSPTFTLWLGRIGVLVVALVAGLLALDPDSSVLELVSFAWAGF +GAAFGPVILLALYWPRFTSWGAMAAMVTGAAVAWVWSEASAETWEWFGLYELLPGFVAAF +VVGVVVSLVTQRSRRVQRRIDAEFTGAIDIVAGREPDPDVAPAAMTRDAAGGSTAAAADP +RAQA +>PROKKA_00497 +MDTNTVFLLAAIGLYFLAMIAIGLYASRKNTDLDDYMLAGRDMKPSVAALSAGASDMSGW +LLMGLPGAIYAAGLVEGWMAVGLTVGAWVNWRVVAPRLRSYTEVAGNSITIPSFLENRFK +DRTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPDSFYAQGISINYLTGMLVVAG +ITVLYTLFGGFLGASLTDVAQGILMFLSLLAVPIVVILTMGGWDAVVEGIRAADAAGGGV +NHFSMFENATLIGVLSSLAWGLGYFGQPHIIVRFMALRTPHDAAVARRVGIGWMALSVFG +AVMVALVGIAYFQANPGTTLEDPETVFLVLASIMFHPFVAGLVLAAVLAAIMSTLSSQLI +VCSSALVEDLYMLRGRTGSSTFTLWLGRIGVLVVALVAGLLALNPDSSVLELVSFAWAGF +GAAFGPVILLALYWPRFTSWGAMAAMVTGAAVAWAWSEASAETWEWFGLYELLPGFVAAL +VVGVVVSLVTQRSRRVQRRIDAEFTGAIDIVAGREPHPDVAPAAMTRDAAGGSTAAAADP +RAQA +>PROKKA_02162 +MDQNTFFLILAIGLYFAAMIAIGLWASRKNTDLDDYMLAGRDMKPGVAALSAGASDMSGW +LLMGLPGAVYAAGLVEAWMAIGLTVGAWINWKVVAPRLRAYTQVAGNSITIPSFLENRFQ +DRTHILRIVSGLIILVFFTFYVSSGMVAGGKFVESTFGPESLYAQGVSVNYLTGMLVVAG +ITVLYTLFGGFLGASLTDVAQGTIMFLALIAVPIATIVAMGGWGAMVEGLRAADAASAAA +GEAVDHLSLFHNATLIGVLSSLAWGLGYFGQPHIIVRFMALRTVQDASTARRIGIGWMAL +SVFGAVMVALVGIAYFQANPGTTLADPETVFLVLASILFHPFIAGLVLAAVLAAIMSTLS +SQLIVCSSALVEDLYKLTGRQGSPRAMVWLGRIGVLVVAVVAGLLALDPESSVLELVSFA +WAGFGAAFGPVILLALYWQRFTSWGAMAAVVTGALVAWLWSEASAETWEWFGLYELLPGF +IAALVVGVVVSLLTQRSRPVQTRIEREFTGAVDVVAGRAAPTA +>PROKKA_02058 +MDSNTAFLLAAIGLYFVAMIAIGLYAARRNNDLDDYMLAGRDMKPGVAALSAGASDMSGW +LLMGLPGAVYASGLIEGWMAIGLIVGAWVNWKVVAPRLRSYTEVAGDSITIPTFLENRFK +DHTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPDSIYAQGVSVNYLTGMVVVAG +ITVLYTLFGGFLGASLTDVAQGVLMFLALLVVPVAVIATMGGWDQVLEGIRAADAAVGPE +ADRFSLFQNATRIGVLSSLAWGLGYFGQPHIIVRFMALRTPQDAAAARRIGIGWMVLSVF +GAVMVGLVGLAYFQANPGTELNDPETVFLVLASILFHPFVAGLVLAAVLAAIMSTLSSQL +IVCSSALVEDLYMLRGRRGSPRTMVWLGRIGVLVVALIAGLLALNPDASVLELVSFAWAG +FGAAFGPVILLALYWERFTSWGAMAAMVVGAAVAWFWSTASADTWDWFGLYELLPGFVAA +LAAGVVVSRLTRRPDHVQEHISGEFTGAADIVAGREPTALTGSTGAVGGSTAAPRA +>PROKKA_00731 +MDTNTVFLLAAIGLYFLAMIAIGLYASRKNTDLDDYMLAGRDMKPSVAALSAGASDMSGW +LLMGLPGAIYAAGLVEGWMAVGLTVGAWVNWRVVAPRLRSYTEVAGNSITIPSFLENRFK +DRTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPDSFYAQGISINYLTGMLVVAG +ITVLYTLFGGFLGASLTDVAQGILMFLSLLAVPIVVILTMGGWDAVVEGIRAADAAGGGV +NHFSMFENATLIGVLSSLAWGLGYFGQPHIIVRFMALRTPHDAAVARRVGIGWMALSVFG +AVMVALVGIAYFQANPGTTLEDPETVFLVLASIMFHPFVAGLVLAAVLAAIMSTLSSQLI +VCSSALVEDLYMLRGRTGSPTFTLWLGRIGVLVVALVAGLLALNPDSSVLELVSFAWAGF +GAAFGPVILLALYWPRFTSWGAMAAMVTGAAVAWVWSEASAETWEWFGLYELLPGFVAAF +VVGVVVSLVTQRSRRVQRRIDAEFTGAIDIVAGREPDPDVAPAAMTRDAAGGSTASAADP +RAQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000680.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000680.fa new file mode 100644 index 0000000000000000000000000000000000000000..a4b7e00d4b610802eef7d92414043710e680fe85 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000680.fa @@ -0,0 +1,29 @@ +>PROKKA_00770 +MSAHHADDGLPAPVSTLAEDPPADGRQAPPSGVVVGEDGRARPPWAARDPLLREYYDTEW +GLPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFREVFAGFDPDAVAAFGDAEVEALLA +DPGIIRNRRKIEAAVANAQAVVGMRGERFAPLHPGAPGAGPAWHGDGDRPARGLPGLVWA +HQPAATPRPETVAQVPSTSDESRALARALKAHGCRFVGPTTCFALLEAAGIVDTHLLGSW +RRGASGIWE +>PROKKA_00501 +MSAHHADDGLPAPVSTLAEDPPADGRQAPPSGVVVGEDGRARPPWAARDPLLREYYDTEW +GLPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFREVFAGFDADAVAAFGDAEVEALLA +DPGIIRNRRKIEAAIANAQAVVGMRGERFTPLHPGSPGAGPAWHGDGDRPARGLAGLVWA +HQPAATPRPETVAQVPSASEESRALARALKAHGCRFVGPTTCFALMEAAGVVDTHLLGSW +RRGASGIWE +>PROKKA_02160 +MTKEHRTDHDAGDDAGPAAPVRSAAGAAEPPAGVVVGEDGRARAPWADRDPLLRAYYDEE +WGVPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFREAFAGFDPDAVAGFGPERVEELL +QDAGIIRNRAKVEAAIANAQAVVGMRDEPWTPLHPGSPGAGPGWDGPGDRPDRGLAGLVW +AHQPAATPRPGTVAEVPSASDESRALATALKARGCRFVGPTTCFALMEAAGIVDTHLLSS +WRRGASGIWE +>PROKKA_02056 +MDEENSEAAGLVLGADGRARAAWAAADPLLRDYYDAEWGLPVTDERGLFERLTLEAFQSG +LSWRTVLAKRPRFREVFAGFDPDAVAAFGAVEVEALMADAGIIRNRRKIDAALANARAVV +GIRDEVFAPLHPGSPGAGPAWDGEGDRPGTGLPGLVWAHQPAQTPTPRTIGEVPSASPES +TALAKALKARGCRFVGPTTCFALLEAAGVVDTHLVSSWRRGASGIWA +>PROKKA_00734 +MSAHHADDGLPAPVSTPAEDPPADGRQAPPSGVVVGEDGRARPPWAARDPLLREYYDTEW +GLPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFWEVFAGFDADAVAAFGDAEVEALLS +DPGIIRNRRKIEAAIANARAVVGMRGERFAPLHPGAPGAGPAWHGDGDRPARGLPGLVWA +HQPAATPRPETVAQVPSTSDESRALARALKAHGCRFVGPTTCFALLEAAGIVDTHLLGSW +RRGASGIWE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000681.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000681.fa new file mode 100644 index 0000000000000000000000000000000000000000..22bf42e3de09d4ab3d8ddda5c64959ed9c792d70 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000681.fa @@ -0,0 +1,60 @@ +>PROKKA_00771 +MSVSERTPLPAAESTAEVVAEENYPTHRLGWLEDAEHGIRVPVTEVHQDDSPDGTPNAPL +TVYRTMGPGSVPERGLPAQRAEWIRARGDVEEYEGRERDLLDDGRSAVRRGAASQEWAGE +RRPPLRAKEGARVTQMHYARRGEITPEMRYVALREGVDVELVRSEVAAGRAIIPANVNHP +ESEPMIIGKAFAVKVNANIGNSAVTSSIAEEVSKLQWATRWGADTVMDLSTGDDIHTTRE +WILRNSPVPIGTVPIYQALEKVGGDHQALTWEIFRDTVIEQCEQGVDYMTVHAGVLLRHV +PLSADRVTGIVSRGGSIMAGWCLGHHKENFLYENYDELCEIFARYDVAFSLGDGLRPGSV +ADANDAAQFAELDTLAELTERAWAYDVQVMVEGPGHIPLHLVRENVERQQELCKGAPFYT +LGPLVTDIAPAYDHITSAIGATEIARYGTAMLCYVTPKEHLGLPNRDDVKTGVITYKIAA +HAADVAKGHPGARDRDDALSKARFEFRWRDQFGLGLDPQLAEEYHDETLPAEPAKTAHFC +SMCGPKFCSMRISQDIRSEFGGASEQARIAEAGMAAKSAEFRAAGGSVYLPEPSLRRPEG +DAVLARD +>PROKKA_00502 +MSVSEHTPLPAAESTAEVVAEENYPTHRLGWLEDAEHGIRVPVTEVHQDDSPDGTPNAPL +TVYRTMGPGSVPERGLPAQRAEWIRARGDVEEYEGRERDLLDDGRSAVRRGAASQEWAGE +RRAPLRAKEGARVTQMHYARRGEITPEMRYVALREGVDVELVRSEVAAGRAIIPANVNHP +ESEPMIIGKAFAVKVNANIGNSAVTSSIAEEVSKLQWATRWGADTVMDLSTGDDIHTTRE +WILRNSPVPIGTVPIYQALEKVGGDHQALTWEIFRDTVIEQCEQGVDYMTVHAGVLLCHV +PLSADRVTGIVSRGGSIMAGWCLGHHKENFLYENYDELCEIFARYDVAFSLGDGLRPGSV +ADANDAAQFAELDTLAELTERAWAYDVQVMVEGPGHIPLHLVRENVERQQELCKGAPFYT +LGPLVTDIAPAYDHITSAIGATEIARYGTAMLCYVTPKEHLGLPNRDDVKTGVITYKIAA +HAADVAKGHPGARDRDDALSKARFEFRWRDQFGLGLDPQLAEEYHDETLPAEPAKTAHFC +SMCGPKFCSMRISQDIRSEFGGASEQARIAEAGMAAKSAEFRAAGGSVYLPEPSLRRPEG +DAVLARD +>PROKKA_02159 +MSVSERTPLPAAESTAEVVAEENYPTHRLGWLEDAEHGIRVPVTEVHQDDSPDGTPNAPL +TVYRTMGPGSVPEHGLPAQRAEWIRARGDVEEYEGRDRDLLDDGRSAVRRGAASQEWAGE +RRAPLRAKEGARVTQMHYARRGEITPEMRYVALREGVDVELVRSEVAAGRAIIPANVNHP +ESEPMIIGKAFAVKVNANIGNSAVTSSIAEEVSKLQWATRWGADTVMDLSTGDDIHTTRE +WILRNSPVPIGTVPIYQALEKVGGDHQALTWEIFRDTVIEQCEQGVDYMTVHAGVLLRHV +PLSADRVTGIVSRGGSIMAGWCLGHHKENFLYEHYDELCEIFARYDVAFSLGDGLRPGSV +ADANDAAQFAELDTLAELTERAWAYDVQVMVEGPGHIPLHLVRENVERQQELCKGAPFYT +LGPLVTDIAPAYDHITSAIGATEIARYGTAMLCYVTPKEHLGLPNRDDVKTGVITYKIAA +HAADVAKGHPGARDRDDALSKARFEFRWRDQFGLGLDPQLAEEYHDETLPAEPAKTAHFC +SMCGPKFCSMRISQDIRSEFGGASEQARIAEAGMAAKSAEFRAAGGSVYLPEPTLRGAAD +A +>PROKKA_02054 +MSASHHTPVPPQSEAVPTAEENYPTHRLGWLEDAEHGIRVPVTHVHQDDSPDGTPNPPFA +VYRTMGPGSVPERGLPAQRAEWIAARGDVEEYEGRERDLLDDGRSAVRRGAASQEWAGER +RPPLRAKEGARVTQMHYARRGEITPEMRYVALREGVDAELVRSEVAAGRAIIPANVNHPE +SEPMIIGKAFAVKVNANIGNSAVTSSIAEEVSKLQWATRWGADTVMDLSTGDDIHTTREW +ILRNSPVPIGTVPIYQALEKVGGDHQALTWEIFRDTVIEQCEQGVDYMTVHAGVLLRHVP +LSADRVTGIVSRGGSIMAGWCLGHHRENFLYENYDELCEIFARYDVAFSLGDGLRPGSVA +DANDAAQFAELDTLAELTERAWAYDVQVMVEGPGHIPLHLVRENVERQQELCKGAPFYTL +GPLVTDVAPAYDHITSAIGATEIARYGTAMLCYVTPKEHLGLPNRDDVKTGVITYKIAAH +AADVAKGHPGARDRDDALSTARFEFRWRDQFGLGLDPQLAEEYHDETLPAEPAKTAHFCS +MCGPKFCSMRISQDIRSEFGGESEQARIAEAGMAAKSAEFRAAGGSVYLPEPSMRRPEGD +AALAAD +>PROKKA_00738 +MSVSERTPLPAAESTAEVVAEENYPTHRLGWLEDAEHGIRVPVTEVHQDDSPDGTPNPPL +PVYRTMGPGSVPERGLPAQRAEWIRARGDVEEYEGRERDLLDDGRSAVRRGAASQEWAGE +RRPPLRAKEGARVTQMHYARRGEITPEMRYVALREGVDVELVRSEVAAGRAIIPANVNHP +ESEPMIIGKAFAVKVNANIGNSAVTSSIAEEVSKLQWATRWGADTVMDLSTGDDIHTTRE +WILRNSPVPIGTVPIYQALEKVGGDHQALTWEIFRDTVIEQCEQGVDYMTVHAGVLLRHV +PLSADRVTGIVSRGGSIMAGWCLGHHKENFLYENYDELCEIFARYDVAFSLGDGLRPGSV +ADANDAAQFAELDTLAELTERAWAYDVQVMVEGPGHIPLHLVRENVERQQELCKGAPFYT +LGPLVTDIAPAYDHITSAIGATEIARYGTAMLCYVTPKEHLGLPDRDDVKTGVITYKIAA +HAADVAKGHPGARDRDDALSKARFEFRWRDQFGLGLDPQLAEEYHDETLPAEPAKTAHFC +SMCGPKFCSMRISQDIRSEFGGASEQARIAEAGMAAKSAEFRAAGGSVYLPEPTIRTASD +A diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000685.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000685.fa new file mode 100644 index 0000000000000000000000000000000000000000..54fc97dd08b27afb58a29d30e5db479e91246a88 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000685.fa @@ -0,0 +1,40 @@ +>PROKKA_00776 +MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDAAGRPHAVAGATHAAAGMLAPLAETQ +FSQDDLAPLLQAGWEAYPALVDLLAAFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS +ILGRRVEPVSVRALRRAEPALAPGLAAGFDAPDDHQVDPRRLAAACVAALRAETGPDGGP +LPVGAGPAARFVAGRVTAAGPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE +VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED +GLAGTSAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLTVPEAPGAVVAT +GFHRHGILLAPWAAGRILELLHARLKEIA +>PROKKA_00507 +MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDAAGRPHAVAGATHAAAGMLAPLAETQ +FSQDDLAPLLQAGWEAYPALVDLLAAFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS +ILGRRVEPVSVRALRRAEPALAPGLAAGFDAPDDHQVDPRRLAAACVAALRAETGPDGGP +LPVGAGPAARFVAGRVTAAGPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE +VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED +GLAGTSAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLAVPEAPGAVVAT +GFHRHGILLAPWAAGRILELLHARLKEIA +>PROKKA_02154 +MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDAAGRPHAVAGATHAAAGMLAPLAETQ +FSQDDLAPLLQAGWEAYPALVGLLAVFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS +ILGRRVEPVSVRALRRAEPALTPGLAAAFDAPDDHQVDPRRLAAACVAALRAETGPDGGP +LPAGAGPAARFVAGRVTAADPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE +VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED +GLAGTCAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLTVPEAPGAVVAT +GFHRHGILLAPWAAGRILELLHARLKEIA +>PROKKA_02049 +MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDTAGRPHAVAGATHAAAGMLAPLAETQ +FSQDALAPLLHAGWKGWPLLVDLLAGFSDVGTGFRTEGSWIVAADPSDVLAWEHVLAHAS +ALGRRVEPVAVRALRRAEPALAPGLAAGFDAPDDHQVDPRRAAAACLAALVAEAGPDGGP +LPAGAGPAARLVSGTVTSADPVGSGVGLTLADGGILTADGAVLAAGLGHRGIGGAATAEV +PLRPVHGDVLRLRVRPEQLLPGEDHLITRTVRGLVHGRQVYLVPRADGTLVVGASAREDG +LAGTSAGSVLDLLADAAAILPAVRECELAEVTTAARPGTPDDAPRVEVVPGAPVVVATGF +HRHGILLAPWAAGRVLDLLTALPKETA +>PROKKA_00743 +MHVAVVGAGIIGLTAAVRLRAAGHAVTLIAPELDTAGRPHAVAGATHAAAGMLAPLAETQ +FSQDDLAPLLQAGWEAYPALVDLLAAFTDVETGFLAQGAWIVAADPSDARAWDHVLEHAS +ILGRRVEPVSVRALRRAEPALTPGLAAGFDAPDDHQVDPRRLAAACVAALRAETGPDGGP +LPTGAGPAARFVAGRVTAADPEGEGVRLTLADGGVLTADGAVLAAGLGHRGIGGAATAVE +VPLRPVHGDVLRLRVRPEQLLPGESHLITRTVRGLVHGRQVYLVPRADGTLVVGASARED +GLAGTSAGAVLDLLADAAAILPAVRECELVEITTAARPGTPDDAPRVLAVPEAPGAVVAT +GFHRHGILLAPWAAGRILELLHAHLKEIA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000686.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000686.fa new file mode 100644 index 0000000000000000000000000000000000000000..a51f1de41d7117a0d165402f83dac83e94a3dfbc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000686.fa @@ -0,0 +1,15 @@ +>PROKKA_00777 +MSTLTLTLNGEPAELAVATVRDVVAHVTGRAIGEDGAAADGRRLGVAVAVGGEVVPRSAW +ATRELAAGDEVDVVTAVQGG +>PROKKA_00508 +MSTLTLTLNGEPAELAVATVRDVVAHVTGRAIGDDGAAADGRRLGVAVAVGGEVVPRSAW +ATRALAAGDEVDVVTAVQGG +>PROKKA_02153 +MSTLTLTLNGEPAELAAATVRDVVAHVTGRAIGDDGAAADARRLGVAVAVGGEVVPRSAW +ATRELTAGDEVDVVTAVQGG +>PROKKA_02048 +MSALPLTLNGEPAELDGPTVRDVVEHVTGRTVRDDGAAADGRRLGVAVAVDGEVVPRSAW +AARTLAGGEAVEVVTAVQGG +>PROKKA_00744 +MSTLPLTLNGEPAELAVATVRDVVAHVTGRAIGDDGAAADGRRLGVAVAVGGEVVPRSAW +ATRALAAGDEVDVVTAVQGG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000688.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000688.fa new file mode 100644 index 0000000000000000000000000000000000000000..80f73aa834f47a4fb7d4531509111b8757d705e5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000688.fa @@ -0,0 +1,40 @@ +>PROKKA_00779 +MTAALDPAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV +LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH +RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP +GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSV +DALTMRFRELRLVPDPERTPVTDLSAHADQAPRPDDAGAPGSAEACGAAGGEIAPAALAA +LLADPARVASLTLLDVREDWERRLRRVEAPAAVADRHVPLEAVLAEPAALAPGRDRVLVV +YCAAGARSARARDAVVGADPSAGGRVLSLAGGLAAWPA +>PROKKA_00510 +MTAALDPAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV +LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH +RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP +GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIVGSLMAAEAIKLLSGVGEPLVGRLLSV +DALTMRFRELRLVTDPERTPVTDLSAHAAQAPRPDDAGAPGSAEACGAAGEEIAPAALAA +LLADPARAASLTLLDVREDWERRLRRVEAPAAVADRHVPLEAVLAEPAAHAPGQDRVLVV +YCAAGARSARARDAVVGADPSSGGRVLSLAGGLAAWPA +>PROKKA_02151 +MTAAPDPADREPRDLTALSDTQLQRFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPV +LTYLAAAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEH +RERLTAANALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAP +GGPLYRDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSV +DALTMRFRELRLVADPERTPVTDLSAHADQAPGSDDAGAPGSAEACGAAGGEIDPATLAA +LLADPARAASLTLLDVREDWERRLRRVEVPAAVADRHVPLDAVLAEPAAHAPGPDRVLVV +YCAAGARSARARDAVVAADPSAGERVLSLVGGLAAWPA +>PROKKA_02046 +MSRPAGEPLVPEDRAPHSLDELSDTQLQRFARHLGLDGFGPEAQLALLRSRVLVVGAGGL +GAPVLTYLAAAGVGEVHVVDDDVVDRSNLHRQVIHVETDLGRPKTASAAETMRGLHPEIR +VVEHRQRLAAANALELVGAVDLVVDGSDNYATRYLVADAGEITGVPVVWGAILRFAGQVS +VFAPGGPLYRDVFPEEPEPGDVPTCAQAGVLGVLPGIVGSLMAAEAVKLLAGVGEPLTGR +LLSVDALTMRFSTLRLVPDPERTSVTDLSAHTVPRGGADPVESGEITPAGLAALLADPER +AAALTLLDVREDWERGLARISAPAAAEDRHVRLDEVLADPAAHSPESGRTVVVYCAAGAR +SARAREAVVAAAPEAADRVLSLAGGHAAWADRN +>PROKKA_00746 +MTAAREPRDLTALSDTQLERFARHLSLDGFGPEAQLALLRSRVLVVGAGGLGAPVLTYLA +AAGVGEVHVIDDDVVDRSNLHRQVIHAEADLGRPKTASAAATMRGLHPEVRVVEHRERLT +ATNALERVGAVDLVLDGTDNYATRYLVADACEIAGVPVVWGAILRFAGQVSVFAPGGPLY +RDVFPERPEPGEVPSCAQAGVLGVLPGIIGSLMAAEAIKLLSGVGEPLVGRLLSVDALTM +RFRELRLVPDPERTPVTDLSAHADQAPRPDDAGAPGSAEACGAAGGEIAPAALAALLADP +ARAASLTLLDVREDWERRLRRVEAPATVADRHVPLEAVLAEPAALAPGQDRVLVVYCAAG +ARSARARDAVVGADPSAGGRVLSLAGGLAAWPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000689.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000689.fa new file mode 100644 index 0000000000000000000000000000000000000000..d6bc4b5cdb968ac446c81eef8447dab5cad9e530 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000689.fa @@ -0,0 +1,55 @@ +>PROKKA_00780 +MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK +AGMAPRDLAGLVAERLTDKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND +ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV +FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ +DIKDTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLREQGHVEDREGAVWLKTTDFGDDKD +RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN +IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS +TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA +AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV +LANGLGLLGVSAPEKM +>PROKKA_00511 +MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK +AGMAPRDLAGLVAERLTGKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND +ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV +FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ +DIKDTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLRAQGHIEDREGAVWLKTTDFGDDKD +RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN +IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS +TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA +AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV +LANGLGLLGVSAPEKM +>PROKKA_02150 +MKPEDLSALLSAVLTDAVDAGDLPAELREEITPARVKVERPRSREHGDWATNVALQLGKK +AGMAPRDLAGLVAERLTGKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPDYGRNA +ALVGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV +FADSVLARLHGRDVPEGGYPGAYVQELADAVALEHPDVRELTDEAARPVVRQAAYRLQMQ +DIKDTLAAFDVHFDVFTSEQTLHESGAIEQAVERLREQGHIEDREGAVWLKTTDFGDDKD +RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN +IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS +TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVAA +AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVDTLNRTRLWLNDATAQV +LANGLGLLGVSAPEKM +>PROKKA_02044 +MKPEELSALIHAQLLAAVDAGELPAELREQLSADRVKVERPRSREHGDWATNVALQFAKQ +AGMNPREFASALASRVGEQPGVATVDVAGPGFLNITLDAAAAGELARQIVEAGEAYGRNE +ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIVRLLRASGADVTAEYYINDAGNQMNV +FADSVLARMAGRDVPEGGYPGAYVKDLADAVATDHPQVRELTDDAARPVVRQAAYELQMQ +DIKDTLAAFDVHFDVFTSETRLHESGAIQAAVDRLREQGHVEDREGAVWLRTTDFGDDKD +RVMIRANGEPTYFAADAAYYLDKRDRGFEEKVYLLGADHHGYVGRLKAIAAAAGDDPEEN +IEILIGQLISVNGAKLSKRAGNIIELKDLVQWLGKDALRYDLARYPADSPITIDPELLRS +QTNDNPVYYVQYAHARACGAARTAAAHGVDRCAFDASLLTDPTESELLAQLAEFPAVVAS +AARLREPHRVARHLEVIAGAYHSWYAAQRIVPVPLEDGTPAPVEDVNRTRLWLNDAAAQV +LRNGLGLLGVSAPETM +>PROKKA_00747 +MKPEDLSALLSAVLTDAVDAGDLPAALREEITPARVKVERPRSREHGDWATNVALQLGKK +AGMAPRDLAGLVAERLTDKPGIAAVDVAGPGFLNVTLDAASAGALAREIVEAGPEYGRND +ALAGHTVNMEFVSANPTGPLHIGHTRWAALGDAIARLLRASGADVTAEYYVNDAGNQMNV +FADSVLARLHGRDVPAGGYPGAYVQELADAVALEHPDVRELTDEAARPVVREAAYRLQMQ +DIKNTLAAFDVHFDVFTSEQTLHDSGAIEQAVQRLRAQGHVEDREGAVWLKTTDFGDDKD +RVLIRANGEPTYFAADAAYYLHKRDRGFEEKVYLLGADHHGYVNRLKAIAAAAGDDPATN +IEILIGQLISVNGAKLSKRAGNIIELKDLVEWLGRDALRYDLARYPADSPLTIDPELLRS +TTNDNPVYYVQYAHARASGAARTAQAHGVDRSEFDAALLTHATESELLAQLAEFPAVVGA +AARLREPHRVARHLEVIAGAYHSWYAACRIVPMPTDDGTPRPVETLNRTRLWLNDATAQV +LANGLGLLGVTAPEKM diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000690.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000690.fa new file mode 100644 index 0000000000000000000000000000000000000000..3a270e2450eb1b8a6ef648b20558dbd8252b6800 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000690.fa @@ -0,0 +1,50 @@ +>PROKKA_00781 +MRTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP +LLVVDEDDFRARARAFRKGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS +GGELAIALAAGIDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR +RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASTDRDGNVAGRSPAAVAVAAALAA +ESIELLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV +DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDVDA +PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV +RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSGGQARVIIRRETQEDLF +ARETDPRLAR +>PROKKA_00512 +MRTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP +LLVVDEDDFRARARAFRKGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS +GGELAIALAAGIDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR +RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASTDRDGNVAGRSPAAVAVAAALAA +ESIELLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV +DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDVDA +PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV +RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSDGQARVIIRRETQEDLF +AREADPRLAR +>PROKKA_02149 +MTTPQPAPASPLAPAWLPAPGDPDALAPGLWAAGVDRAADGELTVQGLRASALAVEFGTP +LLVVDEDDFRARARAFREGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS +GGELAIALAAGVDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELEHLAALAAEAGH +RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPATTDRDGNVAGRSPAAVAVAAALAA +ESIDLLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV +DEPRPAAEIADALADDVQKTVERLGLACPRISLEPGRAISGPAGLTLYTVGVTKTVDADT +PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSAARTSDAQAVLTRVVGKHCESGDVLV +RDVYLPEDLGRGDLLAVPATGAYTHVMASNYNALTRPAVVAVAGGRARVIIRRETQEDLF +AREADPRLGR +>PROKKA_02043 +MNAGSVNLEETVTETAPQSAHPLAPAWLPAPADPDALAPLVWSSGVARDAAGELAVQGVP +ASVLAERFGTPVLVLDEDDFRARARAFREGFDAAFESLCGGADVYFAGKSMLTLSTARWA +AEEGLRVDTASGGELAIALRAGVLPEHIGLHGNNKSAAELATALDAGVGRIIVDSVDELE +FLAALAAERGQIAPVMLRVTPGVHAHTHDFIATAHEDQKFGLSLTPSATGRDGNEAGVAP +AAVAVRTALQADSIRLLGLHCHIGSQIFEADGFGLAAERVLGFLAEVKDEHGVELPELDL +GGGHGIAYTAVDEPRPAAEIADALADDVQKAVERLGLTCPRISIEPGRAISGPAGLTLYS +VGVTKTVDVDAPDDGTASRRYVAVDGGMSDNPRPVLYDADYTAALASRTSDAAPALSRVV +GKHCESGDILVRDVWLPEDVARGDLLAVPATGAYTHSMSSNYNALLRPAVVAVRDGEARE +IVRRETLDDLLRREVDPQNPA +>PROKKA_00748 +MTTPQPAPASPLAPAWLPAPGDPDALVPGLWAAGVDRAADGELTVQGLRASALAAEFGTP +LLVVDEDDFRARARAFREGFDAAFADLCGGADVYYAGKSMLTLSTARWAAEEGLRVDTAS +GGELAIALAAGVDPAHIGLHGNNKSDAELRTALEAGVGRIIVDSLDELTHLAALAAEAGR +RAPVMLRLTPGVHAHTHDFIATAHEDQKFGLSLAPASSDRDGNVAGRSPAAVAVAAALAA +ESIDLLGVHCHIGSQIFEAEGFGLAAGRVLEFLAEVKAEHGVELAELDLGGGHGIAYTAV +DEPRPAAEIADALADDVQKTVERLGLRCPRVSLEPGRAISGPAGLTLYTVGVTKTVDADA +PDGGTAARRYVAVDGGMSDNPRPVLYDADYTAVSARRTSEAEPVLSRVVGKHCESGDILV +RDVYLPADLGRGDLLAVPATGAYTHVMSSNYNALARPAVVAVSGGQARVIIRRETQEDLF +AREADPRLAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000693.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000693.fa new file mode 100644 index 0000000000000000000000000000000000000000..2aab543da4048f7ce57e7e589346f72778ae632f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000693.fa @@ -0,0 +1,35 @@ +>PROKKA_00784 +MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA +TLPRDGAHLILRLAREQLRGRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL +PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATVRLRLHERVVPVV +AIPDTELSTHVARGVLPADVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA +VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL +VPCVAVDGVRVESLHHG +>PROKKA_00515 +MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA +TLPRDGAHLILRLAREHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL +PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV +AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLLAATRDWLHQEPRA +VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL +VPCVAVDGVRVESLHHG +>PROKKA_02146 +MPAPRTLAAGTAVVVAVPATSANLGPGFDSMGLALELRDEVSLTVVDGPDVAEVTGEGAD +VLPRDGSHLILRLAHEHLRARGVRAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL +PAADRRPPEALLEAATDFEGHPDNVAPALVGGATVSWTRDDDARPATAPLRLHERIVPVV +AIPDTELSTHAARGVLPESVPHAVAAAQAGRAALLVHALAERPELLMAGTRDWLHQGPRA +AAMPASAALVAGLRVRGHAAVVSGAGPTVLALCDGAEAAEQAAAAARALTADDVLAWRVL +VPAVAADGVRVEPLHHG +>PROKKA_02040 +MRELRDLTPGTGARVLAPATSANLGPGFDALGLALELRDEVTLTVVDGPDTAVVTGEGAA +ELPTDGEHLVLRLAHAHLTRRRFRAPGLALTAVNRIPHARGLGSSAAAVVTAVLAAEALL +PADERLSAAELLDVTARREGHPDNVAPALSGGASVSWHRDGGPGWATAAVALHPQITPVI +GIPDVTLSTHAARAALPESVPHAVAAEQAGRAALLTLALASRPDLLLPATRDWLHQDARA +SAMPPSAALVRGLREQGHAAVVSGAGPTVLVLAPTPADAERAAEAMRALAPETGAAWRVL +VPGVAAEGARVEPLHHG +>PROKKA_00751 +MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVVGEGEA +TLPRDGAHLILRLAHEHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL +PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV +AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA +VTMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAAAWRVL +VPCVAVDGVRVESLHHG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000696.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000696.fa new file mode 100644 index 0000000000000000000000000000000000000000..68ec06573ac38ded70f685d271581d561c872168 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000696.fa @@ -0,0 +1,34 @@ +>PROKKA_00788 +MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK +GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG +TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES +RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAADRIAAEDAAAARPAD +REA +>PROKKA_00519 +MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK +GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG +TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES +RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAADRIAAEDAAAARPAD +REA +>PROKKA_02143 +MSAADESEPWGQALRRATGLLAEAGVDSPRVDAELLLAHVLGLGRGELLARVFAGAAGTA +GEAERFAALVARRARREPVQHLTGVAFFHGLDLAVGPGVFLPRPETELLVDAVLAELTAR +PAAATVVDLCTGSGAIAAAVSAWAQEHGRDVAVIAVELDDEAAGWARRNLEPRGVYMRQG +DALVALPELEGRVDVVVSNPPYVPEAETPVQAEARLDPARALYGGDAAGLRIPQAIAHRA +TELLVPGGLFAMEHHETQGPALLGALDADPRFTGVCVHQDLTGRDRFLTARRSCEAAAAA +EDGRMADVSDFIDVSDPAALEDAVARAREVLGDCGCVVLPTDTVYGIGADAFSPRAVAVL +LAAKGRGRTMPPPVLISDRRVLAGLAYDVPDEAEALAERFWPGALTLILKSQPTLTWDLG +ETRGTVALRVPDDAVARELLYAVGPMAVSSANRTGMPAATTAEEARGMLGESVDLYLDAG +PREDRAPSTIVDCTVTPFRVARQGAVPLEALRELVPDLLAEGEEPPVPADRLAAEPVAEA +PAPTPAPDGDDAADRAGREA +>PROKKA_02036 +MSEFIDVSDPSDLTAAVERARAVLADRACVVLPTDTVYGIGADAFSPTAVAVLLAAKGRG +RTMPPPVLISDRSVMAGLAYDVPEAAEELAERFWPGALTLILRSQPTLTWDLGETRGTVA +LRVPDDAVTRELLYAVGPMAVSSANRTGMPAATTARGAEEMLGESVALYLDGGERATQEP +STIVDCTVTPFRVARQGAVSLEALRAVVPDLVAEGEEPPVPAELTTPPAAPEA +>PROKKA_00755 +MTDVSDFIDVSDPAALENAVARAREVLADRGCVVLPTDTVYGIGADAFSPLAVAVLLAAK +GRGRTMPPPVLIADRRVMAGLAYDVPEEAEALAERFWPGALTLILKSQPTLTWDLGETRG +TVALRVPDDAVARELLYAVGPMAVSSANRTGMDAATTADAARSMLGESVALYLDAGPRES +RDPSTIVDCTVTPFRVARQGSVPLEELRAVVPDLLAEGEEPPVAAERIAAADDAAAARPA +DPEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000700.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000700.fa new file mode 100644 index 0000000000000000000000000000000000000000..114997c4d3cc4c2e9609245161e01a2d7e5a35e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000700.fa @@ -0,0 +1,15 @@ +>PROKKA_00792 +MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI +LGLVFAFVIGA +>PROKKA_00523 +MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI +LGLVFAFVIGA +>PROKKA_02139 +MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI +LGLVFAFVIGA +>PROKKA_02032 +MEISGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI +LGLVFAFVIN +>PROKKA_00759 +MELHGSLNMIGYGLAAIGSAIGVGLIFAAYINGVARQPEAQRILQPIALLGFALAEALAI +LGLVFAFVIGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000703.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000703.fa new file mode 100644 index 0000000000000000000000000000000000000000..f84b47826fb4bed9f7dbe5d0096496a5aee170fb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000703.fa @@ -0,0 +1,55 @@ +>PROKKA_00795 +MITKHREQGLQMAELTINADDVRNALNEFAASYEPSGTDRTEVGRVISAADGIARVEGLP +SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG +RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ +LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA +LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL +RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI +TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM +FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVQDVLRFE +REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEEGGVRAGHEEHRAI +EQDQVAQEQITKQKR +>PROKKA_00526 +MITKHREQGLQMAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLP +SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG +RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ +LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA +LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL +RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI +TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM +FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWTGSKGHLDEVPVQDVLRFE +REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEDGGVQAGHEEHRAI +EQDQVAQEQITKQKR +>PROKKA_02136 +MAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLPSVMANELLRFE +NGIQGLAQNLDAREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDGFMGRVVDPLGQPID +DLGPIQAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQLIIGDRQTGKT +AIAVDTILNQKANWESGDVDKQVRCVYVAVGQKASTIAGVRATLEEHGALEYTTIVASPA +SDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLLRRPPGREAYPG +DVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISITDGQIFLQSDL +FNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSMFASDLDPATRR +QLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVEDVLRFEREFIDHLRRRG +SVLTDIGSTGKLEDGTVSALESEIAEFKKGFQSSEDGGVHAGHEEHRAIEQDQVAQEQIT +KQKR +>PROKKA_02029 +MITKHREQGLQMAELTINADDVRNALNDFAASYEPSDTTRTEVGRVISAADGIARVEGLP +SVMANELLRFSNGILGLAQNLDAREIGVVVLGEFQDIREGMEVQRTGEILSVPVGDGFLG +RVVDPLGHPLDDLGPIEAEGRRALELQAPTVTQRKSVHEPLQTGMKAIDAMIPIGRGQRQ +LIIGDRQTGKTAIAVDTILNQKANWQTGDVDKQVRCVYVAVGQKASTIAAVRSTLEEHGA +LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL +RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI +TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM +FASDLDPATRRQLARGERLMELLKQPQYSPYPVEDQVVAIWAGSKGHLDDVAVEDVLRFE +REFLDHLRRKDVVLGEIASTGKLEDETVSALEREIDAFKKGFQASGHDGVAAGHEEHAAI +GQDQVVQEQITKQKR +>PROKKA_00762 +MITKHREQGLQMAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLP +SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG +RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ +LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA +LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL +RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI +TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM +FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVQDVLRFE +REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEDGGVQAGHEEHRAI +EQDQVAQEQITKQKR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000704.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000704.fa new file mode 100644 index 0000000000000000000000000000000000000000..11ff8bbd3bb1f377cdc763bc8f4d1ee0143bc9e6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000704.fa @@ -0,0 +1,30 @@ +>PROKKA_00796 +MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVSASLPYANAITRAVSAVSSQ +HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG +RKAQTYFDFRGRGYKQLWTGQTDAPVAERAAEIGEVLVDAFLTDTADGGVDEIHVVFTEF +VSLVKQNPHVVRLLPLEVVEEEAATAEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML +QSAASELANRQRAMKSAGDNATSLIKDYTLLMNNARQAEITQELTELIAGADALNNS +>PROKKA_00527 +MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVSASLPYANAITRAVSAVSSQ +HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG +RKAQTYFDFRGRGYKQLWTGQTDAPVAERAAEIGEVLVDAFLTDTADGGVDEIHVVFTEF +VSLVKQNPHVVRLLPLEVVEEEAATAEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML +QSAASELANRQRAMKSAGDNATSLIKDYTLLMNNARQAEITQELTELIAGADALNNS +>PROKKA_02135 +MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVNASLPYANAITRAVSAVSSQ +HDIDHVLTTEPENPTRAAVLILSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG +RKAQTYFDFRGREYKQLWTGQTDAPAAERASEIGETLVDAFLTDTAAGGVDEIHIVFTEF +VSLVKQNPHVVRLLPLEVVEEEVAAPEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML +QSAASELANRQRAMKSAGDNASGLIKDYTLLMNNARQAEITQELTELIAGADALNNS +>PROKKA_02028 +MGAQIRVYRQKIASTTSMKKIFKAMELIATSRITKARERVNQSLPYANAITRAVTAVSSQ +HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTALHEEGKDVDVYVVG +RKAQTYFDFRGREYKQLWTGQTDAPKAERAQEIGTILVESFLTDTAAGGVDEIHVVFTEF +VSLVKQNPHVIRLLPLEVVEQDVVSPEEVLPLYEFEPDADEVLDALLPKYIESRIFNAML +QSAASELANRQRAMKSAGDNASSLIKEFTLRMNNARQAEITQELTELIAGADALNNS +>PROKKA_00763 +MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVSASLPYANAITRAVSAVSSQ +HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG +RKAQTYFDFRGRGYKKLWTGQTDAPVAERAAEIGEVLVDAFLTDTADGGVDEIHVVFTEF +VSLVKQNPHVVRLLPLEVVEEEAATAEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML +QSAASELANRQRAMKSAGDNATSLIKDYTLLMNNARQAEITQELTELIAGADALNNS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000705.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000705.fa new file mode 100644 index 0000000000000000000000000000000000000000..50679a3dc1223120f38cae1ee55b02a272d69149 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000705.fa @@ -0,0 +1,50 @@ +>PROKKA_00797 +MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDLNGQRRTVTF +EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDMPTS +QLQAEDRWPIHRPAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI +QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV +ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL +QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA +STSRILDPQYVGQEHYDVAIRVKQILQKNKELQDIIAILGVDELSEEDKITVGRARKIEQ +FLSQNTYTAKQFTGVEGSTVPVKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK +IQAEG +>PROKKA_00528 +MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDLNGQRRTVTF +EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDMPAS +QLQAEDRWPIHRPAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI +QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMEEADVLKDTALVFGQMDEPPGTRLRV +ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL +QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA +STSRILDPQYVGQDHYDVAIRVKQILQKNKELQDIIAILGVDELSEEDKITVGRARKIEQ +FLSQNTYTAKQFTGVEGSTVPVKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK +IQAEG +>PROKKA_02134 +MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDLNGQRRTVTF +EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDVETS +SLNFEERWPIHRAAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI +QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV +ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL +QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA +STSRILDPQYVGQDHYDTAIRVKQILQKNKELQDIIAILGVDELGEEDKITVARARKIEQ +FLSQNTYTAKQFTGVEGSTVPIKDTVEGFKAIADGDLDHIAEQAFYNVGGLDDVEREWAK +IQAEG +>PROKKA_02027 +MTATFTDQGTGTPTAGATGRVARVIGPVIDAEFPANAMPEIYNALTATVELAGQTRVVTF +EVAQHLGDNMVRAISLQSTDGLVRGADVQDTGAPISVPVGDAVKGHLFNVLGETLDMPIS +ELDVQERWPIHRPAPSFAALEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI +QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV +ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL +QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA +STSRILDPQYVGQEHYDVATRVKQILQKNKELQDIIAILGVDELSEEDKITVSRARKMEQ +FLSQNTYTAKQFTGVEGSTVPIKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK +IQAEG +>PROKKA_00764 +MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDFNGQRRTVTF +EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDMPTS +QLQAEDRWPIHRPAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI +QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV +ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL +QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA +STSRILDPQYVGQDHYDVAIRVKQILQKNKELQDIIAILGVDELSEEDKITVGRARKIEQ +FLSQNTYTAKQFTGVEGSTVPVKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK +IQAEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000706.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000706.fa new file mode 100644 index 0000000000000000000000000000000000000000..a730479f169a1c1f79e6423144a19fc96ce48dd9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000706.fa @@ -0,0 +1,15 @@ +>PROKKA_00798 +MAELNVEIVSEERSIWSGAASAVSARTVNGEIGILPGHTPMLAVLGDGEVVVRTTDGGTV +TAQAHGGFFSVDHDRVVIAATSARLGDAAAA +>PROKKA_00529 +MAELNVEIVSEERSIWSGAASAVSARTVNGEIGILPGHTPMLAVLGDGEVVVRTTDGGTV +TAQARGGFFSVDHDRVVIAATSARLGDAAAA +>PROKKA_02133 +MAELNVEIVSEERSIWSGAASAVSARTVNGEIGILPGHTPMLAVLGDGEVVVRAVDGGTV +TAQAHGGFFSVDHDRVVIAATSARLGDAAAA +>PROKKA_02026 +MAELNVEIVSEEKSIWTGTASAVSARTINGEIGILPGHTPMLAVLGDGEVVVRATDGGTI +TAQANGGFFSVDDDRVVIAAATAQLGGAAA +>PROKKA_00765 +MAELNVEIVSEERSIWSGAASAVSARTVNGEIGILPGHTPMLAVLGDGEVVVRTTDGGTV +TAQARGGFFSVDHDRVVIAATSARLGDAAAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000709.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000709.fa new file mode 100644 index 0000000000000000000000000000000000000000..3dbf99a7f41178c287ff2fd88aa0f54ddc269993 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000709.fa @@ -0,0 +1,16 @@ +>PROKKA_00801 +MPRSNRPRRSSAPRRSERGASGASRRSRPSPGRSDPLQELLGLDAGYSRQSGSDGGWHVR +QIPAWRAVKDYTCPGCGRVIRQGQAHLVAWRADWIMGDEDAGEDRRHWHPVCWRTRPSR +>PROKKA_00532 +MPRSNRPRRSSAPRRSERGASGVSRRSRPSPGRSDPLEELLGLDAGYSRQSGSDGGWHVR +QIPAWRAVKDYMCPGCGRVIRQGQAHLVAWRADWIMGDEDAGADRRHWHPVCWRTRPGR +>PROKKA_02129 +MADPLKELLGLDPGYSHQSGGDGGWHVRQIPSWRAVKDYTCPGCGRVIRQGQAHLVAWRS +DWIMGDEDAGADRRHWHPVCWRTRVGR +>PROKKA_02022 +MVTMPRSNRPRRSAAPRRGEGAAGGASRRSRPGPGRADPLEELLGMDPGYSHQSGSDGGW +HVRDIPSWRAVKDYTCPGCGRTIRQGQAHLVAWRSDWIMGDEDAGADRRHWHPTCWRTRA +SR +>PROKKA_00768 +MPRSNRPRRSSAPRRSERGASGASRRSRPSPGRADPLEELLGLDAGYSRQSGSDGGWHVR +QIPAWRAVKDYTCPGCGQVIRQGQAHLVAWRADWIMGDEDAGADRRHWHPVCWRTRPGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000711.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000711.fa new file mode 100644 index 0000000000000000000000000000000000000000..2fe06b3911cd7eb900f8899baf33ae9fe54bda17 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000711.fa @@ -0,0 +1,34 @@ +>PROKKA_00803 +MTDVTAQPPSDAPSHLRGAVDLSSLGTPASAGRTAPGADAGAGGGSWVIADADQGLLQQL +VQLSAQVPVLLHLHVPGDAASEALYRQFADAVDAQAGRLVLARLDVAKEPAVLQALGLGA +GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPAVAPARQDAGAAAA +EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAS +AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFDRLVRFIALHPGDDRETARAHLVDLYT +VVGTDDPRVQASRRQLAAALF +>PROKKA_00534 +MTDVTAQPPSDAPSHLRGAVDLSSLGTPAPAGRTAPGADAGAGGGSWVIADADQGLLQQL +VQLSAQVPVLLHLHVPGDAASEALYRQFADAADAQAGRLVLARLDVAKEPAVLQALGLGA +GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPPVAPARQDADAAAA +EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAA +AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFARLVRFIALHPGDDRETARAHLVDLYT +VVGTDDPRVQASRRRLAAALF +>PROKKA_02127 +MIPDADQRLLQQLVQLSAQVPVLLHLHVPGDASSDALYRQFADAVDAQAGRLVLARIDVA +ADPSVLQALGLGAGPAVMAVVAGQPVPLVNQEVPAETLEQLMGEILEVARQNGVAGTVPA +VAPARADAAEPAPAAPPVPPLHRAAHAALAADDLPGAVAAWEEALKDTPADPVAQQGLSA +ARLMLRTRDADAAAVRSAAADAPDDAAAQLAVADLDVLGGHVEDAFARLVRFIALHPGED +RETVRAHLVDLYTVVGVDDPRVTASRRRLAAALF +>PROKKA_02020 +MTSQPSSPSLRGAVDLSSLRTPRPAPGAQGAGAQGAGAPGEPASWAVLDADSRLLEQLVQ +LSTQVPVILVLHVPGDATSEALSTQFADAADAQAGTVVMARLDVVAEPQLLQAFGIGAGP +AVVAVVAGQPVPLANQELPQEALDGLMGQLLEVARQNGVAGRVPALAPARDGAAAPQPAP +VPPLHRRAHEALAADDLPGAVAAWEDALKESPADETARQGLSAARLMLRTRDMDAAAVRA +AAAERPDELAAQTAVADLDVLGGHVEDAFARLVRFVAAHPGEDREAARAHLVDLYIVVGS +EDPRVHASRRRLAAALY +>PROKKA_00770 +MTDVTAQPPSDAPSHLRGAVDLSSLGTPAPAGRTAPGADAGAGGGSWVIADADQGLLQQL +VQLSAQVPVLLHLHVPGDAASEALYRQFADAVDAQAGRLVLARLDVAKEPTVLQALGLGA +GPAVMAVVAGQPVPLVNQEVPEETLRQLMGEILEVARQNGVAGTVPPVAPARQDAGAAAA +EAPPVPPLHRAAHEALAADDLPGAVSAWEAALADSPADAVAQQGLSAARLMLRTRDADAA +AVRAAAADGPDDVAAQLAVADLDVLGGHVEDAFARLVRFIALHPGDDRETARAHLVDLYT +VVGTDDPRVQASRRRLAAALF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000713.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000713.fa new file mode 100644 index 0000000000000000000000000000000000000000..c931152372af279b1a21b3f301cb95f0bc6c666a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000713.fa @@ -0,0 +1,50 @@ +>PROKKA_00805 +MALTLVRLRWTLTLNQWRRSPFTLVVSVLGALYVLGMAAVAVTLLVTGLPALPDEARGAT +TVLVAAVVVLAWLVIPPFVTGVDATLDPHSFVLFPVPARTLIAGLVLSAFTTPAGLATLA +VLVGLGASWWDRPAALAAGLAGGALTAVTAVAIGSGLAGLLAAYASRRRVRDVVSVLLFI +PLMLGGVALSRAVASFEDFLAIAPQVARGAAWTPFGAGPAAAWAAAEGRGAAAALHLAVA +AAWCLAALALWHLAVRRTVEPVAVGGGGSRRVGAGADPTPLRWLGRPATGPRTAIAARAQ +RYWLADPRYAAGLIIIPLMAVVLWFTGGLASGGGLGPGLLLILGPMTAWSLAYSISADIA +YDHTAFHLHVVSGVRGVDDRWGRVLGLAGWGVPMILLVTTATVAAAGDWSLLAPMLGLAL +GLFGTTAGLSAFLSARFVYPVPKPGDSPFKTPQGAAMRTMLVQGASMLVSLALAVPFLVP +FIVRLATGAAVWGWVTVALGFAWGAVALWLGVRLGARWYDRAQAETYQAVAAF +>PROKKA_00536 +MALTLVRLRWTLTLNQWRRSPFTLVMSVLGALYVLGMAAVAVTLLVTGLPALPDEARGAT +TVLAAAVVVLAWLVIPPFVTGVDATLDPHSFVLFPVPARTLIAGLVLSAFTTPVGLATLA +VLVGLGASWWDRPAALAAGLAGGALTAVTAVAIGSGLAGLLAAYASRRRVRDVVSVLLFI +PLMLGGVALSQAIASFEDFLAIAPQVARGAAWTPFGAGPAAAWAAAEGRGAAVALHLAVA +AAWCLAALALWHLAVRRTVEPVAVGGGRSRRVAAGADPMPLRWLGRRATGPRTAIAARAQ +RYWLADPRYAAGLIIIPLMAVLLWFTGGMAAEGGPGLGLLLILGPITAWSLAYSISADIA +YDHTAFHLQVVSGVRGVDDRWGRVLGLAGWGVPMILLVTTATVAAAGDWSLLAPMLGLAL +GLFGTTAGLSAFVSARFVYPVPKPGDSPFATPQGAAMRTMLVQGAAMLVSLALAVPFLVP +FVVRLVTGAAVWGWVTVALGLAWGAVALWLGVRLGARWYDRAQAETYQAVAAF +>PROKKA_02125 +MALTLVRLRWALTLNQWRRSTFTLVLAVLGALYVLGLAVFVVVMLVTFLPDAWVVDRGTV +TVIVASALALGWLLIPPFITGVDATLDPHSFVLFPVRARTLIAGLTLSAFTTPSGLATLI +VMLGTGLSWWDIPAALAAALVGGALTAVTAVASGYGLAGLMAAYAGRRRVREVLSIALLI +PVMLSGVIVAQTLDSLGDLFDVAPRVAAVAAWTPFGAGPAAAWAVAEGQGLRAAAHLLVA +AAWCLAALALWHLAVRRTVEPVAVGGGSAREAGRADGAPLRWLGRPATGPRTAIAARAQR +YWLRDPRYAAGLVMIPVLAAVLWFASTAGGDAGPGLGMLTMLGPVSAWALAYSISADIAY +DHTAFHLHVVSGVRGADDRWGRVMGLAGWGVPALVVLTVATTAAADRWDLLPALLGLTLG +LFGVTAAMSAFVSARFVYPVPKPGESPFKTPQGATMRIMLVQGAAMLVVVPLAVPVVVPF +VVALVTQSAVWGWATLAVGLAWGAVALWLGVRMGAAWYDRAQAETYQAVAAF +>PROKKA_02018 +MALTLTRLRWALTLNGWRRSTLTLVLSVLGALYFFGMAAMAVAALVVGLPEAELPVRGAV +TVLVAAVVVLLWTILPPLVTGVDATLDPSSFVLFPVPARTLVAGLLLSTFTTPIGALTLL +GLLGVAASWWDTPAALAAAAVGAVLSAVTAVCLGYGVTGLMSSFTGRRRVREAISLLVLI +PLMLGGVALSRVMQSIDDLLWLGPVLANAAVWTPFGAGLGAGWAAAEGRWGLAGLRLLVA +LAWAVAAAALWMLAIRRTVEPAAVGSTDSAAPRGDRATDLRWLGRPATSARTAIAARAQL +YWFKDPRYMASLVTVPLMFVLLWFMGTSGPEGATAILLAAGPVTAWALGYSLSADIAYDH +TAFHLHVLAGVKGIDDRLGRVMGLLGWALPVVAGVTLATVAMHGDWSVLPAILGVSLGVL +GACLGLSALVSARWVYPVPKPGDSPLKTPQGAAMRIMLVQGTSLLVTLVLLVPMAVPFVV +LLVTGAAVWSWVTLAVGLAWGALALWLGVRAGAAWYDRAQAETLQAVQSW +>PROKKA_00772 +MALTLVRLRWTLTLNQWRRSPFTLVMSVLGALYVLGMAAVAVTLLVTGLPALPDEARGAT +TVLAAAVVVLAWLVIPPFVTGVDATLDPHSFVLFPVPARTLIAGLVLSAFTTPVGLATLA +VLVGLGASWWDRPAALAVGLVGGALTAVTAVAIGSGLAGLLAAYASRRRVRDVVSVLLFI +PLMLGGLALSRAIASFEDFLAIAPQIARGAAWTPFGAGPAAAWAVAEGRGAAVALHLAVA +AAWCLAALALWHLAVRRTVEPVAVGGGRSRRVAAGADPTPLRWLGRPATGPRTAIAARAQ +RYWLADPRYAAGLIIIPLMAVLLWFTGGMAGEGGPGLGLLLVLGPITAWSLAYSISADIA +YDHTAFHLHVVSGVRGVDDRWGRVLGLAGWGVPMILLVTTATVAAAGDWSLLAPMLGLAL +GLFGTTAGLSAFVSARFVYPVPKPGDSPFATPQGAAMRTMLVQGAAMLVSLALAVPFLVP +FVVRLVTGAAVWGWITVALGLAWGAVALWLGVRLGARWYDRAQAETYQAVAAF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000715.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000715.fa new file mode 100644 index 0000000000000000000000000000000000000000..ca5228e310c267527567a9337bd9821294ed6e77 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000715.fa @@ -0,0 +1,60 @@ +>PROKKA_00807 +MADGRSLTSGTPDGSVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALERYLQTAPQ +DFLTVATPGAGKTTFALRVAKILLDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF +KNADGRHGAEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGEGIREA +FEPATRRLSLTGTPFRSDTASIPFVRYELGADGIERSKADYTYGYGPALRDHVVRPVIFM +AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLSEVRR +NVPDAGGLVIASDHQDARAYAAQLEALTGQRPAVILSDDKGASDRIEEFAASDERWMVAV +RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGETASVFLPSVPALMLLANE +MELERDHALDRKEGAVEVEDLEDAPEEDLIAEANRAESGSDALTREKFEALESRASFDKV +LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQIQRRPRAQAAEPADVV +DHRRMKELRSELSKTVSAWATRSGQPHGVIHNRLREISGGPAVAQASREQLEKRLSTLRG +WFVGRT +>PROKKA_00538 +MADGRSLTSGTPDGSVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALERYLQTAPQ +DFLAVATPGAGKTTFALRVAKILLDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF +KNADGRHGAEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGEGIREA +FEPATRRLSLTGTPFRSDTASIPFVRYELGQDGIERSKADYTYGYGPALRDHVVRPVIFM +AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLTEVRR +NVPDAGGLVIATDHQDARAYAAQLEALTGQRPAVILSDDKGASDRIEEFAASDERWMVAV +RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGETASVFLPSVPALMLLANE +MELERDHALDRKEGAVEVEDLEDAPEEDLIAEANRAESGSDALTREKFEALESRASFDKV +LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQIQRRPRAQAAEPADVV +DHRRMKELRSELSKTVSAWAARSGQPHGVIHNRLREISGGPAVAQASREQLEKRLSTLRG +WFVGRT +>PROKKA_02123 +MAERRSSASGTPDGAVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALEKYLETGPQ +DFLAVATPGAGKTTFALRVAKILLDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF +KNADGRHGSEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGDGIREA +FEPAARRLALTGTPFRSDTSTIPFVEYVDGPDGLSRSKADYTYGYGPALRDHVVRPVLFM +AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPKGEWIPAVLRAADRRLSEVRR +GVPDAGGLVIATDHEDARAYAAQLEALTGQRPALILSDDKGASDRIEEFAASDERWMVAV +RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGEVASVFLPSVPQLMLLANE +MELERDHALDRREGGVDVEDLEDAPEEDLLAQANREESGSDALLRGKFEAMESRASFDKV +LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQVQRRPKAPAKEPADVV +DHRRMKELRSELSKTVSAWSARSGTPHGVIHNRLREVSGGPAVAQASRDQLEKRLSTLRG +WFVGRT +>PROKKA_02016 +MAEGRSETSGAPTPDGIQPDLFHVGEDLPPALPERAAWGTAPKLRQWQQEALEKYLREAP +QDFLAVATPGAGKTTFALRVAKILMDSGVVQRLTVVAPTDHLKRQWADNAARVGLAIDPN +FKNADGRHGPEYRGVALTYAQVANKPVLHRNRTEAARTLVILDEIHHGGDARSWGEGIRE +AFEPASRRLSLTGTPFRSDDAYIPFVRYERGEDGFERSRADYTYGYGPALRDHVVRPVIF +LAYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLTEIR +RGIPDAGGLVIASDHEDARAYAAQLQAVTGQAPAVILSDDKGASDRIEEFAASDERWMVA +VRMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGEVASVFLPSVPQLMLLAN +EMELERDHALDRREGAVTVEELEDLSQAPEEDLIAEANRAERGSETLTRASFEALESRAS +FDKVLFDGGEFGLGGDVGSEEELDFLGIPGLLDAEQVSELLRQRQNEQIRRKPAAAPKES +RDVVDHRRMKELRAELSTTVSAWSARSGQPHGVIHNRLREISGGPAVAQASREQLEKRLE +TLRGWFVGRR +>PROKKA_00774 +MADGRSLTSGTPDGSVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALERYLQTAPQ +DFLAVATPGAGKTTFALRVAKILMDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF +KNADGRHGAEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGEGIREA +FEPATRRLSLTGTPFRSDTASIPFVRYELGQDGIERSKADYTYGYGPALRDHVVRPVIFM +AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLSEVRR +NVPDAGGLVIATDHQDARAYAAQLEALTGQRPAVILSDDKGASDRIEEFAASDERWMVAV +RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGETASVFLPSVPALMLLANE +MELERDHALDRKEGAVDVEDLEDAPEEDLIAEANRAESGSDALTREKFEALESRASFDKV +LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQIQRRPRAQAVEPADVV +DHRRMKELRAELSKTVSAWAARSGQPHGVIHNRLREISGGPAVAQASREQLEKRLSTLRG +WFVGRT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000716.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000716.fa new file mode 100644 index 0000000000000000000000000000000000000000..74780e8e8b28543ccd5c951507b2e91436e9703b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000716.fa @@ -0,0 +1,25 @@ +>PROKKA_00809 +MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYAAVAATRDWHVDPG +THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG +EPDAVPTGAAGERPSGTVGPYGATAVAAAAVEAGAPGLDEWLREQGVDAITVVGIATDHC +VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS +>PROKKA_00541 +MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYASVAATRDWHVDPG +THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG +EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESGAPGLDEWLREQGVDAITVVGIATDHC +VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS +>PROKKA_02121 +MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYAAVAATRDWHVDPG +THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDIEHLDAEFLKGLHTDAYSGFDGALG +EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESDAPGLDEWLREQGVDAITVVGIATDHC +VRATVLDALDAGYEVTVLTDLVAGVDEAASQAALHEMEAAGADLELSEGR +>PROKKA_02012 +MSEQNRALVIVDVQNDFCEGGALAVAGGADVAAAIADHVNEAREDYAAVVTTRDWHVDPV +GHFAAASLEDRDAEPDYVRTWPVHCVAGTPGAELHPGLSAEDLEIDAEFLKGQHSDGYSG +FDGHAGDPDAVRSGDEARAAAGPYGATQGAAHAADGGLGLDEWLREQDVDALTVVGLATD +HCVRATVLDGLEAGYEVTVRTDLVAGVDDAAGEAALHEMEAAGALLRAGD +>PROKKA_00778 +MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYASVAATRDWHVDPG +THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG +EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESGAPGLDEWLREQGVDAITVVGIATDHC +VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000717.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000717.fa new file mode 100644 index 0000000000000000000000000000000000000000..47a7269d44fff7897409bc9fb642c755a88128dd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000717.fa @@ -0,0 +1,45 @@ +>PROKKA_00810 +MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY +GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP +HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA +VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL +LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD +EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG +GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE +RHAASLRELPASVGRLQPGDPAIPTIFLED +>PROKKA_00542 +MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY +GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP +HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA +VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL +LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD +EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG +GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE +RHAASLRELPASVGRLQPGDPAIPTIFLED +>PROKKA_02120 +MSQNPVTSAPQTPDDWRIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY +GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP +HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA +VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTSL +LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTQTGIMVTSDLD +EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG +GRKEAARRRDRRGRATAEVVGVNRGAAPDADDRPLLHRFVHAGELAAGWTGPEAVTRAAE +RHAASLRELPATVGRLQPGDPAIPTIFLED +>PROKKA_02011 +MTQNASAPAPSAAPWHVPTSLMTDHYELTMLCAARRAGTAERRSRFELFSRRLPDGRRYG +VVAGTGRILEGLSRFRFSTAEVDFLADHSVVDDATLQWLADFRFSGDITGYAEGEVYFPH +SPVLQVESTFAEACILETYLLSILNYDSAVASAASRMASAAQGRPCIEMGARRIHEEAAV +AAARAAVIAGFAATSNLEAGRRYGVRTVGTAAHSFTLLHDSERAAFEAQVAALGRDTTLL +VDTYDVEQGVRTAVEVAGRALRNVRLDSGDLVQQAHEVRELLDSLGNTETGIMVTSDLDE +YAIASLRSAPVASYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASHGG +RKDAVRRRDARGRAVAELVGVNRAPAADADDRPLLHTFVKDGELQEGWTGPEAVTRAAER +HAASLAELPRAAARLQPGEALIPTIFQED +>PROKKA_00779 +MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY +GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP +HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA +VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL +LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD +EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG +GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE +RHAASLRELPASVGRLQPGDPAIPTIFLED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000718.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000718.fa new file mode 100644 index 0000000000000000000000000000000000000000..7c20d45522042527ae24f79e04f11da304f184da --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000718.fa @@ -0,0 +1,15 @@ +>PROKKA_00811 +MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY +VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED +>PROKKA_00543 +MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY +VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED +>PROKKA_02119 +MSVLTSHDPTAPRAAGPAPGEAVPGGATDTAVLERPREDLALDRPWNVVVWNDPVNLMSY +VAYVFRTHFGYSESRAHRLMLEVHERGRSVVATGTREKAELHVGAMHGYGLWATLEQAED +>PROKKA_02010 +MPHPAPPAPGADTALLERPREDLAAARPWHVVVWNDPVNLMSYVAYVFRSHFGYSAARAQ +SLMLEVHERGRSVVFTGSREVAEGHVTAMHGFGLWATLEQAED +>PROKKA_00780 +MSVLTRHDPSAPRAVRPAPGESVPAGATDTALLERPHEDTARDRPWNVVVWNDPVNLMSY +VAYVFRTHFGYSAAKAQRLMLEVHERGRSVVATGTKEKAELHVGAMHGYGLWATLEQAED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000722.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000722.fa new file mode 100644 index 0000000000000000000000000000000000000000..4f0d8442a740e51c3d4d60647ddaccc22267a852 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000722.fa @@ -0,0 +1,30 @@ +>PROKKA_00815 +MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK +GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI +VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV +PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR +IQAETLAAATEDRA +>PROKKA_00547 +MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK +GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI +VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV +PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR +VQAETLAAATEDRA +>PROKKA_02115 +MTSPASTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGDTRVLCTASFTQGVPRWLK +GEGTGWVTAEYAMLPRATNERNQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI +VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILRKDAEVLKDSVAAVSVGIVDGV +PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGVPFSRAELDTLLDLALTGTGELAR +IQAETLAGAAGSAEAQA +>PROKKA_02006 +MTESSPSTSPSVTRQDGRAVDELRPITITRGFSRQAEGSALIEFGGTRVLCTASFTEGVP +RWLKGEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALG +ENTIVLDCDVLDADGGTRTASITGAYVALAEAVAWAQGRGILKKDARVLTDSVSAVSVGI +IDGVPMLDLPYVEDVKAETDMNVVVTGSGDFVEVQGTAEGVPFRRAELDVLLDLALAGTA +ELSRIQAETLAGDVAGRA +>PROKKA_00784 +MSSPAPTAPRPDGRAVDELRPITITRGWSRQAEGSALIEFGNTRVLCTASFTEGVPRWLK +GEGTGWVTAEYAMLPRATNERSQRESVKGRIGGRTHEISRLIGRSLRAVIDLSALGENTI +VLDCDVLDADGGTRTAAITGAYVALAEAVAWARREGILAKGAAVLKDSVAAVSVGIVDGV +PVLDLPYVEDVKAETDMNVVVTGAGEFVEVQGTAEGAPFTRAELDTLLDLALIGTGELAR +IQAETLAAATEDRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000723.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000723.fa new file mode 100644 index 0000000000000000000000000000000000000000..412ce64da6677efc474ac46a75e8e4e959fce177 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000723.fa @@ -0,0 +1,25 @@ +>PROKKA_00816 +MSAPASSSAGLPEGARVVLATHNAGKVRELRQLLAGAVPGLEVETAVVDAGAVGAPDVVE +DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL +LLAQLADVPDEHRGAQFVCAAALAVPSGPDAAGARAIHVEHVEHGRLPGTLLREPVGDGG +FGYDPILRPEGRDVSTAQLSPEDKNAISHRGHAFRALLPYLVDALDARP +>PROKKA_00548 +MSAPASSSAGLPEGARVVLATHNAGKVRELRQLLAGAVPGLDVEAAVVDAGAVGAPDVVE +DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL +LLAQLADVPDEHRGAQFVCAAALAVPSGPDAAGARAIHVEHVEHGRLPGTLLREPVGDGG +FGYDPILRPEGRDVSTAQLSPEDKNAISHRGHAFRALLPYLVDALDARP +>PROKKA_02114 +MSGAATGVPEGARVVLATHNAGKVRELRQLLEGAVPGLDASVAVVDAGAVGAPDIVEDGV +TFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLELLLA +QLADVPDAHRGAEFVCAAALAVPSSADARGTHAIHVEHVEHGRLRGTLLRAPVGDGGFGY +DPILRPDGRDESTAQLSAADKNAISHRGHAFRALLPYLVDALDARA +>PROKKA_02005 +MSTPTAPVAPAGARVVLATHNAGKVRELRSLLAEALPALDVETAVVDAGAVGAPDVVEDG +VTFEQNALKKARAVAAHTGLIAVADDSGLAVDVLGGAPGIFSARWAGRHGDDKANLELLL +AQLGDVPDEHRGAAFVCAAALATPRGGDHVELGRMPGMLLREPVGDGGFGYDPILRPAGE +DRSTAQLSSAEKNAISHRGQAFRALLPHLVAALSADS +>PROKKA_00785 +MSAPASSSAGLPEGARIVLATHNAGKVRELRQLLAGAVPGLDVEAAVVDAGAVGAPDVVE +DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL +LLAQLADVPDEHRGAQFVCAAALAVPSGPDAAGARAIHVEHVEHGRLPGTLLREPVGDGG +FGYDPILRPEGRDVSTAQLSPEDKNAISHRGHAFRALLPYLVDALDARP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000726.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000726.fa new file mode 100644 index 0000000000000000000000000000000000000000..7eb5e9f8871f35c3b92a4016cabdfd66fa515e3e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000726.fa @@ -0,0 +1,40 @@ +>PROKKA_00819 +MILLHTSDWHLGRSFHGTGLLEAQEEVLDALVATVTERGVDAVLLAGDVYDRALPPADAV +RLLDRTLTRLHAAGAQVVLTSGNHDSAVRLGFGGGLLAAAGVHVRADAVELDRPVLLTEP +GVDGGAGQTVAVYGIPYLEPRHQGPAWGVEPHHTAVLTEAVRRVHADLAARRAETPEPVA +AVVLAHLFAAGGHGSESERDIGEGEHVEPDAPPEMLVGTLGQVPVSVFDGLDYAALGHLH +GRQRLAEHVRYSGSPLPYSFSEAGHRKGGWLVHVTGGAVTDVEAVDWDAGRRLAVLSGPI +EDLLESPEFAWAEQCWVQVTVTDDERPERALERLKTRFPSVLVFRHEPAGGRRARERTYA +QVLRQAPSDHALAVGFVDHVRQRPASGAEQDLLRDALEAARAGEVRA +>PROKKA_00551 +MILLHTSDWHLGRSFHGTGLLEAQEEVLDALVATVTERGVDAVLLAGDVYDRALPPADAV +RLLDRTLTRLHAAGAQVVLTSGNHDSAVRLGFGGGLLAAAGVHVRADAAELDRPVLLTEP +GVDGGAGQTVAVYGIPYLEPRHQGPAWGVEPHHTAVLTEAVRRVHADLAARRAETPEPVA +AVVLAHLFAAGGHGSESERDIGEGEHVEPDAPPEMLVGTLGQVPVSVFDGLDYAALGHLH +GRQRLAEHVRYSGSPLPYSFAEAGHRKGGWLVHVTGGAVTDVEAVDWDAGRRLAVLSGPI +EDLLESPEFAWAEQCWVQVTVTDDERPERALERLKTRFPSVLVFRHEPAGGRRARERTYA +QVLRQAPSDHALAVGFVDHVRQRPASEAEQDLLRDALEAARAAEVRA +>PROKKA_02111 +MLLLHTSDWHLGRSFHGTGLLEGQRQVLDALVDTVRERGVDAVLLAGDVYDRALPSADAV +ALLDATLARLREAGAQVVLTSGNHDSAVRLGFGAGLLSAAGVHVLTDPARLDEPVLLEDA +AGERAAVYGVPYLEPRHLGQAWEVDPTHTGVMTEAVRRIRADLEDRRAGSPTPLAGVVLA +HLFAAGGDASDSERDIGAGGSSWPASPAPADPAGRDAGCGAEPEGLVGTLGQVPVTVFDG +LDYAALGHLHGRQTMAEHVRYSGSPLPYSFSEAKHVKGGWLVHVHGGAVTEVEPVDWRAG +RRLAVLADRIGPLLDSPEYAFAENRWVQATVTDPERPEKALERLRSRFPHLLVFRHEPEG +GRPERVRTYAQALRQAPTDLALTTGFVDHVRGRPASAEESALLDDALTASRTREAQA +>PROKKA_02002 +MLLLHTSDWHLGRSFHGTGLLDSQRRVLAQLVDTVRERGVDAVLLAGDVYDRALPAADAV +TLLDETLAALRAAGSQVVLTSGNHDSAIRLGFGSALMAAGGVHVRTDPERLAEPVLLEDA +AGERAAVYGIPYLEPRHLGEAWGVDPHHTAVMTEAVRRVLADLEERRAADGPLAGVVLAH +LFAAGAEGTESERDIGEGPHTDAHGTAPEGLVGTLGQVPVSVFSGLDYAALGHLHGRQTM +APHVRYSGSPLPYSFSEARHTKGGWLVHVAGGAVTEVESVDWDAGRRLAVLEDRIQPLLD +SPGYAWAEDRFVQATVTDPERPEKALERLRSRFPHLLVFRHEPEGGHAARERTYAQALRQ +APDDLALTTGFVDHVRGRPASEAERELLDEALTASRIGEAQA +>PROKKA_00788 +MILLHTSDWHLGRSFHGTGLLEAQEEVLDALVATVTERGVDAVLLAGDVYDRALPPADAV +RLLDRTLTRLHAAGAQVVLTSGNHDSAVRLGFGGGLLAAAGVHVRADAAELDRPVLLTEP +GVDGGAGQTVAVYGIPYLEPRHQGPAWGVEPHHTAVLTEAVRRVHADLAARRAETPEPVA +AVVLAHLFAAGGHGSESERDIGEGEHVEPDAPPEMLVGTLGQVPVSVFDGLDYAALGHLH +GRQRLAEHVRYSGSPLPYSFSEAGHRKGGWLVHVTGGAVTDVEAVDWDAGRRLAVLSGPI +EDLLESPEFAWAEQCWVQVTVTDDERPERALERLKTRFPSVLVFRHEPAGGRRARERTYA +QVLRQAPSDHALAVGFVDHVRQRPASGAEQDLLRDALEAARAGEVRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000729.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000729.fa new file mode 100644 index 0000000000000000000000000000000000000000..6d14aa17eb7874fafd4f443de32c2a8acacd7b3c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000729.fa @@ -0,0 +1,50 @@ +>PROKKA_00822 +MPTTSSTATHDVVLIGGGIMSATLGVLLQKLEPTWSIALYESLDQAGLESSDPWNNAGTG +HAALCELNYSPMDKNGRVDVTKALGINEQFWTTRQFWSSLVADGTLKDPKSFINPLPHMS +FVWGDDHADYLRTRYEAMSAQPLFAGMEHSEDPEQIRAWAPLLIEGREPGQRLAASRNTG +GTDVDFGSLTRQLITAMAGAGAEVRFGHKVTGLTRGTDGRWEVKVKNKAAGSELVDRARF +VFVGAGGGALPLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNQHMAKVYGQAAVGAPPM +SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSVRPHNLSTMLDVAKDNMDLT +KYLVTEVLKSRDKKIDALHEFYPEADGGEWELITAGQRVQVMKRKGRFGGVLQFGTEVVT +HADGSLGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGTLKELIPSLGHTLNDDPALL +DEVRTVTDAALKLA +>PROKKA_00554 +MPTTSSTATHDVVLIGGGIMSATLGVLLQKLEPTWSIALYESLDQAGLESSDPWNNAGTG +HAALCELNYSPMDKNGRVDVTKALGINEQFWTTRQFWSSLVADGTLKDPKSFINPLPHMS +FVWGDDHADYLRTRYEAMSAQPLFAGMEHSEDPEQIRAWAPLLIEGREPGQRLAASRNTG +GTDVDFGSLTRQLITAMAGAGAEVRFGHKVTGLTRGTDGRWEVKVKNKAAGSELVDRARF +VFVGAGGGALPLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNQHMAKVYGQAAVGAPPM +SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSVRPHNLSTMLDVAKDNMDLT +KYLVTEVLKSRDKKIDALHEFYPEADGGEWELITAGQRVQVMKRKGRFGGVLQFGTEVVT +HADGSLGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGTLKELIPSLGHTLNDDPALL +DEVRTVTDAALKLA +>PROKKA_02108 +MPTPSSATTHDVVLIGGGIMSATLGVLLQRLEPTWSIALYENLDQAGLESSDPWNNAGTG +HAALCELNYAPLGKDGTVDVTKALGINEQFWTSRQFWSSLVKDGTLQDPKTFINPLPHMS +FVWGDAHADYLRTRYEAMSAQPLFAQMEHTEDPATIAEWAPLLIEGREDAGRIAASRVVG +GTDVDFGSLTRQLVTAMAGAGADVRFGHKVTGLSRGTDGRWEVSVKNKAAGTEVVDRARF +VFVGAGGGALSLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNRHMAKVYGQAAVGAPPM +SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSIRPHNLTTMLDVAKDNMDLT +KYLVAEVVKSQNKKVESLKEFYPEAEGGDWELITAGQRVQVMKRKGRFGGVLQFGTEVVT +HGDGSIGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGALKELIPSLGRTLNDDPALL +AEVSASTDAALKLA +>PROKKA_01999 +MWIPPDGVRRCTILALEHQEHIVSTPTSTTHDVVLIGGGIMSATLGVMLQKLEPSWSIAL +YENLDQSGLESSDPWNNAGTGHAALCELNYSPLGKDGKVDTAKAKGINEQFWITRQFWSS +LVKDGTLADPKNFINPLPHMSFVVGDAHADYLKTRYEAMSAEPLFADMEHTEDPDVIGEW +APLLMDGRTGTERLAASRVPTGTDVDFGSLTRQLVTALAAGGADVRFGHKVTGLSRGTDG +RWDVTVKNKAAGTEVRDRARFVFVGAGGGALGLLQNSGIPEIKGFGGFPVSGQFLRCTDE +KVVNQHMAKVYGQAAVGAPPMSVPHLDTRFVNGKRSLLFGPYAGFSTNFLKSGSYLDLPL +SIRPHNLPTMLNVAKDNMDLTKYLVTEVLKSNEKKVDTLHEFYPAADGSEWELITAGQRV +QVMKKKGKLGGVLQFGTEVVSHADGSIAGLLGASPGASTAAPIMVKLLERCFPAKMAGWD +AALKDMIPTLGRTLNDDPSLLAEVRSATDAALQLG +>PROKKA_00791 +MPTTSSTATHDVVLIGGGIMSATLGVLLQKLEPTWSIALYESLDQAGLESSDPWNNAGTG +HAALCELNYSPMDKNGRVDVTKALGINEQFWTTRQFWSSLVADGTLKDPKSFINPLPHMS +FVWGDDHADYLRTRYETMSAQPLFAGMEHSEDPEQIRAWAPLLIEGRASGQRLAASRNTG +GTDVDFGSLTRQLITAMAGAGAEVRFGHKVTGLTRGTDGRWEVKVKNKAAGSELVDRARF +VFVGAGGGALPLLQKSGIPEAKGFGGFPVSGQFLRCTDESVVNQHMAKVYGQAAVGAPPM +SVPHLDTRFVNGKRSLLFGPYAGFSTNFLKTGSYLDLPLSVRPHNLSTMLDVAKDNMDLT +KYLVTEVLKSRDKKIDALHEFYPEADGAEWELITAGQRVQVMKRKGRFGGVLQFGTEVVT +HADGSLGGLLGASPGASTAAPIMVKLLERCFPAKMAGWDGTLKELIPSLGHTLNDDPALL +DEVRTVTDAALKLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000730.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000730.fa new file mode 100644 index 0000000000000000000000000000000000000000..ee694a04084139af16115e8b19d1d55c30c3c2a2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000730.fa @@ -0,0 +1,55 @@ +>PROKKA_00823 +MQPTRRAFLGGGLGLLGLGVAGCTTSPAAPSSAAPSSSGPGRLLVVGAPARALTRDPARA +LDVESFRLIRQVFETLLGVDADTGAPTPRLAERHEESDGGRLHTFHLVSGVVFDDGEPCD +AAAVVANIERWAAAPAPVDGTVSPPSSFVSAFGGYAGDADSAFAGVEAHGELEVRLRLHS +PRRHLAAALASPAFAISSPASWDRTVDVDGSEVTTPAGTGPYRWADAAETAELTRAHPGA +SGATFLVPSARHRGSDPAAHPVAVQAWGRASVRLRELRRGTADVIDVVAPGQLRPLVEAG +TQVLPRDPLGVLYVGMNLDHPLVHAQYLRQAIAYAVDRPRIAGSDVFLEGTRLAHDLVPP +SLGVGDEEARRYDVNPGRAREFLGLAGYDGEPLEFLYPAGTARPSLPEPERVYAMVARDL +GAVGMHIVPVPVPEDQDYLHAVVSRPTRALHLMGRTGDYRDPHAFLEPFARSGRAETGYR +NPRVVEDVDAAAAETDDDTRRALFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSP +QLDEPFSRVRLTEG +>PROKKA_00555 +MQPTRRAFLGGGLGLLGLGVAGCTTSPAAPSSAAPSSSGPGRLLVVGAPARALTRDPARA +LDVESFRLIRQVFETLLGVDADTGAPTPRLAERHEESDGGRLHTFHLVSGVVFDDGEPCD +AAAVVANIERWAAAPAPVDGTVSPPSSFVSAFGGYAGDADSAFAGVEAHGELEVRLRLHS +PRRHLAAALASPAFAISSPASWDRTVDVDGSEVTTPAGTGPYRWADAAETAELTRAHPGA +SGATFLVPSARHRGSDPAAHPVAVQAWGRASVRLRELRRGTADVIDVVAPGQLRPLVEAG +TQVLPRDPLGVLYVGMNLDHPLVHAQYLRQAIAYAVDRPRIAGSDVFLEGTRLAHDLVPP +SLGVGDEEARRYDVNPGRAREFLGLAGYDGEPLEFLYPAGTARPSLPEPERVYAMVARDL +GAVGMHIVPVPVPEDQDYLHAVVSRPTRALHLMGRTGDYRDPHAFLEPFARSGRAETGYR +NPRVVEDVDAAAAETDDDTRRALFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSP +QLDEPFSRVRLTEG +>PROKKA_02107 +MQPSRRALLGAGLGALGLGLGGCAGTPTPAPSASGTAPATPSGPSRLLVVGAPGRPFTRD +SARAWDSESFRIIRQVLETLLGVDPDTGAPTPRLAERHEVSADGRVHAFHLVPGLVFDDG +EPCDADAVVANIRRWAQAPAPVEGSVPMPSSFVSAFGGHEGEEGSVYAGVEARGAHEVRL +RLTSPLRHLAAALSSPAFAISSPASWERTVPVDGVETVTPAGTGPYRWATEAEVAELSRD +QPDGADVAYLVPSASHRGEEPAVRPVVVHPWGRATTRLRELRRGTADVIDVVAPGQLRPL +VEAGTQVLPRDPLAVLYVGMNLDHPRIRSQYLRQAIAYAVDRPRIAASDVFLEGTRLAHD +LVPPALGVGDEEARRYDVNPAQARRLVELSGYDGEELEFLYPAGTSSPSLPEPERVYAMV +AQDLGAIGLHITPVPVPADHDYLRAVVSRPTRALHLMGRNGAYRDPHAFLEPFARSWRAE +TGYRNPRVIQDVDAAASEQDDEARRGLFRRVVRAMALDLPALPLVYPISALATGPRVASY +PTSPQLDEPFARVRLTEG +>PROKKA_01998 +MDASRRSVLSLGLAGLGLGLSACGAGRATPASSSSSAASAPAVRPLVLGAPGRPLTRTPA +LAWDTESLRLIAQVLEPLLGVDQDTGAPTPLLAEHRESEDGLTHTFVLTPDLRFSDGVAC +DADAVVANLRRWSEGEPAEAVAMPSPFVAAFGGLAGEDSTAFRDATAADARTVRLRLRRR +LRHLPAALASPRFAISSPASWKRTQDVDGAPVATPAGTGPHRWADPTESVEVLEPLGGTG +PATVLVPNEHARAGLPTPPTAVVHSWGRASTRLRELRRGNADVIDVVAPGQLRPLVEAGT +QVLPRDPFSVLYLGMNLDHPLLHSLYLRQAVAYAVDRPRLASSDVFLQGTALAHDLVPPA +LGVAVEDGPRYDVDPARARRLLELAGYRGEPLEFLYPSGHAWPSLPEPERVFAMVSSDLG +VVGLRVVPVPVPADQDYRRAVLGRRGRALHLMGRDGHYRDPHAFLEPFARSARTETGYVN +AALTADVDAAASETDDERRRELHRRAGRTLLLDLPALPLVHPISALATGPRVASYPTSPQ +LDEPLAQVRLADS +>PROKKA_00792 +MQPTRRAFLGGGLGLLGLGVAGCTTSPAVPSSAAPSSSGPGRLLVVGAPARALTRDPARA +LDVESFRLIRQVFETLLGVDADTGAPTPRLAERHEESDGGRLHTFHLVSGVVFDDGEPCD +AAAVVANIERWASAPAPVDGTVAPPSSFVSAFGGYAGDADSAFAGVEARGELEVRLRLHS +PRRHLAAALASPAFAISSPASWDRTVDVDGSEVTTPAGTGPYRWADAAETAELTRAHPGA +SGATILVPSARHRGSDPAAYPVAVQAWGRASVRLRELRRGSADVIDVVAPGQLRPLVEAG +TQVLPRDPLGVLYVGMNLDHPRVRSQYLRQAIAYAVDRPRIAGSDVFLEGTRLAHDLVPP +SLGVGDEEARRYDVNPGRAREFLHLAGYDGEPLEFLYPAGTARPSLPEPERVYAMVARDL +GAVGMHIVPVPVPEDQDYLHAVVSRPTRALHLMGRTGDYRDPHAFLEPFARSGRAETGYR +NPRVVEDVDAAAAETDDDARRALFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSP +QLDEPFSRVRLTEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000734.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000734.fa new file mode 100644 index 0000000000000000000000000000000000000000..0cdf41fc5ec5db87c1d9950295822e1182babba9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000734.fa @@ -0,0 +1,41 @@ +>PROKKA_00830 +MPDPHPAPPRVEPATPPADVPPSVLRADRVHDGERLGGPGWIALAEGRVVAVGTGDPPRT +HGPVHDLGDALLAPGCVDVHCHGGGGHAVESGAAAARAAAAAHARAGTTTVVASLVTDEV +DALAAQLTALTALCAEGVLAGVHLEGPWLSPLHRGAHRAASLRAPEPEDVARLVEVGAGH +LAMVTLAPELPGALDAVGRLAGAGVVVAIGHTDASYETTRAAIEAGARMATHLHNACRPT +HHREPGPAVALLEDPRVGIETIVDGVHLHPATVRRVAREAGERWILVSDSMAAAGCGDGE +FPLGPLRVRVHDGVARVVGADGAAGAIAGSTATVTGSVRSAVAAGVDLDAALRAATAAPA +DALGLPDVGRLRAGSRADAVVFGPELEVRGVLHHGTWVKAAAPAAAD +>PROKKA_00562 +MPDPHPAPPRVEPATPPADVPPSVLRADRVHDGERLGGPGWIALAEGRVTAVGAGDPPRT +HGPVHELGDALLAPGCVDVHCHGGGGHAVESGPDAARAAAAAHARAGTTTVVASLVTDEV +DALVAQLTALAPLRAEGVLAGVHLEGPWLSPLHRGAHRAASLRAPEPEDVARLVEAGAGS +LAMVTLAPELPGALDAVGRLAEAGVLVAIGHTDASYEVTRAAIEAGARMATHLHNACRPA +HHREPGPAVALLEDPRVGIETIVDGVHLHPATVRRVAREAGERWILVSDAMAAAGCGDGD +FSLGPLRARVHDGVARVVGADGAAGAIAGSTATVAGSVRSAVAAGVDLDAALRAATAAPA +DALGLPDVGRLRAGSRADAVVFGPELEVRGVLRHGAWVEAAAPAAAD +>PROKKA_02131 +MRPGGHARARRITPPLADHHVHGGAGVDLATSGAEDVRRWLAELRAAGASVVLGSLPALV +PADLAAALERLRPLWEDGALAGVHLEGPFLSPARAGAQHPDALCAPDSAAGRRVRALLRA +QPRGFVRTLTLAPELPGAREVAAELEAAGTVLCLGHTDAGPAEVAAALDWPRPRAAATPV +ATHLFNGMRPFHHRDPGPVPTLLAAARRGRLRLELVADGAHVAPELMELILEDPDLAAQT +CLVSDAIAATGAPCGTVHRLGPAVVHAAPDAPRLGEPAEDGQGSKATGPEDGGRAPLAGG +RRTLVEAVTALLDADLDADAVLRAAVHVPRRSLPETPAPELEDGALVWDEGRPLVALPAA +RA +>PROKKA_02024 +MTASALLRTTAPWVGADPGATPVRVSAVWSAGPDGALLVWAGLAERVPQELWETAVDAPA +LRLSPALTSHHVHGGAGVDLATSPAADVRSWLAAQRQAGVGAVVGSLPTLAEDALAAALD +RLRPLWAEGLLAGVHLEGPFLSPARAGAHDPALLLTPPSPAGRRVRALIAAQPEGFVRTL +TLAPELPGADALTRELTGTGVVVCPGHTDADGATTRAWLQTADDARAAATAAGLPAPTPV +ATHLFNGMRGFHHRAPGPLPALLGAARAGRARLELIGDGVHVDDEVLTAILGDPGLAPAA +CLVSDAVAATGATRGTAHRLGSLPIHAAQDGPRVGADEPTGPAEAALAGGAADLPEIVGR +LLHSDLDPDAVLRAATHVPARTLGGSHAVPVGTPETTEHAAPGGDVLVWAPDGAVTVLRS +QAAPGGRHHD +>PROKKA_00799 +MPASVPHRPRAEQAPQAAASPSVLRADRVHDGERLGGPGWIALAEGRVVAVGTGDPPRTH +GPVHDLGDALLAPGCVDVHCHGGGGHAVESGAAAARAAAAAHARAGTTTVVASLVTDEVD +ALAAQLTALTPLCAEGVLAGVHLEGPWLSPRHRGAHRAASLRAPEPEDVARLVEVGAGHL +AMVTLAPELPGALDAVGRLAEAGVVVAIGHTDASYETTRAAIDAGARMATHLHNACRPTH +HREPGPAVALLEDPRVGIETIVDGVHLHPATVRRVAREAGERWILVSDAMAAAGCGDGEF +PLGPLRVQVHDGVARVVGADGAAGAIAGSTATVAGSVRSAVAAGVDLDAALRAATAAPAD +ALGLPDVGRLRVGSRADAVVFGPELEVRGVLRHGTWVKAAAPAVAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000735.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000735.fa new file mode 100644 index 0000000000000000000000000000000000000000..6b502c86e9892047a8fbc79a6adda6df2a4f79bf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000735.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000740.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000740.fa new file mode 100644 index 0000000000000000000000000000000000000000..217f7490fcd0f5300bb7eb8320524fadb8723c81 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000740.fa @@ -0,0 +1,36 @@ +>PROKKA_00848 +MTETTRSSADPLDIAVIGGDGIGPEVTDQAAAVLQAALRAEGRPEARLTPYPLGAEHWLE +TGEALTDEVLESLRRHDAILFGAVGAAPGDERIPSGLIERGMLLKLRFALDHGVNLRPAT +LLPGAVSPLAAPGEIDFTVVREGTEGPYVGNGGAIRVDTPHEIATEVSVNTAFGVRRVVE +DAFRRADAGERKRLTLVHKHNVLVHAGHLWRRTVESVGADFPAVTWDYMHVDAAMIFLAT +DPARFDVIVTDNLFGDIITDLAAAVTGGIGLAASGNINVEGTAPSMFEPVHGSAPDIAGQ +GIADPVAAILSAALLLEHVGETGAAARVRTAVWAHLKDRVDGARGTTAEVGADVAARV +>PROKKA_00570 +MTETTRSSADPLDIAVIGGDGIGPEVTDQAAAVLQAALRAEGRPEARLTPYPLGAEHWLE +TGEALTDEVLESLRRHDAILFGAVGAAPGDERIPSGLIERGMLLKLRFALDHGVNLRPAT +LLPGAVSPLAAPGEIDFTVVREGTEGPYVGNGGAIRVDTPHEIATEVSVNTAFGVRRVVE +DAFRRADAGERKRLTLVHKHNVLVHAGHLWRRTVESVAADFPAVTWDYMHVDAAMIFLAT +DPARFDVIVTDNLFGDIITDLAAAVTGGIGLAASGNINVEGTAPSMFEPVHGSAPDIAGQ +GIADPVAAILSAALLLEHVGETGAAARVRTAVWAHLKDRVDGARGTTAEVGADVVARV +>PROKKA_02087 +MTESTRPSADPLDIAVIGGDGIGPEVTEQAAAVLQAALGAEGRPEARLTPYPLGAEHWLR +TGEALPDETLEALRGHDAILFGAVGAAPGDERIPSGLIERGMLLRLRFELDHGVNLRPAA +LLPGAVSPLAEPGTIDFTVVREGTEGPYVGNGGAIRTGTPHEIATEVSVNTAHGVRRVVE +DAFARAAAGERKRLTLVHKHNVLVHAGHLWRRTVEAVAADFPEVSWDYMHVDAATIFLTT +DPARFDVIVTDNLFGDILTDLAAAVTGGIGLAASGNINVEGTAPSMFEPVHGSAPDIAGQ +GVADPVAAILSAALLLEHVGETGAAQRVRTAVWAHLKDRVDGARGSTAEVGADVAARV +>PROKKA_01987 +MTESTRTSAAPLDIAVIGGDGIGPEVTDQAVAVLEAALAAEGRPAPRLTPYALGAEHWLA +TGEALTDETLEALRGHEAILFGAVGAAPGDQRIPSGLIERGILLRLRFELDHGVNLRPSR +LYPGTTSPLAEPGEIAFTVVREGTEGPYVGNGGAIRTGTEHEIATEVSVNTAHGVRRVVR +DAFRRASATERRRLTLVHKHNVLVHAGHLWRRTVEEVAAEFPEVAHDYMHVDAATIVMTT +DPARFDVIVTDNLFGDILTDLAGAVTGGIGLAASANINVERTAPSMFEPVHGSAPDIAGQ +GIADPVAAILSAGLLLEHVGERAAADRIDRAVWAHLAERGPQRGSTAEVGVDVVRRVRES +SAA +>PROKKA_00807 +MTETTRSSADPLDIAVIGGDGIGPEVTDQAAAVLQAALRAEGRPEARLTPYPLGAEHWLE +TGEALTDEVLESLRRHDAILFGAVGAAPGDERIPSGLIERGMLLKLRFALDHGVNLRPAT +LLPGAVSPLAAPGEIDFTVVREGTEGPYVGNGGAIRVDTPHEIATEVSVNTAFGVRRVVE +DAFRRADAGERKRLTLVHKHNVLVHAGHLWRRTVESVAADFPAVTWDYMHVDAAMIFLAT +DPARFDVIVTDNLFGDIITDLAAAVTGGIGLAASGNINVEGTAPSMFEPVHGSAPDIAGQ +GIADPVAAILSAALLLEHVGETGAAARVRTAVWAHLKDRVDGARGTTAEVGADVVARV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000741.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000741.fa new file mode 100644 index 0000000000000000000000000000000000000000..46b525b1256eeda86b364a4da9ac7b8129d82d70 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000741.fa @@ -0,0 +1,40 @@ +>PROKKA_00849 +MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG +PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF +LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE +LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE +LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS +GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGADVALKIRTELEGIQTGRVEDRHGWLH +RLV +>PROKKA_00571 +MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG +PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF +LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE +LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE +LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS +GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGTDVTLRIRAELEGIQTGRVEDRHGWLH +RLV +>PROKKA_02086 +MSETVFTRQPHLSPLSEEERVEILQDPGFGKVFTDHMVSIDWTWSEDGGAWHDARVEPYG +PLSLDPSASVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEEMF +LGSLKAQLEADRDWVPTGEGQSLYLRPFMFATEAFLGVRPAKEVRYMVIASPAGNYFGGE +LKPVTIWVSREYARAGRGGMGAAKTGGNYAASLLPQLEAASKGADQVVFLDQYHDDSIEE +LGGMNVFFVFDDGRLVTPELTGTILEGVTRSSILQLGRDMGLTVEERRITLAEWAEGVRS +GAIREVFACGTAAVVTPIGRLLDGDDVIESAGGTEVTLKIRAELEGIQTGRVEDRHGWLH +RLV +>PROKKA_01986 +MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG +PLSLDPSAAVLHYGQEIFEGLKAYGHEDGSVWTFRPEANAARLNRSARRLALPELPEELF +LGSLRAQLEADQAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE +LTPVTIWVSRDYARAGKGGMGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE +LGGMNVFFVHADGRLVTPELTGTILEGVTRSSILQLGRDMGMSVEERRVTLAEWAEGVRT +GAITEVFACGTAAVVTPIGRLLDGDDVIESTGGTEVAMKIRAELEGIQTGTVEDRYGWMH +RLV +>PROKKA_00808 +MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG +PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF +LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE +LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE +LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS +GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGTDVTLRIRAELEGIQTGRVEDRHGWLH +RLV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000742.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000742.fa new file mode 100644 index 0000000000000000000000000000000000000000..a201b092419d7250ecc62236667282066bf1db65 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000742.fa @@ -0,0 +1,70 @@ +>PROKKA_00850 +MSSHRSSAAAEGAPLPATTPEDLPPTEAAGRPRWTPAKIAVWVAVALLGGVAWTMLALHR +GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL +YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG +QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV +YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA +VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP +FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR +GIYFAMNAPAALTGGTPETAAAWVMSLGLAGVDVTPEQLTALANLVGEDTVVSRTGGAPT +LAVGLSIIMGQLIGGEALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF +KDTGWRVGAWVCTGIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLAI +VAGRRHFRGLWIVALPLGFITVVTTVASFQKIFSSVPAVGYWAQHNAFKDALASGATSFG +AAKSVPAMEAVVRNTFIQGTLSIVFLVLALVVITTSVLATVRAFRGTEVIDHQDPYVPSQ +RFAPAGLFATAEEKELQAQWDALPAEKQPVRGH +>PROKKA_00572 +MSSHRSSAPAEGAPRPATTPEDLPPTEAADRPRWTPVKIAVWVAVALLGGVAWTMLALHR +GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL +YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG +QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV +YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA +VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP +FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR +GIYFAMNAPAALTGGTPETAADFVMGLGLAGVNLAPGDLTHLADLVGEETVVSRTGGAPT +LAVGLAHIMGQLVGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF +KDTSWRVGAWVCTAIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLTI +VARRRDFRGLWIVALPLAFITVVTTVASFQKIFSSIPAVGYWAQHRAFQDALAAGKTSFG +AAKSVPAMEAVVRNTFIQGTLSVVFLVLALIVITTSVLATVRAFRGTEVIDHQDPYVPSQ +RFAPAGLFATAEEKELQRKWDALPADRQPVRGH +>PROKKA_02085 +MSSHRSAAPAEGMAPRDPARDGGPDGLPPVEAAQRPRWTPLKIAVWVVVALVGGVAWTML +ALHRGESINAIWFVFAAVATFAIGYRFYSKYVERMIVRPDDTRATPAEYRADGRDYVATD +RRVLYGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGG +RSLGQMARDELGRIGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVALTIPIAI +FMGLYLRYLRPGRITEVSIIGFVLLMAAIIGGGWVAETDWGVALFTLDRVTIAWGIIIYG +FVAAVLPVWLLLAPRDYLSTFMKIGVIAGLAVAIVIVQPQITAPAISEFASGQTGPVWPG +SLFPFLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAV +SIDRGIYFAMNAPAALTGGTPETAAAWVMSLGLAGVDVTPEQLTALANLVGEDTVVSRTG +GAPTLAVGLSIIMGQLIGGEALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNV +APRFKDTGWRVGAWVCTGIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAV +VLAIVAGRRHFRGLWIVALPLGFITVVTTVASFQKIFSSVPAVGYWAQHNAFKDALASGA +TSFGAAKSVPAMEAVVRNTFIQGTLSIVFLVLALVVITTSVLATIRAFRSTEVVDHADPY +VPSRRFAPAGLIATAEEKELQRQWDALPADQRPERGH +>PROKKA_01985 +MSSTRSVIPTGGSAPHDARPDGLPPVEAPHEQRWTPARVAVWAVIALLGAVAWTMLALHR +GESINAIWFVFAAVSTFLIGYRFYSKYVERAIVRPDDTRATPAEYNADGRDFVATDRRVL +FGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG +QMARDELGRIGGTAAIIATLLIMVIITAILALIVVNALGDSPWGVFSVGMTIPIALFMGL +YLRYLRPGAITEVSIIGFVLLLAAIIGGGFIAETPWGAALFTLDRVTLAWAVIVYGFVAA +VLPVWLLLAPRDYLSTFMKIGVIAGLAIAIVIVQPRVQAPAFSEFAGGQAGPVWAGSLFP +FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAIMALVAAVTIDR +GVYFAMNAPTALTGGAVDSAVAWVNGLGLANADLTPDQLTTLANQVGEETVVSRTGGAPT +LAVGLAQIMGQLIGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDTLGNVFPKF +KDHNWTPGAWLATAVMVAAWGAVLVMGVTDPLGGINTLFPLFGIANQLLASIALAVVMAI +VAKRRTFKGLWIVALPLAFITVVTTVASLHKIFSPVPAVGYWAQHRAFQDALAAGKTSFG +AATTVPAMEAVVRNTFVQGTLSVLFLALALIVITSSIVATVRAFRSTEVVDHQDPYVPSR +RFAPAGLTATPAEKEIQAQWDALPADRQPVRGH +>PROKKA_00809 +MSSHRSSAPAEGAPRPATTPEDLPPTEAADRPRWTPVKIAVWVAVALLGGVAWTMLALHR +GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL +YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG +QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV +YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA +VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP +FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR +GIYFAMNAPAALTGGTPETAADFVMGLGLAGVNLAPGDLTHLADLVGEETVVSRTGGAPT +LAVGLAHIMGQLVGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF +KDTSWRVGAWVCTAIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLTI +VARRRDFRGLWIVALPLAFITVVTTVASFQKIFSSIPAVGYWAQHRAFQDALAAGKTSFG +AAKSVPAMEAVVRNTFIQGTLSVVFLVLALIVITTSVLATVRAFRGTEVIDHQDPYVPSQ +RFAPAGLFATAEEKELQRKWDALPADRQPVRGH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000743.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000743.fa new file mode 100644 index 0000000000000000000000000000000000000000..f9d59fbde4a6bf9fbfb42ba53646b2ec953f4e78 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000743.fa @@ -0,0 +1,14 @@ +>PROKKA_00851 +MVAPRTTPGGAPAAEASPARRTWQAARWWVRQLSGEGKYDAYVAHHRAHHPERAPMTERE +FWRAEYARQEANPGSRCC +>PROKKA_00573 +MRCRRTGSRCGVTDVADPRATPAGPSSAEGPAGPSRPSVWARARWWVRQLSGEGKYDAYV +AHHRAHHPERAPMTEREFWRAEYARQEANPGSRCC +>PROKKA_02084 +MAASGTCPTPTGGSAAEPAAARRAGDGTGPAAGSGLRAAWASARWWVRQLAGEGKYDAYL +AHHRAQHPGVEPMSEREFWRDEYAKQEANPGSRCC +>PROKKA_01984 +MAGIWASTRWWVRQLTGEGKYDAYLAHHRAHHPGEVPMTEREFWRDEYARQDANPGSRCC +>PROKKA_00810 +MRCRRTGSRCGVTDVADPRATPAGPSSAEGPAGPSRPSVWARARWWVRQLSGEGKYDAYV +AHHRAHHPERAPMTEREFWRAEYARQEANPGSRCC diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000751.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000751.fa new file mode 100644 index 0000000000000000000000000000000000000000..9db7ccf9eaf4708f88947425a34b66f9befe98c5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000751.fa @@ -0,0 +1,25 @@ +>PROKKA_00864 +MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS +GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV +ERIWKELENRPGTPVTVDLVTRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLGHQAEI +DAYEADRPAYKPTTLPARTAG +>PROKKA_00586 +MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS +GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV +ERIWKELENRPGTTVTVDLVTRTVECGDVTAPFQIDDDTRRRLLEGLDDIAVTLGHQAEI +DAYEADRPAYKPTTLPARTAG +>PROKKA_02071 +MEKFTTHTGIGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS +AGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV +ERIWKELENRPGTTVTVDLVSRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLDHQDEI +DAYERARPSYKPTTLPARTAG +>PROKKA_01965 +MDKFTTHTGIGVPLRASNVDTDQIIPAVYLKRVSRTGFEDALFAGWRQDPDFILNTEPYS +AGSVLVAGPDFGTGSSREHAVWALKDYGFKVVVSSRFADIFRGNSAKQGLVAAQVEPEDV +ERIMKQLENQPGAAVTVDLEHLTVECGGVTAAFEIDEDARHRLLHGLDDIAITLSHADAI +AAYEAGRPSYKPTTLPARTAD +>PROKKA_00823 +MEKFTTHTGVGVPLRASNVDTDQIIPAVYLKRISRTGFEDALFAGWRQDPDFILNTEPFS +GGTVLVAGSDFGTGSSREHAVWALKDYGFRAVISPRFADIFRGNSAKQGLVAAQVEQEDV +ERIWKELENRPGTPVTVDLVTRTVECGDVTAPFQIDDDTRHRLLEGLDDIAVTLGHQAEI +DAYEADRPAYKPTTLPARTAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000752.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000752.fa new file mode 100644 index 0000000000000000000000000000000000000000..66b337a739dad687025c79db7852880b2e86f874 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000752.fa @@ -0,0 +1,45 @@ +>PROKKA_00865 +MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNSPSVLRNIPEIKDVDVVSSLLEI +HGVSVEWDKETGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG +CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV +KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVSEMRGYNHIALPDRNE +SASWASAALATRGDIYVRGAEQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL +ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS +VPCRFGQRNFLHSAVISGPTPLHGVEFDIPDLRGGFSHLIAALTAEGTSTATGLEIINRG +YEHFMAKLEGLGADVELTERDR +>PROKKA_00587 +MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNSPSVLRNIPEIKDVDVVSSLLEI +HGVSVEWDKETGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG +CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV +KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVSEMRGYNHIALPDRNE +SASWASAALATRGDIYVRGAEQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL +ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS +VPCRFGQRNFLHSAVISGPKPLHGVEFDIPDLRGGFSHLIAALTAEGTSTATGLEIINRG +YEHFMAKLEGLGADVELTERDR +>PROKKA_02070 +MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNTPSVLRSIPEIKDVDVVSSLLEI +HGVSVEWDKESGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG +CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV +KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVTEMRGYNHEALPDRNE +SASWASAALATGGDIFVRGASQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL +ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS +VPCRFGQRNFLHSAVISGPTPLHGVEIDIPDLRGGFSHLIAALAAEGTSTATGLEIINRG +YEHFMDKLQGLGADVELSDRTR +>PROKKA_01964 +MAKLLTIHGGKPLQGEVTVRGAKNLVPKAMVAALLGTGPSVLRSIPEIKDVDVVSSLLEI +HGVTVDWDKESGTITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG +CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV +KAEGITELKGAAVEPEIHDLIHVLQKMGAIITVQTDRTIRIEGVPELRGYNHVAIPDRNE +SASWASAALATKGDIFVRGASQRDLTAFLNTYRKIGGEFEVTDEGIRFWHGGGELNPLVL +ETDVHPGFMTDWQQPLVVALTQATGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS +VPCRFGQRNFLHSAVISGPTPLHGVDFDVPDLRGGFSHLIAALAAEGTSHATGLEIINRG +YEHFMAKLQGLGADVELSERPR +>PROKKA_00824 +MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNSPSVLRNIPEIKDVDVVSSLLEI +HGVSVEWDKETGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG +CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV +KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVSEMRGYNHIALPDRNE +SASWASAALATRGDIYVRGAEQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL +ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS +VPCRFGQRNFLHSAVISGPTPLHGVEFDIPDLRGGFSHLIAALTAEGTSTATGLEIINRG +YEHFMAKLEGLGADVEPTERDR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000753.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000753.fa new file mode 100644 index 0000000000000000000000000000000000000000..bbcf592fda927c666585f1a91d06f649a6cffe2c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000753.fa @@ -0,0 +1,30 @@ +>PROKKA_00866 +MSGVDAQSPAAAGGRPTRTARAPYVIPGVIVRPAMRALVRQVWEGTEHLPETGAILAVNH +ISEVDPLSVAHMVYNQGLLPTFLAKAELWKVPVLKQVLEATRMIPVERTRDGGRSLAAAR +EAVATGRAIIVYPEGTVTRDPDGWPMAGRNGAVRLALQTGAPLIPVGQWGIQELLPYGGR +SLRVLPRKTARIRVGAPVDLADLRDRPVTAGTLREGTGRMMGAITDLVAELRGEPAPEGR +WDPTAGARVAEA +>PROKKA_00588 +MSGVDAQSPAAAGGRPTRAARAPYVIPGVIVRPAMRALVRQVWEGTEHLPETGAILAVNH +ISEVDPLSVAHMVYNQGLLPTFLAKAELWKVPVLKQVLEATRMIPVERTRDGGRSLAAAR +EAVATGRAIIVYPEGTVTRDPDGWPMAGRNGAVRLALQTGAPLIPVGQWGIQELLPYGGR +SLRVLPRKTARIRVGAPVDLADLRDRPVTAATLREGTGRMMAAITDLVAELRGEPAPEGR +WDPTTGARVTGA +>PROKKA_02069 +MSTVDPQTPAPAAGRPSRAARAGYVIPAAIVRPALRGLVSQVWEGTENLPETGAILAVNH +ISELDPLSVAHMVYNQGLLPTFLAKAELWKVPGFKQALQATRTIPVERSRDGGRSLAAAR +EALATGRAIIVYPEGTVTRDPDGWPMAAQSGAVRLALQTGAPLIPVGQWGIQELLPYGGR +APRPFPRKTARIRVGTPVDLDDLRGGPLTATALRAGTERMMDAITAIVADLRGEPAPAGR +WDPRTGRREPGA +>PROKKA_01963 +MNDGERPIAQPSRGLRRGFVAPAAVVRPALRALVRQEWLHAERIPRTGAILAVNHISELD +PLSVAHMVYNQGLLPAVLAKAELWKVPVLRRVLQSTRMIPVERSRDGGRSLAAAQAALDE +GRVIIVYPEGTVTRDPEGWPMSARSGAVRLALQTGAPLIPVGQWGMQELLPYPGFRLSPF +PRKTARVLVGEPVDLDDLRGGPLTAAVLRVGTERMMDAVTELVAQLRGEPAPAWRWDLRT +GRREGAA +>PROKKA_00825 +MSGVDAQSPAAAGGRPTRAARAAYVIPGVIVRPAMRALVRQVWEGTEHLPETGAILAVNH +ISEVDPLSVAHMVYNQGLLPTFLAKAELWKVPVLKQVLEATRMIPVERTRDGGRSLAAAR +EAVATGRAIIVYPEGTVTRDPDGWPMAGRNGAVRLALQTGAPLIPVGQWGIQELLPYGGR +SLRVLPRKTARIRVGAPVDLADLRDRPVTAATLREGTGRMMAAITDLVAELRGEPAPEGR +WDPTAGARVIGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000754.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000754.fa new file mode 100644 index 0000000000000000000000000000000000000000..09ec782a368158d0afef3f5284b4bd97ae1fb733 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000754.fa @@ -0,0 +1,36 @@ +>PROKKA_00867 +MSDPRTVAVLGAGSWGSAFARVLGLSTSPESARASEIVMWSRRAEVAEAITERHENPEYL +PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLRTVRADLAPDAVVVSLVKGLER +GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG +RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG +GDTDTMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV +HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA +>PROKKA_00589 +MSDPRTVAVLGAGSWGSAFARVLGLSTSPESARASEIVMWSRRAEVAEAITERHENPEYL +PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLHAVRADLAPDAVVVSLVKGLER +GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG +RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG +GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV +HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA +>PROKKA_02068 +MSDPQTVAVLGAGSWGSAFARVLGTSTSPEGARARDVVIWSRRPEVAEVVNRDHANPEYL +PGIELPACVRAVTDAFEAVRGAGVVVVAVPAQHVRETLRTLREDLAPDAVVVSLVKGLER +GTDARMSQVCTEELGLTPDRFAVVSGPNLALEIARGEPTATVVASGSSATAERIAALTAG +PTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG +GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGMSAEEAVAAMSQTAEGIKSVSAVV +HVARAHGVEMPISELMDRVVAGDVAVHRLAELLLARDLKSEGRTA +>PROKKA_01962 +MSPAPSAGPEPAFASASAGDRAGDPTRVAVLGAGSWGTAFACVLGSSTSPAGRRAREVVV +WSRRAEVARAITEDHANPEYLPDVALPECVRAVTDAREAVAEAGVVVVAVPAQQARTVLE +GLADALAPDAIAVSLMKGLERGTDARPSQVCQEALGIGPERFAVLSGPNLALEIARGEPT +ATVVASASRATADRVAALTAGPTFRPYTNGDVVGVEIGGIVKNVIALAVGICDGQGLGDN +SKASVITRGLAETTRLAVALGGEASTLAGLAGLGDLVATCASPLSRNRSAGRLMGTGLSA +DEAVAAMKQTAEGIKSVSAVVHVARAHGVEMPISEAMDRVVAGTLDVDRLAGLLLARDLK +SEGRHA +>PROKKA_00826 +MSDPRTVAVLGAGSWGSAFARVLGLSTSPEPARASEIVMWSRRAEVAEAITERHENPEYL +PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLRTVRADLAPDAVVVSLVKGLER +GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG +RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG +GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV +HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000757.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000757.fa new file mode 100644 index 0000000000000000000000000000000000000000..2f67cab375c83129b8325f34a5d4d7eee1ac8de1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000757.fa @@ -0,0 +1,39 @@ +>PROKKA_00870 +MSSTADPRPRPPQEDVAVGRRRRRRRPWLIALAVVLVALLAVGIAAAVYVGGIARTIDQD +TQRFDGGAFPAESGRPGAAGASAQQPTAPPPGMDADQAAEGAQGPVAPDADEKADEQALD +VLLVGEDAGAEGRDSAGRSDTLMWVHVPGDRSEIQVMSIMRDMWVPIPGHGDHKVNAAYQ +YGGIPLTVATAENMFQARVDHVIAVDLAGFKGLVDALGGVSVDNPSAFVSTGGIDFPAGT +VQMDGDKALAYARERYNLPRSDFDRVENQQRLVKAIVAAFLSRDTLSDPSRVQAAVEEFA +PFLTLDDELDSSTLANLAWSLRDARDAPIVTSTVPSVGVGYTDTGEDVVWPDWAAIARLG +EGIRTGTLGETVAQ +>PROKKA_00592 +MSSTADPRPRPPQEDVAVGRRRRRRRPWLIALAVVLVALLAVGIAAAVYVGGIARTIDQD +TQRFDGGAFPAESGRPGAAGASAQQPTAPPPGMDAEQAAEGAQGPVAPGADEKADEQALD +VLLVGEDAGAEGRDSAGRSDTLMWVHVPGDRSEIQVMSIMRDMWVPIPGHGDHKVNAAYQ +YGGIPLTVATAENMFQARVDHVIAVDLAGFKGLVDALGGVSVDNPAAFVSTGGIDFPAGT +VQMDGDKALAYARERYNLPRSDFDRVENQQRLVKAIVAAFLSRDTLSDPSRVQAAVEEFA +PFLTLDDELDSGTLANLAWSLRDARDAPIVTSTVPSVGVGYTDTGEDVVWPDWAAIARLG +EGIRAGTLGEAVAQ +>PROKKA_02065 +MALLAVGIAAAVYVGGIARTIDQDTQRFDGGAFPAESGRPGAAGASAQQPTAPPPGMDAE +QAAEGAQGPVAPDRDEKADEQALDVLLVGEDAGAEGRDSAGRSDTLMWVHVPGDRSEIQV +MSIMRDMWVPIPGHGDHKVNAAYQYGGIPLTVATAENMFQARVDHVIAVDLAGFKGLVDA +LGGVSVDNPAAFVSTGGIDFPAGTVQMDGDKALAYARERYNLPRSDFDRVENQQRLVKAI +VAAFLSRDTLSDPSRVQAAVEEFAPFLTLDDELGSSTLANLAWSLRDARDAPIVTSTVPS +VGVGYTDTGEDVVWPDWAAIARLGEGIRTGTLGEAVAP +>PROKKA_01959 +MSTAEPTATPRRRRRPLLIVLVALLVLLLAAGLTAALWLGGLGRTVDEGVQRFEGQALPE +ESLRPAEPGSAAAPGSAADGRNASGVYSPSAPPPGTAPAGVDPATALAGPAGPAADEVAD +GKAVDFLLVGEDSGVEGRDPNGRSDTLMWVHIPGDRSAVQVRSIMRDTWVPIPGHGDHKV +NAAYQYGQIPLTVATVENMFQARVDHVVAVDMAGFQGLVDALGGITVDNPIAFTADDGHA +YPAGAIQMDGATALVYARERYNLPRGDFDRVENQQRVVKAVFSKALSLDTLSDPGRVQQA +VERFSPFLTLDSELHSGDLAALAWSMRNLRGSDIQTSTVPAAGVGYSADGQAVVWPDWAA +IHEIGRQIRTSEAR +>PROKKA_00829 +MSSTADPRPRPPQEDVAVGRRRRRRRPWLIALAVVLVALLAVGIAAAVYVGGIARIIDQD +TQRFDGGAFPAESGRPGAAGASAQQPTAPPPGMDADQAAEGAQGPVAPDADEKADEQALD +VLLVGEDAGAEGRDSAGRSDTLMWVHVPGDRSEIQVMSIMRDMWVPIPGHGDHKVNAAYQ +YGGIPLTVATAENMFQARVDHVIAVDLAGFKGLVDALGGVSVDNPSAFVSTGGIDFPAGT +VQMDGDKALAYARERYNLPRSDFDRVENQQRLVKAIVAAFLSRDTLSDPSRVQAAVEEFA +PFLTLDDELDSSTLANLAWSLRDARDAPIVTSTVPSVGVGYTDTGEDVVWPDWAAIARLG +EGIRTGTLGEAVAQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000759.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000759.fa new file mode 100644 index 0000000000000000000000000000000000000000..69d94651231e2812de4a6d014a75f1804689422a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000759.fa @@ -0,0 +1,70 @@ +>PROKKA_00872 +MAAEAPVTDLPLSEVLGGKLPARLERELGLTTVGDLLDHVPRRWIERGELTPIAALPYDA +EVTVVAVVESVTTRRMHSRPGFIVDVTVADPSVAGVPGASLSMAFFNGHDARRRLAPGMT +AMFQGRTTEYRGRITLNNPDFALLDDDVAPGEVDVRPVPLYRATGKLPSWTVRSAVARVL +ETVDLGRIPELLTERIRAEAAAALDLDVPLPGTAQAYRDLHAPNDVAATGPARTALALRE +ALLVQAALAWRRNRERAVPAVPRPPRAGGLLEALDARLPFALTPGQVAVGEQLSAELARD +APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLRLMGPLAEA +GTLGAGDGPATRIALVTGSLKTAARREALLALASGEAGIAVGTHALLSEKVGFAELALAV +VDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVT +THVARMAHGPRVIGRVWELIAEHVAAGHQAFVVCPRIDPDDADPGHANVEEMTPRLRGLP +ALAGLRIDAVHGRMDQAEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAILDADDF +GLSTLHQLRGRVGRGPGAAVCLLATRLPDGHPSLRRLEVLAQEQDGMRIAQEDLAQRGVG +DVLGAAQSGLASGLHHVDVIADAPLIAVAADAVAQVMAAGPGLSAHPALAAEVARWEAEH +LTAADYLEKG +>PROKKA_00594 +MAAEAPVTDLPLSEVLGGKLPARLEKELGLTTVGDLLDHVPRRWIERGELTPIAALPHDA +EVTVVAVVESVTTRRMHSRPGFIVDVTVADPSVAGVPGASLSMAFFNGHDARRRLAPGMT +AMFQGRTTEYRGRITLNNPDFALLDDDVAPGEVDVRPVPLYRATGKLPSWTVRSAVARVL +ETVDLGRIPELLTERIRAEAAAALDLDAPLPGTAQAYRDLHAPHDVAATGPARTALALRE +ALLVQAALAWRRDRERAVPAVPRPPRPGGLLEALDARLPFALTPGQVAVGEQLSAELARD +APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLRLMGPLAEA +GTLGAGDGPATRVALVTGSLKTTARREALLALASGEAGIAVGTHALLSEKVGFAELALAV +VDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVT +THVARMAHGPRVIGRVWELIAEHVAAGHQAFVVCPRIDPDDADPGHANVEEMTPRLRSLP +ALAGLRIDAVHGRMDQAEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAILDADDF +GLSTLHQLRGRVGRGPGAAVCLLATRLPDGHPSLRRLEVLAQEQDGMRIAQEDLAQRGVG +DVLGAAQSGLASGLRHVDVIADAPLIAVAADAVTRVMAAGPGLSAHPALAAEVARWEAEH +LTAADYLEKG +>PROKKA_02063 +MGAEVRVTDLPLSEVLDGRLPARLDKELGLATVGDLLDHVPRRWIERGELTPIAALPWDA +EVTVVAVVESVTTRRMHSRPGFIVDVTVADPAADGAPGASLSMAFFNGHDARRRLAPGMT +AMFQGRTTAYRGRITLNNPDFALLDDDVAPGDVDVRPVPLYRATGKLPSWTVRSAVARVL +ADVDLTRIPELLTPRLRAEAAAALDLDAPLPDTARAYRDLHAPEEVEATGPARTALALRE +ALVVQAALAWRRDRERAVPAVPRPPRAGGLLDALDARLPFALTPGQAEVGEQLAAELTRD +APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLALMGPLAEA +GTLGAGDGPATKVVLVTGSLKTQARREALLALASGEAGIAVGTHALLSDKVGFAELALAV +VDEQHRFGVDQREALRRSNPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVA +THVARMDHGPRVIGRVWELIAEHAAAGRQAFVVCPRIDPDDADPGHANVEEMAPRLRSLP +ALAGLRIEAVHGRMDQAEQDAAMQAFARGETDVLVATTVIEVGVDVPNATVMAVLDADDF +GLSTLHQLRGRVGRGPDAAVCLLATRLPDEHPSLRRLEVLAQEQDGMRIAQEDLATRGVG +DVLGAAQSGLASGLRHVDVLRDAPLIAVAADAVGRIMAEGPGLSAHPALAAEVARWESEH +LTAADYLEKG +>PROKKA_01957 +MAADGVLDLPLGEVLSGRLPGRLEKELGLATVGGLLDHVPRRWVERGELTPIAALPVDAE +VTVVARVEHVATRRMRSRAGFIVDVTVADPSVAGTAGASLSMAFFNGHDAQRRLAPGVTA +MFQGKTSLYRGAVTLNNPDFALLDDDVAPGEVDTRPVPIYRATGRMPSWTVRSAVRRVLE +TVDLDAIPELLTEPIRARATLALGLPETLPGTAEAYRRLHAPDAVEQTGPARTALSLREA +LVVQGALAWRRSREKAVPAVPRPRRAGGLLEALDARLPFELTPGQRAVGEELAAELSGPH +PMSRLLQGDVGAGKTLVALRAMAQAVDAGGQAAFVAPTEVLAAQHHRALLALLGPLAREA +GTLGAAAQEGPGTDVVLVTGSQRSAQRRAALLKLASGEAGIAVGTHALLAERVQFAELAL +AVVDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRTP +VATHVARMAHGPRVIARVWEVVAEHCAAGRQAFVVCPRIDPDDADPAHANVTEMAERLRA +LPVLGGLRIGEVHGRMDQAEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAVLDAD +DFGLSTLHQLRGRVGRGQDAAICLLATRLADGHPSLRRLEVLEATRDGMRIAQADLAQRG +VGDVLGAAQSGLASGLTHVDVIGDADVIGVAADVVADLMAAAPGLSAHPALAAEVSRWEA +AHLTAADYLEKG +>PROKKA_00831 +MAAEAPVTDLPLSEVLGGKLPARLEKELGLTTVGDLLDHVPRRWIERGELTPIAALPYDA +EVTVVAVVESVTTRRMHSRPGFIVDVTVADPSVAGVPGASLSMAFFNGHDARRRLAPGMT +AMFQGRTTEYRGRITLNNPDFALLDDDVAPGEVDVRPVPLYRATGKLPSWTVRSAVARVL +ETVDLGRIPELLTERIRAEAAAALDLDAPLPGTAQAYRDLHAPHDVAATGPARTALALRE +ALLVQAALAWRRDRERAVPAVPRPPRAGGLLEALDARLPFALTPGQVAVGEQLSAELARE +APMSRLLQGDVGAGKTLVALRAMLQVVDAGGQAALVAPTEVLAAQHHRALLRLMGPLAEA +CTLGAGDGPATRVVLVTGSLKTAARREALLALASGEAGIAVGTHALLSEKVGFAELALAV +VDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQPVT +THVAQMAHGPRVIGRVWELIAEHVAAGHQAFVVCPRIDPDDADPGHANVEEMTPRLRGLP +ALAGLRIDAVHGRMDQVEQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAILDADDF +GLSTLHQLRGRVGRGPGAAVCLLATRLPDGHPSLRRLEVLAQEQDGMRIAQEDLAQRGVG +DVLGAAQSGLASGLHHVDVIADAPLIAVAADAVAQVMAAGPGLSAHPALAAEVARWEAEH +LTAADYLEKG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000760.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000760.fa new file mode 100644 index 0000000000000000000000000000000000000000..08ca3c3476d29222e01d8404ce5f501debfc2ebe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000760.fa @@ -0,0 +1,25 @@ +>PROKKA_00873 +MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC +EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAAPVDLI +LADPPYPVAGPPLEAVVEAAAERLAPGGLLVLERAARDAAPRRPRGLEEVEVRVYGETAL +YLWQDER +>PROKKA_00595 +MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC +EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAAPVDLI +LADPPYPVAGAPLEAVLEAAAGRLAPGGLFVLERAARDAAPRRPRGLEEVEVRVYGETAL +YLWQDER +>PROKKA_02062 +MSRIIAGAAAGRPLTSVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLFAGSGALGC +EAASRGAASVLLVERERRAVAACRANAALVNRARGADVVQVRAGTVEQALAAGGEPADLI +LADPPYPLAGPALEAVLEAAAARLTPGGLIVLERAARDAPPRRPAGLEEVEVRAYGETAL +YLWQDER +>PROKKA_01956 +MSRIIAGAAAGRPLRSVPGTGTRPTTDRTKEALFSWLQARDWLDGTRVLDLYAGSGALGC +EAASRGAAHVTLVEKARRAAEVCRANAAALNAVLGAPVVQVAASSVEQALALPGDSADLI +LADPPYPESGPAFHAVLAAAAARLAAGGLLVLERSARDPAPERPAGLEQVEVRTYGETAL +YFWQDEG +>PROKKA_00832 +MSRIIAGAAAGRPLTAVPGTGTRPTTDRTKEALFSWLEARDWLDGTAVLDLYAGSGALGC +EAASRGAASVLLVERDRKAVTACRANAALVNRARGADVVRVRAGSVEQALAAEAASVDLI +LADPPYPVAGPPLEAVVEAAAGRLAPGGLLVLERAARDVAPRRPRGLEEVEVRVYGETAL +YLWQDER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000761.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000761.fa new file mode 100644 index 0000000000000000000000000000000000000000..de9803eb5ea69c99f6fb3fab5bf85321c833277e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000761.fa @@ -0,0 +1,41 @@ +>PROKKA_00874 +MDGTQPTPGAAPHDVDVDAPWRRTAAAAGLLGDAGPVPTVFETMTGLAVEHGAVNLGQGF +PDADGPDALLRLAADAVLAGPNQYAPGTGDPALRQAVAEHRRRHWGVTEDPATQVMITTG +ATEGIAATVLAFVRPGDEVVTVEPFYDSHAATIALAGARHVSVPVEAPDFLPDPARVAAA +MTDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVLILSDEVYDHLVYEGEHVSLRS +VAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVKQFLTYSSGPAFQRALGAY +LPTDGAERHLAGQRERYRDARDRLVAGLREAGLDPVVPAAGYFVVVDLAPWGVTDAAEAA +VRWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDEAMRRLAEAAPRLRAA +>PROKKA_00596 +MDGTQPTPGSARHDVDVDAPWRRTAAAAGLLGDTGPVPTVFETMTGLAVEHGAVNLGQGF +PDADGPDALLRLAADAVLAGPNQYAPGTGDPVLRQAVAEHRRRHWGVTEDPATQAMITTG +ATEGIASTVLAFVRPGDEVITVEPFYDSHAATIALAGGRHVSVPVEAPDFLPDPARVADA +ITDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVLMLSDEVYDHLVYEGEHVSLRS +VAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVKQFLTYSSGPAFQRALGAY +LPTDDAERHLAGQRERYRDARDRLVAGLREAGLDPVVPAAGYFVVVDLAPWGVTDAAEAA +VQWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDEAMRRLAEAAPRLRAP +>PROKKA_02061 +MNADASDRTRPPRTGPAPAPATGPAPADVAGTAFVAGPWRRTAAAAGLLDDGAPVPTVFE +TMTGLAVEHGAVNLGQGFPDADGPDALLRLAAEAVLAGPNQYAPGTGDPVLRQAVAEHRR +RHWGVTEDPATQVMITTGATEGIAATVLAFVRPGDEVITVEPFYDSHAATIALAGGRHVS +VPVEAPDFLPDPARVADAITDRTRLLIVNTPHNPTGAVYPRELLEELVTLCRSRGVLILS +DEVYDHLVYEGEHVSLRSVAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVK +QFLTYSSGPAFQRALGAYLPTEDAKRHLAGQRERYRDARDRLVAGLRAADLDPVVPAAGY +FVVVDLAPWGVTDAAEAAVRWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDE +AMRRLAAAAPALDGRRPRP +>PROKKA_01955 +MSHDSPSPTDAAAAPSDVRLAGPWRAASAAAGVLRDGAPVPTVFETMTALAVEHGAVNLG +QGFPDADGPPELLALAAEAVTTGPNQYAPGTGRADLRAAVAAHRARHWGVAEDPDTQVLA +TTGATEAIAATVLALVRPGDEVITVEPFYDSHAAVVALAGGRHVTVPVHAPDFLPDPARI +AAAITPRTRLLIVNTPHNPTGAVYPRALLEELVALCRARDVLMLSDEVYDHLVHEGRHVT +LRAIPGAERIALTASSAGKSLAVTGWKVGWLTGPADLVAAVRGVKQFLSYSSGPAFQQAV +AAFLPRADDFLAGQLARHRRSRDLLVSGLRDIGLDPVVPAAGYFTVVDLAPWGVRDAAAA +ARTWTERAGVAGIPVSALCRPDGDHLRSWLRLTFCKSEDTVAEAVARLTRHAADLRAG +>PROKKA_00833 +MDGTQPTPRSAPHDVDVDAPWRRTAAAAGLLGDAGPVPTVFETMTGLAVEHGAVNLGQGF +PDADGPDALLRLAADAVLAGPNQYAPGTGDPALRRAVAEHRRRHWGVTEDPATQVMITTG +ATEGIAATVLAFVRPGDEVVTVEPFYDSHAATIALAGGRHVSVPVEAPDFLPDPARVAAA +MTDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVLILADEVYDHLVYEGEHVGLRS +VAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVKQFLTYSSGPAFQRALGAY +LPTDDAERHLAGQRERYRDARDRLVAGLREAGLDPVVPAAGYFVVVDLAPWGVTDAAEAA +VQWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDEAMRRLAEAAPRLRAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000762.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000762.fa new file mode 100644 index 0000000000000000000000000000000000000000..1557f95b569863856791e71b23db729f6e761b94 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000762.fa @@ -0,0 +1,20 @@ +>PROKKA_00875 +MRRAVCPGSFDPLHKGHVEVIARAANLFEEVVVAVSANPAKTYRFSVDERIAMIEATVSS +LAGVAVRPMGPGLLAEFCRQIGADAIVKGLRGGADLEFEAPMAAMNRHLTGVETVYLPAD +ARYTHVSSSLIKEVHGLGGDVAEFVPAAVLRGLDGGA +>PROKKA_00597 +MRRAVCPGSFDPLHMGHVEVIARAANLFEEVVVAVSANPAKTYRFSVDERIAMIEATVSS +LAGVAVRPMGPGLLAEFCRQIGADAIVKGLRGGADLEFEAPMAAMNRHLTGVETVYLPAD +ARYTHVSSSLIKEVHGLGGDVAEFVPAAVLRGLDGGA +>PROKKA_02060 +MRRAVCPGSFDPLHKGHVEVIARAANLFDEVVVAVSVNPAKRYRFSTEERIAMIETTLSS +LAGVTVRPMGLGLLAEFCREIGADAIVKGLRNGTDLEFEAPMAAMNRHLTGVETVYLPAD +ARYTHLSSSLIKEVHGLGGDVAELVPAAVLRGLDGEP +>PROKKA_01954 +MRRAVCPGSFDPLHKGHLEVIARAASMFDEVVVAVSDNPAKRYRFSTDERLELIRASVQG +LAGVSAEAMGPGLLAEFCREIGAGVIVKGLRNGTDLEFEAPMAAMNRHLTGVETVFLTAD +ARYTHLSSSLIKEVHGLGGDVREFVPAVVHARLEATRP +>PROKKA_00834 +MRRAVCPGSFDPLHKGHVEVIARAANLFEEVVVAVSSNPAKTYRFSVDERIAMIEATVSS +LAGVAVRPMGPGLLAEFCRQIGADAIVKGLRGGADLEFEAPMAAMNRHLTGVETVYLPAD +ARYTHVSSSLIKEVHGLGGDVAEFVPAAVLRGLDGGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000764.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000764.fa new file mode 100644 index 0000000000000000000000000000000000000000..be5375e793edacdb3343779989cb44de505d5503 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000764.fa @@ -0,0 +1,25 @@ +>PROKKA_00877 +MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE +SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD +LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS +ETSITETEER +>PROKKA_00599 +MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE +SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD +LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS +ETSITETEER +>PROKKA_02058 +MDTTQRQDADSSWVIPVRDLTRGAGVQRELTAQWPAPAGVTTPLLGIPEGDPVELDLRLE +SVHEGVLVTGTADATLKGECSRCLLPLHEGITVDLQELYLTGASEDEAGEQPLVVRETVD +LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS +ETSITETEER +>PROKKA_01952 +MATTVPSGAPSPWVLSVRDLARGAGVQRELTTRLPAPAAVSMPMLGIPEGDPVDLELRLE +AVHEGVLVTGTAHADLTGECSRCLLPLHEGITVDLQELFLADPPAEGDDEQPLVEHETVD +LEPVFRDAVVTALPFQPLCRPDCEGLCADCGIRLEDAPAGHAHERVDPRWAALAALADTT +EETSITETEKR +>PROKKA_00836 +MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWRAPAGVSTPLLGIPEGDPVELDLRLE +SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD +LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS +ETSITETEER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000765.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000765.fa new file mode 100644 index 0000000000000000000000000000000000000000..7f4413fdd64ac3487495af843f71b8c1b1b88e10 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000765.fa @@ -0,0 +1,15 @@ +>PROKKA_00878 +MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK +GRKVADA +>PROKKA_00600 +MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK +GRKVADA +>PROKKA_02057 +MAVPKRKMSRANTRARRSQWKATAPTLVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK +GRKVADA +>PROKKA_01951 +MAVPKRKMSRANTRARRSQWKAEAPSLVKTVENGRVSYRLPHQAELKTDAAGTPLFYEYK +GRKVADA +>PROKKA_00837 +MAVPKRKMSRANTRARRSQWKATAPALVKSVENGRVSYRLPHQAELKTDAAGTPLFFEYK +GRKVADA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000767.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000767.fa new file mode 100644 index 0000000000000000000000000000000000000000..c14caa74ce0f0e8bc96da891055ae7e2e355139b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000767.fa @@ -0,0 +1,34 @@ +>PROKKA_00880 +MPELPEAEVVRRGLARWATDAVAAELEVLDPRSLRRSPGGADALRERLRGARLAEPARRG +KFLWLPLAEGDDAVVVHLGMSGQILVDEPGAADQRHLRLRLPVTAVDGSARELRFVDQRI +FGGWWLDALRPDDAAGGERIPTTAAHIALDPLHPLFDPAAVHARLARRRSTLKRALLDQS +LVSGIGNIYADEALWGARLHPERPTERMRRADTLRLLAAVQDVMRRALEVGGTSFDALYV +NVDGRSGYFARSLAAYGRTGQPCRRCAAEGVDSRIVREPFMNRASHLCPRCQPRPRRRRA +AAADA +>PROKKA_00602 +MPELPEAEVVRRGLARWATDAVAAELEVLDPRSLRRSPGGADALRERLRGAQLAEPARRG +KFLWLPLAEGDDAVVVHLGMSGQILVDEPGAADQRHLRLRLPVTAADGSARELRFVDQRI +FGGWWLDALRPDDAAGGERIPTTAAHIALDPLHPLFDPAAVHARLARRRSTLKRALLDQS +LVSGIGNIYADEALWGARLHPERPTERMRRADTLRLMAAVQDVMRRALEVGGTSFDALYV +NVDGRSGYFARSLAAYGRTGQPCRRCAAEGIDSRIVREPFMNRASHLCPRCQPRPRRRRA +VAADA +>PROKKA_02055 +MPELPEAEVVRRGLARWATDAVAGALQVHDPRSLRRSPGGAEALRARLEGARLAEPARRG +KFLWLPLADADEAVVVHLGMSGQILVDEPGAPDQRHLRLRLPVTAADGAARELRFVDQRI +FGGWWLDALHPDFAAGGEPIPATAAHIALDPLHPLFDADAVHARLARRRSTLKRALLDQS +LVSGIGNIYADEALWGARLHPERPTERMRRADTRRLMAAVQDVMRRALAVGGTSFDALYV +NVDGRSGYFARSLDAYGRTGQPCRRCAAEGVESRIVREPFMNRASHRCPRCQPTPRRRRT +ATPADGPARP +>PROKKA_01949 +MPELPEAEVVRRGMARWASGARAADLDVLDARSVRRSPGGAEALRERLSGAVLAEPARRG +KFLWLPLEDADDAVVVHLGMSGQVRVDEPGAPDQRHLRLRLPITAADGSDRELRFVDQRL +FGGWWLDPVVVGPETGDAVPASAAHIALDPLHPDFDPDAVHRRLVRRRSTLKRSLLDQTL +VSGIGNIYADEALWAARLHPERPTQRMARAQTRAVLAAVQDVMRRALAVGGTSFDALYVN +VDGRSGYFARSLEAYGRTGQPCRRCTAEGRRTLIVREPFMGRASHRCPVCQPVPRRSPSR +>PROKKA_00839 +MPELPEAEVVRRGLARWATDAVAAELEVLDPRSLRRSPGGADALRERLRGARLAEPARRG +KFLWLPLAEGDDAVVVHLGMSGQILVDGPGAADQRHLRLRLPVTAADGSARELRFVDQRI +FGGWWLDALRPDDAAGGERIPTTAAHIALDPLHPLFDPVAVHARLARRRSTLKRALLDQS +LVSGIGNIYADEALWGARLHPERPTERMRRADTLRLLAAVQDVMRRALEVGGTSFDALYV +NVDGRSGYFARSLAAYGRTGQPCRRCAAEGVDSRIVREPFMNRASHLCPRCQPRPRRRRA +AVADA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000769.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000769.fa new file mode 100644 index 0000000000000000000000000000000000000000..9b5754ba6b04a97b7d09d300466bc9963e7d0d46 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000769.fa @@ -0,0 +1,40 @@ +>PROKKA_00882 +MTTESRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER +VLPTPRLPLGEAGRNGRFAEAVVHALLAVPRGMATRRPDVVVATVPALPVVVPGVVLSRL +WRRPLVLEMRDAWPDLAHEAGVHQGLLGAAMERVVTGGQRAARLVVTVTDGFAETLRGRG +VRVVRTLGNGVDLARLAVAPRRERAAGELHVLYLGNMGESQGLERLIDAAATLRRTRPGV +RVRLVGEGTRRPALEARNAELGSPAEILGPVHGAAVAEQYAWADTLVVALRPDWPSFRHT +VPSKTYEVLAVGRHVTGLVTGEAARTLEAAGGADVIGPDVDDLVRHLTALADDPHRTDVG +AGGRDWVRRHADLPAVARRYERVLRRVAGR +>PROKKA_00604 +MTTEPRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER +VLPTPRLPLGEAGRNGRFAEAVVHALLAIPRGMATRRPDVVVATVPALPVVVPGVVLSRL +WRRPLVLEMRDAWPDLAHEAGVHQGLLGVAMERVVTGGQRAARLVVTVTDGFAETLRGRG +VRVVRTLGNGVDLARLAVAPRRERDAGELHVLYLGNMGESQGLERLIDAAATLRRTRPGV +RVRLVGEGTRRPALEARNAELGSPAEILGPVHGAAVAQQYAWADTLVVALRPDWPSFRHT +VPSKTYEVLAVGRHVTGLVTGEAARTLEAAGGAEVIGPDVDDLVRHLTALADDPHRTDVG +AGGRDWVRRHADLPAVARRYERLLRRVAGR +>PROKKA_02053 +MPTEPRRPRVLLITHSYRPERTPPARRWAAVVAALRAGGWDVDVVAPGGLRAVAGDDGER +ILRTPRLPAGRSGRNGRFLEAAVHAVLAVPRGLAARRPDVVVATVPALPVVVPGVVLSRL +WRRPLVLEMRDAWPDLAHEAGVHQGLLGVAMERVVTGGQRAARLVVTVTDGFAETLRGRG +VERVETLCNGVELAGLARAPARRREPGDLHVLYLGNMGESQGLERLVEAAAELRQSRPGV +RVRLVGAGTRRGELEARNAELGSPAEILPACYGEEAAAQYAWADTLVVALRPDWPSFRHT +VPSKTYEVLAVGRHVTGMVTGEAARTLEDAGGADVIGSRVADLVAHLTALADDPARTDVG +EGGRPWVRLHADLPSVARRYVRLLGQLVPDYRRHA +>PROKKA_01947 +MGERRTRAGGRAPRLLLVTHSYRPERTPPARRWAAVVQALRAAGWEVDVLVPGGLRTRVG +EHGERLRPTPRLLGSGDGRNGRFAAAAVHAVLAVPRGLVLPRPDVVVATLPALPVVVAGR +ALAVLRRRPLVVEMRDAWPDLAREAGVHPGLLGTLMERVVTGGQRAADLVVTVTEGFAAT +LRGRGMRRVEVLANGVDLERVPVAPPRDRTAGELHVLYLGNLGESQGLERLVEAAARQRA +THPGVHVRIVGDGTRRAALEALNAELEAGVEFVPPVSGAALTEQYAWADTLVVCLRPDWP +SFRHTIPSKTYEALAVGRHVTGQLSGEAALMLERSGAADVVGPGVEDLVAHLDALADDPA +RTRVGDAGRRWAAAHGDLPTTARRYEALLRRVAARPSRRTRTETTA +>PROKKA_00841 +MTTEPRRPRLLLVSHSYRPERTPPARRWGAVVAALRSAGWDVDVVAPGGVRPFAGPDGER +VLPTPRLPLGEAGRNGRFAEAVVHALLAIPRGMATRRPDVVVATVPALPVVVPGVVLSRL +WRRPLVLEMRDAWPDLAHEAGVHQGLLGAAMERVVTGGQRAARLVVTVTDGFAETLRGRG +VERAETLCNGVELAGLAWAPARRREPGDLHVLYLGNMGESQGLERLMEAAAELRQSRPGV +RVRLVGAGTRRGELEARNAELGSPAEILPACYGEDAAAQYAWADTLVVALRPDWPSFRHT +VPSKTYEVLAVGRHVTGMVTGEAARTLEDAGGADVIGPRVADLVAHLTALADDPARTDVG +EGGRPWVRRHADLPSVARRYVRLLGQLVPDYRRHA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000771.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000771.fa new file mode 100644 index 0000000000000000000000000000000000000000..c4f48864e78407962cbbb9202619a46e076c0e67 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000771.fa @@ -0,0 +1,29 @@ +>PROKKA_00895 +MSADPLTPSVVVDEASMTYRVLSAEAVQPRRGLRGRVRAARGVRTTEVQALQPLSFVVGR +GESVGVIGTNGSGKSTLMKLITGQMRPTTGHIYATSTPVMLGVNAALVRQVSGEDNIRLG +CLAMGMSRAEAEAKRDAVVALSGLDDHALQLPLKAYSSGMAARLQFAIATSVDPDILVID +EALNTGDAQFRERTRQRLDELREQAGCVFLVSHSLSTIQEMCQRVIWIERGVLTMDGSPR +AVTRGYNLYARAMAQGRTEEAQEILERKQSELVRERIAWSGGERPTGITAL +>PROKKA_00617 +MSAEPLTPSVVVDEASMTYRVLSAEAVQPRRGLRGRVRAARGVRTTEVQALQPLSFVVGR +GESVGVIGTNGSGKSTLMKLITGQMRPTTGHIYATSTPVMLGVNAALVRQVSGEDNIRLG +CLAMGMSRAEAEAKRDAVVALSGLDDHALQLPLKAYSSGMAARLQFAIATSVDPDILVID +EALNTGDAQFRERTRQRLDELREQAGCVFLVSHSLSTIQEMCQRVIWIERGVLTMDGSPR +AVTRGYNLYARAMAQGRTEEAQEMLERKRSELVRERIAWTGGERPTGITAL +>PROKKA_02042 +MSGSRPLDPAVVLDEAGMTYTVRSSDTGARRAGIGGMLRGVRGVRTDQVQALAPLSLIVD +RGESVGIIGTNGSGKSTLMKLITGEIHPTTGRVYATSTPVMLGVNAALVRQISGEDNIRL +GCLAMGMTTAEAAEKRDDVVRLAGLDDQALQLPLKAYSSGMASRLQFAIATSVDPDILLI +DEALNTGDAQFRARTRARIDELRARAGCVFLVSHSLTTLKQMCSRVIWIEQGILTMDGNP +EVVTGNYARYTRHRSNGADEVAERLLAEARAGVKRVAVRWAGGQRPSGVIAD +>PROKKA_01940 +MTDTTVDYALVLDRVSMTYRVPSSAADSVAALPAWRRGLARALRQPPRVPVHALHEMTLG +LEQGRTLGLVGRNGSGKSTLSQIIAGKLAPSTGRVLATATPMMLGVNAALVPAMSGRQNI +VLGCLALGMAKDEVMAKTPEIAASTGLGEAIDLPIETYSSGMSARLRFAIATSRDPEVLV +IDEALNVGDSQFRARAKERMQELKRKAGAVVLVSHDNKTILDSSNKVLWLDKGRPVMEGS +PQRVMDRYEQYNEMLAAQKVDEARAFVEDLRTTYRPRVVLPATDMHLPSVQEVEFSPRHA +L +>PROKKA_00846 +MPNLTGLDNIRIGLLAMGLTPAEVHDRIPQVAELADIGKSIRMPMRTYSSGMRARLRFAI +SVASQPDIIMIDEALATGDDAFRERSNQAMRDLIARSGTGFLVNHSAGVIREMCTRVVWM +DEGAIIEDGDTLDVMQHYSYFMSALRKHGEEKALEARARYETTEAERIVALKGTTGH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000775.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000775.fa new file mode 100644 index 0000000000000000000000000000000000000000..e63b2dfa85b940699bd1274cc55b9db9d052faeb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000775.fa @@ -0,0 +1,40 @@ +>PROKKA_00902 +MCETGHVEIVLIISVVLALLVGGLIVGLLDRRPAPPKGSYQGVRDADDPRPGPRHAAPGG +STAVLERPDAEEATVDVAEPEVVEEVETAPAAPELERPEAAGSRLSRLRARLLKSNNVFG +KGLLALLSQDRIDEDVWDEIEETLLMADLGTEPTMELVDRLKARVTVEGTRDPEQVRALL +REELVAMVDPSMDRRLAATRRDGRPAVTLVVGVNGVGKTTTVGKLARVLVAEDRDVVLGA +ADTFRAAAAEQLATWGARVGVPTVRSEKEGADPASVAFEAVAEGIRAEADVVLVDTAGRL +QNKSNLMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLD +GTAKGGIVVAIQRQLGVPVKLIGLGEGADDLAPFTAEGFVDALLAD +>PROKKA_00621 +MLIVSVVAALLLGGVLVGLLDRRPAPPKGSYQGVRDADDPRPSPRHAAPSGSTAVLERPE +VDEAPAVVAEPEPAVVEEVEPAPAKPEYERPEAAGSRLARLRARLLKSNNVFGKGLLALL +SQDRIDDDVWDEIEETLLMADLGTEPTLELVDRLKARVTVEGTRDPEQVRTLLREELVAM +VDPSMDRRLAATRKGDRPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFRAA +AAEQLATWGARVGVETVRSEKEGADPASVAFEAVELGIAEGVDVVLVDTAGRLQNKANLM +DELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKGGI +VIAIQRQLGVPVKLIGLGEGPDDLAPFTAEGFVDALLTD +>PROKKA_02040 +MCQTGHVEIVLIISVVLALLVGGLIVGLLDRRPAPPKGSYQGVRDADDPRPAPRHAAPGG +STAVLERPEAEEAPVDLVEPEVVEEVEAEPAAPELERPEAAGSRLARLRARLLKSNNVFG +KGLLALLSRDRIDEDTWDEIEETLLMADLGTEPTMVLVDRLKSRVTVEGTREPEQVRELL +REELVAMVDPSMDRRLAASRRDGRPAVTLVVGVNGVGKTTTVGKLARVLVAEDRDVVLGA +ADTFRAAAAEQLATWGARVGVPTVRSEKEGADPASVAYEAVAEGIRLEADVVLVDTAGRL +QNKSNLMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLD +GTAKGGIVVAIQRQLGVPVKLIGLGEGADDLAPFTAEGFVDALLAD +>PROKKA_01938 +MITVIVISVVLALLLGVVLVGLLDRPVAPPKGTYTELRDSDDPAPAGLVADPSSAPAPEE +ALEETGRAGSHAAAPVAEPVEAAEAPERQLERPEAAGTRLQRLRARLLKSNNVFGKGLLA +LLSRDHIDEDVWDEIEETLLMADLGTEPTMELVDRLKARVTVDGTRDPESVRALLREELV +AMVDPSMDRRLAATPHDGHPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFR +AAAAEQLATWGARVGVETVRSDVEGADPASVAFEAVKTGIEREADVVLVDTAGRLQNKAN +LMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKG +GIVVAIQRQLGVPVKLIGLGEGADDLAPFSAEGFVDALLAA +>PROKKA_00850 +MLIVSVVAALLLGGVLVGLLDRRPAPPKGSYQGVRDADDPRPSPRHAAPSGSTAVLKRPE +VDEAPAVVAEPEPAVVEEVEPAPAKPEYERPEAAGSRLARLRARLLKSNNVFGKGLLALL +SQDRIDDDVWDEIEETLLMADLGTEPTLELVDRLKARVTVEGTRDPEQVRTLLREELVAM +VDPSMDRRLAATRKGDRPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFRAA +AAEQLATWGARVGVETVRSEKEGADPASVAFEAVEHGIAEGVDVVLVDTAGRLQNKANLM +DELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKGGI +VIAIQRQLGVPVKLIGLGEGPDDLAPFTAEGFVDALLAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000777.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000777.fa new file mode 100644 index 0000000000000000000000000000000000000000..f7185e56555aa6e3bf4212fb1b8f72f1e7d905fa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000777.fa @@ -0,0 +1,50 @@ +>PROKKA_00904 +MFNSLSDRLTATFRSLKGKGRLSEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL +SAEVAQALNPGQQVVKIVNEELVGILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL +AHLLKSQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVYAPHPGVSSEFEAATGDPVQVA +RDGVAEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVDPDEVLFVIDAMIGQDAVAT +AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS +RILDMGDVLSLIEQAEQNWDRTEAEKMARKFADQEDFTLDDFLAQMQQLKKMGSLKKMLM +MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIARGSGVSVSEV +NGLLERFAEAQKMMKRMAAGGGIPGMPGTPGGASRKGKGKGKNAKRDRVKSGNPAKAAAE +RKAIEERRARAAQAQAGAVFGRDGAGMDGFDPSTLNLPAGFEKYLKDR +>PROKKA_00623 +MFNSLSDRLTATFRSLKGKGRLSEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL +GAEVAQALNPGQQVVKIVNEELVGILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL +AHLLKSQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVYAPHPGVSSEFEAATGDPVQVA +RDGVAEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVDPDEVLFVIDAMIGQDAVAT +AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS +RILDMGDVLSLIEQAEQNWDRTEAEKMARKFADQEDFTLDDFLAQMQQLKKMGSLKKMLM +MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIARGSGVSVSEV +NGLLERFAEAQKMMKRMAAGGGIPGVPGMPGGASRKAKGKGKNAKRDRVKSGNPAKAAAE +RKAIEERRARAAQAQAGAVFGRDGAGMDGFDPSTLNLPAGFEKYLKDR +>PROKKA_02038 +MFNSLSDRLTATFRSLKGKGRLTEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL +GEEVAQALNPGQQVVKIVNEELVGILGGETRRIRHAKTGTTVIMLVGLQGAGKTTLAGKL +AHLLKAQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVFAPHPGVSSEFEAATGDPVQVA +RDGVAEANAKYHDVVIIDTAGRLGVDAELMQQAADVRAAVEPDEVLFVIDAMIGQDAVAT +AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS +RILDMGDVLSLIEQAEQNWDRSEAEKMAKKFADQEDFTLDDFLNQMQQLKKMGSLKKMLM +MMPGAQGMRQQLEQFDESSIGRVEAVIHSMTPHERVAPKIINGSRRARIAKGSGVSVSEV +NGLLERFAEAQKMMKRMAAGGGMPGMPGAPGGVSRKAKGKNAKRNKVKSGNPAKAAAERK +ALEERQARAAQAQAGAVFGRDGGAGMDGFDPSSLNLPAGFEKYLKDR +>PROKKA_01936 +MFTSLSDRLTATFRNLKGKGRLTEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL +GEEVSQALNPGQQVVKIVNEELVAILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL +AHLLKSQGHTPLLVACDLQRPNAVKQLQVNGERAGVPVFAPHPGVSSEFEAATGDPVQVA +RAGIDEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVQPDEVLFVIDAMIGQDAVAT +AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS +RILDMGDVLSLIEQAEQNWDRAEAEKMAKKFADQEDFTFDDFLTQMQQLKKMGSMKKLLG +MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIAKGSGVQVTEV +NALLERFAEAQKMMKKLAGGGVPGMPGMGPGPGRKSKGRNAKKTKVKSGNPAKAAAERRA +LEERRSRPAAGGVFGQGGTMPDMTDFDPSQLNLPAGFEKYLKDR +>PROKKA_00852 +MFNSLSDRLTATFRSLKGKGRLSEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL +GAEVAQALNPGQQVVKIVNEELVGILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL +AHLLKSQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVYAPHPGVSSEFEAATGDPVQVA +RDGVAEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVDPDEVLFVIDAMIGQDAVAT +AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS +RILDMGDVLSLIEQAEQNWDRSEAEKMARKFADQEDFTLDDFLAQMQQLKKMGSLKKMLM +MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIARGSGVSVSEV +NGLLERFAEAQKMMKRMAAGGGIPGMPGMPGGASRKAKGKGKNAKRDRVKSGNPAKAAAE +RKAIEERRARAAQAQAGAVFGRDGAGMDGFDPSTLNLPAGFEKYLKDR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000779.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000779.fa new file mode 100644 index 0000000000000000000000000000000000000000..b5f7d35114f79e04a873bc8d1f1b15323f9b6919 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000779.fa @@ -0,0 +1,15 @@ +>PROKKA_00906 +MLTEALEHLVRGIVDTPEAVRVDARSQRRGDMLEVRVAPEDLGRVIGRQGRTATALRTVL +DGLAGHPVRVDVVETDRRS +>PROKKA_00625 +MLTEALEHLVRGIVDTPEAVRVDARSQRRGDMLEVRVAPEDLGRVIGRQGRTATALRTVL +DGLAGHPVRVDVVETDRRS +>PROKKA_02036 +MLTEALEHLVRGIVDTPEAVRVDARSQRRGDMLEVRVAPEDLGRVIGRQGRTATALRTVL +DGLAGHPVRVDVVETDRRR +>PROKKA_01934 +MLAEALEHLVRGIVDTPDAVRVASRPQRRGEMLEVRVAPEDLGRVIGRQGRTATALRTVL +DGLAGHPVRVDVVETDRAR +>PROKKA_00854 +MLTEALEHLVRGIVDTPEAVRVDARSQRRGDMLEVRVAPEDLGRVIGRQGRTATALRTVL +DGLAGHPVRVDVVETDRRS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000781.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000781.fa new file mode 100644 index 0000000000000000000000000000000000000000..62662fc1b52c4050b3c36afd3be44eb7c6bf82bd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000781.fa @@ -0,0 +1,29 @@ +>PROKKA_00908 +MRFDVVTIFPEYLAVLDVSLLGRARREGLVDVHVHDLRDFTFDRHRTVDDTPYGGGAGMV +MKPEPWALALEHVAAQGPVSPAPAESSSAEPGDRPVLLVPTPSGERFTQRFARELAGREH +VAIACGRYEGIDERVFGWAEELFEVRLVSLGDYVLNGGEVAALAMIEAVGRLVPGVVGNP +ASLVEESHEDGLLEYPVYTKPADWRGRAVPPVLLSGDHGKVAAWRRAQQEERTRERRPDL +WAAYDSED +>PROKKA_00627 +MRFDVVTIFPEYLAVLDVSLLGRARREGLVDVHVHDLRDFTVDRHRTVDDTPYGGGAGMV +MKPEPWALALEHVAAQGPVSPAPAESSSAEPGDRPVLLVPTPSGERFTQRFARELAGREH +VAIACGRYEGIDERVFGWAEELFEVRLVSLGDYVLNGGEVAALAMIEAVGRLVPGVVGNP +ASLVEESHEDGLLEYPVYTKPADWRGRAVPPVLLSGDHGKVAAWRRAQQEERTRERRPDL +WAAYDSED +>PROKKA_02034 +MRFDVVTIFPEYLAVLDVSLLGRARREGLVDVHVHDLRDFTFDRHRTVDDTPYGGGAGMV +MKPEPWALALEHVAAQAPADAGERPVLLVPTPSGERFSQGLARELAQREHVAIACGRYEG +IDERVFGWAEELFEVRLVSLGDYVLNGGEVAALAMIEAVGRLVPGVVGNPASLVEESHED +GLLEYPVYTKPADWRGREVPPVLLSGDHGKVAAWRRAQQEERTRARRPDLWEALGRDG +>PROKKA_01932 +MRIDVVSIFPEYMAVLDVSLLGKARREGLVDVHVHDLRDVTTDRHRTVDDTPYGGGAGMV +MKPEPWALSLEAVAAASPMAAPAKPILMVPTPSGTPFTQATARELAQAEHLAFACGRYEG +IDERVFGWAEDLFDVRLFSLGDYVLNGGEVAALAVIEAVGRLVPGVVGNPESLVEESHED +GLLEYPVYTKPSMWRDREVPPVLLSGDHGRIAAWRRDQQEERTRIRRPDLWAAHHAGSAA +ED +>PROKKA_00856 +MRFDVVTIFPEYLAVLDVSLLGRARREGLVDVHVHDLRDFTFDRHRTVDDTPYGGGAGMV +MKPEPWALALEHVAAQGPVSPAPAESSSAEPGDRPVLLVPTPSGERFTQRFARELAGREH +VAIACGRYEGIDERVFGWAEELFEVRLVSLGDYVLNGGEVAALAMIEAVGRLVPGVVGNP +ASLVEESHEDGLLEYPVYTKPADWRGRAVPPVLLSGDHGKVAAWRRAQQEERTRERRPDL +WAAYDSED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000784.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000784.fa new file mode 100644 index 0000000000000000000000000000000000000000..30ff176e3791c1d2b9d6f44a47383e3a12030991 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000784.fa @@ -0,0 +1,26 @@ +>PROKKA_00911 +MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR +GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ +EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG +TDPDAFATVPDAPAPEART +>PROKKA_00630 +MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR +GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ +EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG +TDPDAFATVPDAPAPEART +>PROKKA_02031 +MSRPDHRLVPPAAGHAHDSGAAPADDAARPAGPTGALLGHAVPSGAGSQALPAEPGRGPL +RAVLAVVVLTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPEPYPVRRGDVV +VFDDTKGWLADGGHVIKRVVGLPGDTVSFTPGEAALRVNGVPVAEPYLAPGDAPAQDAFE +ATVPAGRLWVLGDHRSASADSRAHRDGPGGGFVSLDDVVGRARFVVWPLDRIGGAGAAPE +AFEAVPDARGAGS +>PROKKA_01929 +MAEAPVTPAAAGTADPAAAPAAEHPGHPLRAAAVTVAVTLALLLAVQLLLVRMFAIPSAS +MEPTLRPGDRVAVDLLVPGPLELRRGDVVVFRDARGWLAGAEAVHADPLHAAVAALGLGT +QEGHLVKRVVGLPGDRVRWSPEDARLEVNGVPVDEPYVAGPAAQEAFDVVVPDGGLWVLG +DHRSASQDSRQHQHGPGGGMVSVDDVVGRVEGVVWPLDRAGAVGPGPLAKLP +>PROKKA_00859 +MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR +GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ +EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG +TDPDAFATVPDAPAPEART diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000785.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000785.fa new file mode 100644 index 0000000000000000000000000000000000000000..bfcdc357ce7d98030e3672074d1ebc7b4702fd9f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000785.fa @@ -0,0 +1,30 @@ +>PROKKA_00912 +MTARRGGGRPTVRAGLDVEAGLAAPALAARGADRVLVAGMDEVGRGALAGPVVVGVCAAW +LPAAGQIPPVRDSKALTDRRRRALVPQIEDWAAGVALGEAGPAEIDALGISAALGLAGRR +AWAALCAAVGQEPVALVLDGRDDWLSRSDPDAGPAPAPRPLPPEPTMLVRAEDRCATVAA +ASIAAKVARDDVMIALDAAHPGYGWAGNKGYGSAAHRAALAERGASEQHRRSWNLGLPGA +PAQAPPTLFD +>PROKKA_00631 +MTARRGGGRPTVRAGLDVEAGLAAPALAARGADRVLVAGMDEVGRGALAGPVVVGVCAAW +LPAAGQIPPVRDSKALTDRRRRALVPQIEDWAAGVALGEAGPAEIDALGISAALGLAGRR +AWAALCAAVGQEPVALVLDGRDDWLSRSDPDAGPAPAPRPLPPEPTMLVRAEDRCATVAA +ASIAAKVARDDVMIALDAAHPGYGWAGNKGYGSAAHRAALAERGASEQHRRSWNLGLPGA +PAQAPPTLFD +>PROKKA_02030 +MTGSERAPRAGARTAVRAGLDVEAGLAAPFLAAGGTDRVLVAGMDEVGRGALAGPVVVGV +CAAWLPAEGEIPAVRDSKALTDRRRRALVPEIRAWAAAVALGEANPAEIDALGISAALGL +AGRRAWAAVCAAAGQEPVALVLDGRDDWLTRSDPDAGPAPAPRPVPPVPTMLVKAEDRCA +TVAAASIAAKVARDDTMIALHADHPAYGWAGNKGYGAAAHRAAILDHGAGEHHRRSWSLG +LPAAPADEPPTLFD +>PROKKA_01928 +MSPRPPVVRAGLDVEASLAEAAIGPGASALVAGMDEVGRGALAGPVTVGVCAARVPALGV +VPAVRDSKALTDRRRRALASEIEAWAAGVVLGEASPAEIDRLGITRALALAGCRAWAGLL +AALGEEPVALILDGSDDWLRHARGGGMDDVVTGPVPPAPHMMVKAEDRCATVAAASIAAK +VGRDDAMIALSAAHPAYGWAGNKGYGAAAHRSALVELGVTEHHRRSWNLGVPGTGAEPDV +LF +>PROKKA_00860 +MTARRGGGRPTVRAGLDVEAGLAAPALAARGADRVLVAGMDEVGRGALAGPVVVGVCAAW +LPAAGQIPPVRDSKALTDRRRRALVPQIEDWAAGVALGEAGPAEIDALGISAALGLAGRR +AWAALCAAVGQEPVALVLDGRDDWLSRSDPDAGPAPAPRPLPPEPTMLVRAEDRCATVAA +ASIAAKVARDDVMIALDAAHPGYGWAGNKGYGSAAHRAALAERGASEQHRRSWNLGLPGA +PAQAPPTLFD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000786.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000786.fa new file mode 100644 index 0000000000000000000000000000000000000000..8577e8163e0a635b3435b8f2c796c48fe16407ca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000786.fa @@ -0,0 +1,15 @@ +>PROKKA_00913 +MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL +LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS +>PROKKA_00632 +MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL +LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS +>PROKKA_02029 +MSTDDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQSDGDVFFEIL +LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPRDELQVPPDGQLPD +>PROKKA_01927 +MSTDDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANAVTLTPHQTDGEVFFELT +LEDAWVWDVYRTARFIRRVRVLTFKDVNIEELPRDELQVPEDGGLRGDLGR +>PROKKA_00861 +MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL +LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000788.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000788.fa new file mode 100644 index 0000000000000000000000000000000000000000..ba97a7e56f95f806fc84509a4bdb7752db2abb63 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000788.fa @@ -0,0 +1,50 @@ +>PROKKA_00915 +MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP +LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE +TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA +RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG +ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG +GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ +LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP +ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR +PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA +>PROKKA_00634 +MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP +LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE +TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA +RRQVTAPEPEPARAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG +ILPPLDRRTALECAALRSLRGGDARVRRRGGTAQGFDGDIDRTPPFEAPHHSASRSALVG +GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ +LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP +ASETTSQVAARVAAAADRQARRWATAAERGLAPSGLRRNAHVPAGVLRHGPYAVPRAARR +PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA +>PROKKA_02027 +MSGIGRTRSISLSGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP +LTRRHLTVNLLPAGVHKRGAGHDLAIVLAAYAADGRVRGVEGPVFLAELGLDGALHRSPE +TVAMVMASVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVILAFGGEPEGEAPQRRP +VRPADDDGAPGLGPGAPDLSEVAGQAEARFALEVAAAGAHHLLLRGAPGAGKTMLAERLP +GILPPLDRRTALECAALRSLRGADALARRGVGQGSAGTRAAGDLDRTPPFEAPHHSASMA +ALVGGGANLARPGAVSLAHGGVLFLDEAPEFERRALESLRQPLESGEVLLHRARGTVAYP +ARFQLVLAANPCPCGKGGGNGVECRCSVTERRRYGQRLSGPLLDRVDLQVTVRPVQARQL +AGAPAAETSAQVAARVAEAARRQAERWARAAEEGLVAPGLRRNAHAPAGVLRHGPYAVPR +AARRAADEAVDHGLLSARGHARVLRLAWTLADLRGAETPAPEDTDVALTLRHQEEDET +>PROKKA_01925 +MSGIGRTRSISLTGLRGTVVDVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP +LTRRHLTVNLLPAGVHKRGAAHDLAIVLAAYAADGRVQGVDGPVFLAELGLDGTLHRAPE +TVAMVMAAVDAGHDRVVVAADAVAEAELVPGARVRGFAHLHEAILAFGGRPDASVARPSG +PSGTAGRGPAAGQEGPSGPVPDLAEVAGQAEARFALEVAAAGGHHLLLSGPPGAGKTMLA +ERLPGILPPLDDRTALETAALRSLRGLEPSARGLRRTPPFEAPHHSASMAALVGGGTGLG +RPGAVSLAHGGVLFLDEAPEFERRALDALRQPLESGEMIVHRAHGSVAYPARFQLVLAAN +PCPCGFGSGTGAHCRCTSLQRRKYAARLSGPLLDRVDVQVSVRPVRADQLAAAPEAEPSR +AVAARVAAAVAAQDARWAAAAREGSLPPGVCRNAHVPAALLRSGRFAVPPEARATADRAV +DRGELSARGHGRVLRLAWTLADLRGASCPEAQDVEIALQLRIRSEEDR +>PROKKA_00863 +MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP +LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE +TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA +RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG +ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG +GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ +LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP +ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR +PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000791.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000791.fa new file mode 100644 index 0000000000000000000000000000000000000000..d6af2ce698810071e1c3775dfb82b1fdc54c49b1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000791.fa @@ -0,0 +1,20 @@ +>PROKKA_00918 +MTSTHTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG +TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY +AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV +>PROKKA_00637 +MTSTHTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG +TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY +AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV +>PROKKA_02023 +MTSTTTRGVVHILSAPTALCPHVEWALSSVLGPETPVEWQGQPVAPGQHRTELRWTAPAG +TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNTMVSEDRIRY +AYEAGAGEPAVLLHELSLALGEAWDEELEPFRLAAADANVRWLHRVG +>PROKKA_01922 +MPDITTNGVVHLLSAPTAVCPHVEWTLTSVLGPGDPVDWRDQPAEAGTVCAELHWSAAQG +SGARLASALRRWPGLRFEITETPSAGVDGSRWSHTPELGVFHATTDVSGNIMVSEERIRY +AYEAGGGDPTVLVHELSLALGEAWDDELEPFRRAAAGAPVRWLHRAG +>PROKKA_00866 +MTSTQTRGVVHILSAPTALCPHVEWALSSVLGPATSVEWEGQPVAPGQHRAEVHWTAPAG +TGARLASALRGWPHLRFEITEEPSAGVDGSRWSHTPDLGIFHATTDVSGNIMVSEDRIRY +AYEAGAGDPSVLMHELSLALGEAWDDELEPFRLAAAHANVRWLHRAV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000792.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000792.fa new file mode 100644 index 0000000000000000000000000000000000000000..d0b6260b50a4e2a249912f212b74a9523853e966 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000792.fa @@ -0,0 +1,40 @@ +>PROKKA_00919 +MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS +EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD +TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLVRS +GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV +IESEEHAKARGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADITPEDVCH +VNAHATSTPKGDAPEYLAMRAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH +GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV +>PROKKA_00638 +MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS +EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD +TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLIRS +GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV +IESEEHAKARGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADIAPEDVCH +VNAHATSTPKGDAPEYLAMRAVFGEHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH +GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV +>PROKKA_02022 +MTRTAVITGLGATTPIGGDVPTFWSNALKGVSGARTMEHEWVEELGLPVTFAAELAVPTA +DVLSKVEQKRQDPGTQMATVAAREAWRDAGLEGVELDGDRLAVAFGTGIGGVWTLLDGWD +ILRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLIRS +GQADVVICGASEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV +VESEEHARARGARVYAELAGTGVTSDSHHITAPEPEGLGATRAMRAALKAADLTPEDVCH +VNAHATSTPKGDAPEYLAMKAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH +GQAPVTINLENQDPEIPLNVVTGSPAQLPEGPRVAVKNSFGFGGHNAVAVFRSV +>PROKKA_01921 +MTRTALITGLGATTPIGGDVPTFWANAQKGVSGAATMQHEWVEQYDLPVTFAAELAVPTS +EVLSKVELKRQDPSTQMATVAAREAWADAGLADADVDPERLAVAMGTGIGGVWTILDAWD +ALRERGPRRVMPMTVPMLMPNGAAGALSLEFGARAGARTVVAACAAGTEALDTALTLIRT +GQADVVLCGATEAAVHPMPMAAFAAMQALSKRNDDPQSASRPYDVDRDGFVLGEGAGVMV +VESEEHAAARGARVYARLAGTGVTSDSHHITAPEPEGLGATRAMRRALADAGLRPEDVGH +VNAHATSTPKGDAPEYLAMKAVFGTGLDDVLVSATKSQTGHLLGASGAIESILSVLAVHH +GVAPVTINLENQDPEIPLNVVTGTPAALPADRRVVVKNSFGFGGHNAVAVFTGV +>PROKKA_00867 +MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS +EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD +TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLVRS +GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV +IESEEHAKTRGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADITPEDVCH +VNAHATSTPKGDAPEYLAMRAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH +GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000793.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000793.fa new file mode 100644 index 0000000000000000000000000000000000000000..b58a7b20c84ebc47780b2d2c32c8212e1dc1ff8f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000793.fa @@ -0,0 +1,15 @@ +>PROKKA_00920 +MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD +EEVKNLKTVQDAVDFIDGAQA +>PROKKA_00639 +MASKEEILAGLAEIVNEETGLDAAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD +EEVKNLKTVQDAVDFIDGAQA +>PROKKA_02021 +MASKEEILAGLAEIVNEETGLDTADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD +EEVKNLKTVQDAVDFIDNAQA +>PROKKA_01920 +MASKEEILAGLAEIVNEETGLETADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD +EEVKNLKTVQDAVDFIDQAQA +>PROKKA_00868 +MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD +EEVKNLKTVQDAVDFIDGAQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000794.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000794.fa new file mode 100644 index 0000000000000000000000000000000000000000..27635b5fecb35cbcce2b7145d61d2922c9aa846b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000794.fa @@ -0,0 +1,35 @@ +>PROKKA_00921 +MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLIGPIDSSDEWIRQRTGIVTRQRATAEE +TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS +AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA +DEPGISPSVWGSDGERWSTISMTHSQLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG +PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD +IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP +>PROKKA_00640 +MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATAEE +TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS +AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA +DEPGISPSVWGSDGERWSTISMTHSQLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG +PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD +IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP +>PROKKA_02020 +MTVTLKQHERPAASRIVSVGAYRPKNLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATAGE +TVPAMAVAAGREALERAGLTGADLDAVIVSTVTFPHATPPRPPSWPTSSAPPPAPAFDVS +AACAGYCYGVAQADALVRAGTAKHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA +DEPGISPSVWGSDGERWETISFTHSQLELRDVVEQARTSGDASAITGSEEMVWPTLRQDG +PSVFRWAVWSMAKVAREALDAAGVEPEDLVAFIPHQANMRIIDEFAKQLKLPESVTVARD +IADAGNTSAASIPLAMHRLLEEDPSLSGGLALQIGFGAGLVYGAQVVRLP +>PROKKA_01919 +MTVTLKQHERPAGSRIVSVGAYRPATLVPNEDLVGPIDSSDEWIRQRTGIVTRQRATPEE +TVVTMAVGAGREALQRAGLEASDLGAVVVATVTFPYPTPSAAAAVADALGATPAPAYDIS +AACAGYCYGVAQADALVRAGSAQHVLVVGVERLSDFIDPTDRSISFLLGDGAGAVVVSAS +DEAGIAPSVWGSDGSRWSTISPTRSLLDLRAEVEHARETGDASAIIGAEEMLWPTLRQDG +PSVFRWAVWSMAEKAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD +IAEAGNTSAASIPLAMHRLLQEHPELSGGLALQIGFGAGLVYGAQVVRLP +>PROKKA_00869 +MTVTLKQHERPAASRIVAVGAYRPANLVPNEDLIGPIDSSDEWIRQRTGIVTRQRATAEE +TVPVMAVGAAREALERAGLQGSDLDAVIVSTVTFPHATPSAAALVAHEIGATPAPAYDVS +AACAGYCYGVAQADALVRSGTARHVLVVGVERLSDVVDPTDRSISFLLGDGAGAVIVSAA +DEPGISPSVWGSDGERWSTISMTHSRLELRDAVEHARTTGDASAITGAEGMLWPTLRQDG +PSVFRWAVWSMAKVAREALDAAGVEPEDLAAFIPHQANMRIIDEFAKQLKLPESVVVARD +IADAGNTSAASIPLAMHRLLEENPELSGGLALQIGFGAGLVYGAQVVRLP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000797.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000797.fa new file mode 100644 index 0000000000000000000000000000000000000000..225ecf905f94056e1135c8e67be89cdb2b6eaa3d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000797.fa @@ -0,0 +1,85 @@ +>PROKKA_00924 +MSAAEESSQIRSGLTDQLPDKDPQETSEWIESLDGLIEERGTERAQYIMRSLMQRASAQS +VALPYVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDGVGVGGHIS +SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEEDLDGFRQE +KSRQGHGLPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA +FLGDGEMDEPESRGQLHIAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG +WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSVTKE +MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT +HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV +PERRSDYHAIPLPPESAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE +ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG +TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD +GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHDRGDDVRNVIYYLTVYNEPIT +HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW +SVTSYNELYRDAVAAEKDALKDPSATPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF +VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGEVERGTAAKAHEKYR +LDDVNAGTTGIAGGDA +>PROKKA_00643 +MSAAEESSQIRSGLTDQLPDKDPQETSEWIESLDGLIEERGTERAQYIMRSLMQRASAQS +VALPYVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDAVGVGGHIS +SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEQDLDGFRQE +KSRQGHALPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA +FLGDGEMDEPESRGQLHVAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG +WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSVTKE +MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT +HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV +PERRSDYHAIPLPPESAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE +ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG +TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD +GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHDRGDDVRNVIYYLTVYNEPIT +HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW +SVTSYNELYRDAVAAEKDALKDPSASPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF +VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGEVERGTAAKAHEKYR +LDDVNAGTTGIAGGDA +>PROKKA_02017 +MSAAEESSQILSGLTQQFPDKDPQETAEWIESLDGLIEERGTERAQFIMRSLLQRAGAKS +VGVPMVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAAAIVQRAQKEGIGVGGHIS +SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEEDLDGFRQE +KSRQGHALSSYPHPRMMPDFWQFPTVSMGLGPMNAIFQAQTNRYLHNHGIKDTSDQHVWA +FLGDGEMDEPESRGQLHVAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG +WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSATKE +MVADMSDEEIWGLKRGGHDYRKVYAAYKSAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT +HQMKKMTVEDIKVFRDRHRIPVTDEQIERDPYDIPYYHPGKDAPEIKYLMERRKELGGFV +PERRAKHHSIPVPPEAAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGSRIVPIIPDE +ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAVG +TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD +GHSPVIAGTNPAVKHYDPAYSYEIAHIVRQGFEDMYGEHDRGEDVRNVIYYLTVYNEPIH +HIDEPEDLDVEGLLKGIYRLSEGQGDGPKVQLMGSGVSLPWAVEAQGILAEEWGVNASVW +SVTSYNELYRDAVAAEKDALKDPSAAPRVPYVTQKLEGAEGPVVATSDFATSWTNQIRPF +IPNRFAALGADEFGFADTRSAARRYFLIDSHSMVVRALQLLEEEGSVEKGTAAKAHEKYR +LDDVNAGTTGNAGGDA +>PROKKA_01916 +MSAAEESSQIVSGLTSQRPDKDPQETAEWIESFDGLVDERGTERAEYIMRSLMQRAGAKS +VALPHVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDAVGVGGHIS +SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEEDLDGFRQE +KSRQGHALPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA +FLGDGEMDEPESRGQLHVAANDKLDNLTFVVNCNLQRLDGPVRGNGKIVQELESYFRGAG +WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVREHFFGRSSVTKE +MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT +HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV +PERRSTYHQIPLPPESVYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE +ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG +TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD +GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHEDGDARRNVIYYLTVYNEPIT +HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW +SVTSYNELYRDAVAAEKDALKDPSATPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF +VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGGVERGTAAKAHEKYR +LDDVTAGTTGIAGGDA +>PROKKA_00872 +MSAAEESSQIRSGLTDQLPDKDPQETSEWIESLDGLIEERGTERAQYIMRSLMQRASAQS +VALPYVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDAVGVGGHIS +SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEQDLDGFRQE +KSRQGHALPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA +FLGDGEMDEPESRGQLHVAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG +WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSVTKE +MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT +HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV +PERRSDYHAIPLPPESAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE +ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG +TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD +GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHDRGDDVRNVIYYLTVYNEPIT +HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW +SVTSYNELYRDAVAAEKDALKDPSATPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF +VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGEVERGTAAKAHEKYR +LDDVNAGTTGIAGGDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000798.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000798.fa new file mode 100644 index 0000000000000000000000000000000000000000..79caf4574bd665d7b896582e1f7161df2ef7259a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000798.fa @@ -0,0 +1,20 @@ +>PROKKA_00925 +MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEDALGEELLTEDDQEPA +DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL +HATTGAGASEDWAAQKLVQKRGG +>PROKKA_00644 +MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEGALGEELLTEDDQEPA +DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL +HATTGAGASEDWAAQKLVQKRGG +>PROKKA_02016 +MEAGSTPTSTDSALLAELALAQGDLVQEWGYDDDVDFTFRDGLEDALGEELLTEEDQEPA +DAVLYWWRAEDGDVTDLADALVDAQRSLDSGPVWLMTPRKGRAGHVNPADVQEAAGTAGL +HATTGAGVSEDWAAQRLVQKRGG +>PROKKA_01915 +METPSDGTSTHQELLDAYGLTAGELVQEWGYDDYIDFDFRDALEDALGEELLTEEDQEPA +DAVLFWWRTDDGDVSDLTDALVDAQRSLDAGPVWLMTPRNGRPGHVSPTDVAEAAATAGL +HVTTGAGGSADWAAVRLEKRGG +>PROKKA_00873 +MQAGSTPTSTDSALLAELALSRGDLVQEWGYDDDVDVTFRDALEDALGEELLTEDDQEPA +DAVLFWWRADDGDVMDLADALVDAQRSLDAGPVWIMTPRKGRPGHVSPADVAEAASTAGL +HATTGAGASEDWAAQKLVQKRGG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000799.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000799.fa new file mode 100644 index 0000000000000000000000000000000000000000..95a70e6944b1be691a21f21d435d314fbbd0394f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000799.fa @@ -0,0 +1,20 @@ +>PROKKA_00926 +MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL +GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF +DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR +>PROKKA_00645 +MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL +GWIGALAEDVAVDEVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF +DAETGRPRRVSVLLDADGVEAARVVAAPGQARTRGEHEAATRDLLVDR +>PROKKA_02015 +MAEEPGAVPALRDDRGQDWPWPPTRGPEDAAAPRATWLVLLPGAFTPVCTGELGWLGELA +TDLAADDVAVRVIACDAAPVLRRVREELGLPEDLVLLSDFWPHGAACAALDAFDAASGRA +RRVSVLLDADGVEVSRVTAAPGRPRSRTEHEAATRALLGDR +>PROKKA_01914 +MAEPALRDIHGTPWPWPPVVSGERAAWLVFLPGAFTPVCAGELAWLGPLAVELAAEDVGL +RVVSCDAAPVLREVADRTGLPAECVLLSDFWPHGAAAARFGLLDETTGRPRRVSVLVDES +GTELVRVRPGEPGGPRTAQAHRRAAEGALGRRR +>PROKKA_00874 +MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL +GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF +DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000800.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000800.fa new file mode 100644 index 0000000000000000000000000000000000000000..bd9f289e9730ee52aa2c038ea90fd857d2ca675d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000800.fa @@ -0,0 +1,30 @@ +>PROKKA_00928 +MLTIMSSSTESLRAPVTPSRWAEVRSGVAVTLGAGLGLFPLGMAFGMLVVQAGLPAWVAP +LFSVVVFAGSVELLLVSLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRFARIYS +MGALIDEAYAIAAARPRGWTGPRLVAMQVALHAYWVLGGLAGVAVAWLLPGPVEGLEFAL +VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR +GTALPLPEPVPVTGPVPVVAATGERAGTDAEPGAGEDPR +>PROKKA_00647 +MLTIMGSSSASSRASAPPSRWAEVRSGVAVTLGAGLGLFPLGVAFGMLVVQAGLPAWVAP +LFSVVVFAGSVELLLVSLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRLARIYS +MGALIDEAYAIAAAQPRGWTAPRLLAMQIALHAYWVLGGLAGVAVAWLLPVPVEGLEFAL +VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR +GTALPLPEPVPVTGPVPVVAAAGERAVTDAEPGVEEDPR +>PROKKA_02012 +MNAPSLQPSPYPAPPPSRGAEVRAGVRLSLAAGLGLFPLGVAFGMLVVQAGLPAWVAPLF +SVVVFAGSVELLLVSLAVAATPLLTIAVTVFLVNFRHVFYAFSFPLRVVRHPLARLYSMG +ALIDEAYAIAAAHPRGWTAPRLIALQVALHAYWVLGGLAGVAVAWLLPGPVEGLEFALVA +LFIVLALDAARTRAQAPLVLAAALAVGVGLLVAPGQLLVAAFAVYAAVLIALHVLARRGV +DLPLPAPTPATGPVPVVAGPAPGEEPR +>PROKKA_01911 +MTEITPPSPAASGVPDALPTRRAEVAEGVRLSGPAGLGLFPLGVAFGMLVVQAGLPGWAA +PLLSVVVFAGSVELLLVSLLAAGTSLAGIAVTVFLLNFRHVFYAFGFPLRVVRNPLARLY +SMGGLIDEAYAITAAHPRGWTAPRLLATQVSLHLYWVVGGLVGVVAAGLLPAPVEGLEFA +LTALFIVLALDAARTRRHVLLVLAAAAAVGVGLVVAPSALLVASFLGFVAALMAAHVAAE +RGARLPLPAVKELGATSPGAAEAAELTTVDAEAGR +>PROKKA_00876 +MLTIMGSSSASSRASAPPSRWAEVRSGVAVTLGAGLGLFPLGMAFGMLVVQAGLPAWVAP +LFSVVVFAGSVELLLVPLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRLARIYS +MGALIDEAYAIAAARPRGWTGPRLVAMQVALQAYWVLGGLAGVAVAWLLPGPVEGLEFAL +VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR +GTALPLPEPVPVTGPVPVVAATGERAGTDAEPGAGEDPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000804.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000804.fa new file mode 100644 index 0000000000000000000000000000000000000000..c96c523269b6b02d330e062a02d82ee16710f5e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000804.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000805.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000805.fa new file mode 100644 index 0000000000000000000000000000000000000000..3b5d7d5117a6054c7ff6d29c0cef772abe3c3a51 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000805.fa @@ -0,0 +1,50 @@ +>PROKKA_00933 +MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSRARTDQLVAEHGDEGA +FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHFEDTRR +REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKIAAQFEGEPCCA +WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL +IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS +SQRAVREVARETLAAGVDEEAQRAPQDTDAFVEDVRQALFASKLVAYAQGMDMLAAAAEE +YGWSLDLGTIASLWRDGCIIRADLLDVIMQAFGGRDTSRHPAPGTRAPGQPLNLLFAPEF +AQAIAEALPAWRRVVGTAVAAGVPVPVFSSALAYYDGLRADRLPAALVQGQRDYFGAHTY +LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPTEGDPTQD +>PROKKA_00652 +MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSRARTDQLVAEHGDEGA +FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHFEDTRR +REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKISAQFEGEPCCA +WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL +IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS +SQRAVRQVARETLAAGVDEEAQRAPQDTDTFVEDVRQALFASKLVAYAQGMDMLAAAAEE +YGWSLDLGTIASLWRDGCIIRADLLDVIMQAFGGRDTSRHPAPGTRAPGQPLNLLFAPEF +AQAIAEALPAWRRVVGTAVAAGVPVPVFSSALAYYDGLRADRLPAALVQGQRDFFGAHTY +LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPTEGDPTQD +>PROKKA_02007 +MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSHGRTDQFVAEHGDEGA +FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHYEDTRR +REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKISAQFEGEPCCA +WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL +IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS +SQREVRAAAREVLQAGVDEAAVPAVTDTDAFVEDVRQALFASKLVAYAQGMDMLAAAAEE +YGWSLDLGTIASLWRDGCIIRADLLDVIMKAFGGRDTARHPEPGTRAEGQPLNLLFAPEF +AQAIAEALPAWRRVVGTAVAAGVPVPVFSSALAYYDGLRADRLPAALVQGQRDYFGAHTY +LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPAEGDPTQD +>PROKKA_01903 +MTETSTVRGTADIGVTGLAVMGANLARNFARHGYTVALHNRSRAKTDALVAEHGHEGSFV +ATETLEELVGSLASPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHYEDTRRRE +AALAEKGLHFVGVGVSGGEEGALNGPAIMPGGPEESYAALGPLLEDIAASYDGEPCCAWI +GTDGAGHYVKMVHNGIEYADMEVIGEAFDLLRRVAGIEPAEQAQVFDAWNQTELASYLIE +ITAEVLQQVDAATGAPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLSAQ +TEVRATAREVLAAGVESAPAVSPQDRDAFVEDVRQALFASKLVAYAQGLDMLSAAAIEYG +WALDLGTIASLWRDGCIIRADLLDVIMKAFGGRDTSRHPEPGTRAEGQPLNLLFAPEFAQ +AMAEALPAWRRVVGAAVAAGVPVPVFSSALAYYDGLRADRLPAALIQGQRDFFGAHTYRR +TDRDGSFHTLWSGDRTEVDGDGAPVVMPQPAEGDPTDETAR +>PROKKA_00882 +MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSRARTDQLVAEHGDEGA +FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLEEGDIVIDAGNSHYEDTRR +REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKISAQFEGEPCCA +WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL +IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS +SQRAVREVARETLAAGIDEDAQRVPQDTDAFVEDVRQALFASKLVAYAQGMDMLAAAAEE +YGWSLDLGTIASLWRDGCIIRADLLDVIMQAFGGRDTSRHPAPGTRAPGQPLNLLFAPEF +AQAIAEALPAWRRVVGTAVASGVPVPVFSSALAYYDGLRADRLPAALVQGQRDYFGAHTY +LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPTEGDPTQD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000806.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000806.fa new file mode 100644 index 0000000000000000000000000000000000000000..bc8a5266e3bd54c8f7619731f8fa0ca18f48cadf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000806.fa @@ -0,0 +1,25 @@ +>PROKKA_00934 +MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS +QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH +PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPSEGK +PLVDPAEYVDPALWI +>PROKKA_00653 +MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS +QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH +PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPAEGK +PLVDPAEYVDPALWI +>PROKKA_02005 +MGLLARIKEDLDNVRSHDPAARGDLEVALVYSGLHAVWAHRIAHRMWRHERLRMPARILS +QATRAATGIEIHPGATIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH +PTLRDGVVVGAGAKILGPVEIGAGSAVGANAVVVKDTPADAIATGIPATYRLRRSPAEGK +PLVDPAEYVDPAMWI +>PROKKA_01902 +MGIRSRIKEDIATVRSHDPAARGDLEVVLAYSGLHAVWSHRVAHRMWQVGRLKTPARLLS +QAARALTGIEIHPGATIGRRLFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLEKVKRH +PTLRDGVVVGAGAKILGPVEIGEGTSVGANAVVVKDTPPDSIATGIPASVRLRTSPAEKK +PLVDPAEYVDPAMWI +>PROKKA_00883 +MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS +QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH +PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPAEGK +PLVDPAEYVDPALWI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000807.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000807.fa new file mode 100644 index 0000000000000000000000000000000000000000..8f677cfdb4652b693d507a28f543ad10e14209ef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000807.fa @@ -0,0 +1,35 @@ +>PROKKA_00935 +MARILDDITQAVGGTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEAAG +ELSPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA +DGMRGALERAQEIVRSTPNSIWAQQFANQANVQAHYTGTGPEIWDASEGAVDVFIAGVGT +GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTDLYDE +VYPATFEESIETARRLGTEEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY +ISTALFEDIRG +>PROKKA_00654 +MARILDDITQAVGNTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEAAG +ELTPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA +DGMRGALERAQEIVRSTPNSIWAQQFANQANIQAHYTGTGPEIWDASEGAVDVFIAGVGT +GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTDLYDE +VYPATFEESIETARRLGTEEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY +ISTALFEDIRG +>PROKKA_02004 +MAHILDDITQAVGGTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEASG +ELTPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA +DGMRGALERAQQIVASTPNSIWAQQFANQANVQAHYTGTGPEIWDATEGAVDVFIAGVGT +GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTELYDD +VYAASLEESIETSRTLATQEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY +ISTALFEDIRG +>PROKKA_01901 +MAKILDNITQAVGGTPLVRLNSLTEGLPGDVAVKVEFYNPANSVKDRIGVAIVDAAEKSG +QLTPGGTIVEGTSGNTGIALAMVGAARGYKVILTMPETMSAERRVMLRAFGAEIVLTPGA +DGMRGAVERAQQIVRDTPNSIWAQQFANEANVRAHYTTTGPEIWDATGGAVDTFIAGVGT +GGTITGAGRYLREQKPDVKLIAVEPSDSPILSGGQAGPHKIQGIGANFVPEILDTELYDE +VYAATFEESIATSRALGAREGILGGISTGAIVSAALKEAAKPESEGKLIVAVVCDFGERY +ISTALFEDVRG +>PROKKA_00884 +MARILDDITQAVGNTPLVRLNRLAKDLPGDVAVKVEFYNPANSVKDRIGTAIVDAAEAAG +ELTPGGTIVEGTSGNTGIALAMVGAARGYRVILTMPETMSTERRVMLKAFGAEIVLTPGA +DGMRGALERAQEIVRSTPNSIWAQQFANQANIQAHYTGTGPEIWDASEGAVDVFIAGVGT +GGTITGAGRYLREQKPDVKLIAVEPADSPILSGGQAGPHKIQGIGANFVPEILDTDLYDE +VYPATFEESIETARRLGTEEGILGGISTGAIISAALKEAAKPESEGKLIVAIVCDFGERY +ISTALFEDIRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000808.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000808.fa new file mode 100644 index 0000000000000000000000000000000000000000..d051904ddb455d81f5cf7825251a7adb4ab76e2f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000808.fa @@ -0,0 +1,25 @@ +>PROKKA_00936 +MTDFPRTEPLGASGAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE +SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDE +AEARFFADEIARAQENYDSPIVTRVEPASAWHPAEDIHQDFYARRRSNGYCRVVIDPKLA +KVRRNYSAWLVDA +>PROKKA_00655 +MTDSPRTEPLGASDAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE +SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTSHDPTSLNRQGADVGTQYRSAVFAHDE +AETRFFADEIARAQANYDSPIVTRVEPASAWHPAEDIHQDFYARRRSNGYCRVVIDPKLA +KVRRNYSAWLVDA +>PROKKA_02003 +MTDSPRTEPLGASSAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE +SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDE +AEARFFADEIARAQANYDSPIVTRVEPASAWHPAEDIHQDFYARRRSDGYCRVVIDPKLA +KVRRNYSAWLVDA +>PROKKA_01900 +MSETPETPSTPAAHAPRVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGHTPDPDYEA +VCTGQTGHAEAVRVRFDEAQVPAEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDEA +EADFFRSQLARAQELYEAPIVTTIEPAAAWHPAEWYHQDFYASRPGNGYCRVVIDPKLAA +VRRRHAAWLTDGA +>PROKKA_00885 +MTDSPRTEPLGASGAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE +SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDE +AEARFFADEIARAQANYDSPIVTRVEPASAWHPAEDIHQDFYARRRSNGYCRVVIDPKLA +KVRRNYSAWLVDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000809.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000809.fa new file mode 100644 index 0000000000000000000000000000000000000000..294510fd5102a7b8e5fa2c1b2c4a304e81c6fd9a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000809.fa @@ -0,0 +1,35 @@ +>PROKKA_00937 +MAGMTVSRPAVPASPEHALAPPTLGQVLEVVEGLWPRELAEPWDAVGPVAGRPEAPVRTV +LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAKGRLLHTLIEHRIALL +AAHTNADAVVGGVSDVLARAVGVTGALSPLTASAAGTGAEGIGRVGDLPEETDLAAFARA +VHAALPATAGGVRVAGGPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASEA +RETAASGDGRPALVDVSHWASESLWLEHGARALEAALVERGLGVTTLFSDHRSDPWDFLV +GGERADEGSRA +>PROKKA_00656 +MAGMTVSRPTVPASPEHALAPPTLGQVLEVVQGLWPRELAEPWDAVGPVAGRPEAPVRTV +LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAAKGRLLHTLIEHRVAL +LAAHTNADAVVGGVSDVLARAVGVIGALSPLTTSAAGTGAEGIGRVGDLPEETDLAAFAR +AVHAALPATAGGVRVAGDPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASE +ARETAAPGEGRPALVDVSHWASESLWLEHGARALEAALAERGLGVTTLFSDHRSDPWDFL +VGGERADEGSHA +>PROKKA_02002 +MDRMTVSRPAVPASPEHALAPPTLGHVLEVVQGLWPRDLAEPWDAVGPVAGRPEAPVRTV +LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAAKGRLLHTLIEHRIAL +FAAHTNADAVVGGVSDVLARAVGVTGALSPLTTSAAGTGAEGIGRVGDLPEETDLAAFAR +VVHAALPATAGGVRVAGDPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASE +ARETAVSGDGRPALVDVSHWASESLWLEHGARALEAALAERGLGVTTLFSDHRSDPWDFL +VGGERADEGSHA +>PROKKA_01899 +MTVPDHPLQGAGEGACGRAVATDAVASDVPRLSDVLAAVERLWPARLAESWDAVGPVVGR +AGRPVRHVLWAVDPVQDVVDEAVRIGADLVVTHHPLMLRGTTSVAAVGHGGAFKGEVVHT +LIEHGIALVAAHTNADSAVGGVSDAIAWRLGLTDVSPLQPSAGGSGAEGIGRVGELPAPV +PLVEFARTVAALLPATAGGVRVAGDADLPVRRVAVCGGAGDSLFDAVRAADADVYVTSDL +RHHPASEAREAARHAGGRPALVDTAHFAGEWLWLADGAAALAEELARGGHRARMTVSELV +TDPWDLHLPSGLAERTTS +>PROKKA_00886 +MAGMTVSRPAVPASPEHALAPPTLGHVLEVVQGLWPRELAEPWDAVGPVAGRPEAPVRTV +LWALDPVQAVADEAVARGADLVVTHHPLLLRGTSSVAAVGHAAAAKGRLLHTLIEHRIAL +LAAHTNADAVVGGVSDVLARAVGVTGALSPLTTSAAGTGVEGIGRVGDLPEETDLAAFAR +AVHAALPATAGGVRVAGDPAQRIRRVAVCGGAGDSLFDAVRASGADVYVTADLRHHPASE +AQETAVSGGGRPALVDVSHWASESLWLEHGARALEAALAERGLGVTTLFSDHRSDPWDFL +VGGERADEGSHA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000810.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000810.fa new file mode 100644 index 0000000000000000000000000000000000000000..ac688d3164675685e52ac8d93b55e89441328aa8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000810.fa @@ -0,0 +1,30 @@ +>PROKKA_00938 +MSEVTAPPAVQARLLELQELDTALDQARAAVHRLQADPEHARLRARAQEFEEALPGLQDA +ARTADRAGAEATEKAAATRARRDRTRERLETGQGGPKELQAMQHEDDTLTALLDDHEAAA +LEAMEATDAAESRLSKGHAALERARAEVEARAAEVRREGQAVTQRGRDLIQRRAALAAEF +PASLLALYEQARERNGGIGAARLVGNRSAAAGTELSPAEVARIRALPPAAVARCPESGAI +LIRD +>PROKKA_00657 +MSEVTAPPAVQARLLELQELDTALDQARAAVRRLKADPEHARLRARALELEEALPGLEDA +ARTADRAGAEATEKAAATRARRDRTRERLEAGQGGSKELQAMQHEDDTLTALLDDHEAAA +LEAMETADAAESRLAKGHAALEQARAEVEARAAEVRREGQAVTQRGRDLIQRRAALAAEF +PASLLALYEQARERNGGIGAARLVGNRSAAAGTELSPAEVARIRALPPAAVARCPESGAI +LIRD +>PROKKA_02001 +MSEVTAPPAVQARLLELQELDTALDQARTQIRRLKADPELARLRARAQELEDALPEVEDA +ARTADRAGAEASEKAAATRARRDRTRERLEAGQGGSKELQAMQHEDGTLTALLDEHEGAA +LEAMEAADEAESRLAAARQALEQARAEVDARAAEVRREGQVVTQRGRDLTQRRTALAAVF +PAPLLALYEKARERNGGIGAARLVGRRSQASGTELSPADVARIEALPPAAVARCPESGAI +LVRG +>PROKKA_01898 +MNRVTAPAAEQARLLELQQLDLGIGRAKTRLAQLRADAALADLQKAVAAAEEAAAEQEAH +ERETDAAAAQASERATTTRARRDRTRAHLDAGDGGSKELTALQHELEGLESLLAEHEGAA +LAAMEAADEAEEALARARAAVDEARAAVAARADEVRAEGRRVTEEGRELAALRAGLAGRL +PADLLARYEEARAANAGIGATRLEGRRTGAGTELSPADLDAVLATPADEVAVDPETGILI +IRA +>PROKKA_00887 +MSEVTAPPAVQARLLELQELDTALDQARAAVRRLKADPEHARLRARAQEFEEALPGLQDA +ARTADRAGAEATEKAAATRARRDRTRERLETGQGGSKELQAMQHEDDTLTALLDDHEAAA +LEAMEAADAAESRLAQGHAALERARAEVEARAAEVRREGQAVTQRGRDLIQRRAALAAEF +PASLLALYEQARERNGGIGAARLVGNRSAAAGTELSPAEVARIRALPPAAVARCPESGAI +LIRD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000811.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000811.fa new file mode 100644 index 0000000000000000000000000000000000000000..08326108203f004a3185e7adfd6aca2799ad00a8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000811.fa @@ -0,0 +1,32 @@ +>PROKKA_00939 +MSGRVLQVEADGGSRGNPGVAGYGALVRDPATGEILRTDAAPLGKASNNVAEYSGLVAGL +RMARDLDPEARVHVLMDSKLVVEQMSGRWKIKHDDMRRLAAEARSVLPPERVSYEWIPRN +RNKDADRLSNEAMDAGARGEQWDAGASEVPVAAPAKASTTSASAVAESGLEADADVRAVE +ADGPDAVASPEDATPAPAPTGRLHHVEIWVADLAAAEASLGWLFGELGYVPGEGWAEGRT +YQGAGEYLVLEAGPDVAAGAHERTRPGLNHLAFRAGSRARVDELTAAARDRGFRLLFEDR +HPHAGGPDHYAAYLETADGFEVELVAVED +>PROKKA_00658 +MSGRVLQVEADGGSRGNPGVAGYGALVRDPATGEILRTDAAPLGKASNNVAEYSGLVAGL +RMARDLDPEARVHVLMDSKLVVEQMSGRWKIKHDDMRRLAAEARAVLPPERVSYEWIPRN +RNKDADRLSNEAMDAGARGGQWDAGASEVPVAAPAEASTTSTSAVAESGLDADADVRAVE +ADGPDAVASPEDATPGPAPTGRLHHVEIWVADLAAAEASLGWLFGELGYVPGEGWAEGRT +YQGAGEYLVLEAGPDVAAGAHERTRPGLNHLAFRAGSRSRVDELTAAARGRGFRLLFEDR +HPHAGGADHYAAYLETADGFEVELVAVED +>PROKKA_02000 +MLEADADARAVEAEAPDAVGQDAAAPQAPTPTGRLHHVEVWVADLAAAEAGLGWLLGELG +YVLGEGWAEGRTYQGAGEYIVLESGPDVVGGAHERTRPGLNHLAFRAGTRARVDELTAAA +RERGFRLLFADRHPHAGGADHYAAYLEAPDGFEVELVAVED +>PROKKA_01897 +MAERTLQVEADGGSRGNPGVAGYGALVRDPATGDVLMTDAAPLGKASNNVAEYSGLIAGL +EMAKTLDPDARVHVKMDSKLVVEQMSGRWKIKHEDMRRLAQQARAVLPPSRVTYEWIPRA +QNKDADQLSNEAMDAGARGGRWDAGASKVPVTAPSAPTSAGAPAAEPDKEPLEEPPVPEE +RTRPRPVGRLHHVEIWAADLDAAVESLGWLFEQVGYAPGDAWAEGRVYRGAGDYLVLESG +RDVAPGGHDRLRPGLNHLAFRAGTRADVDRIAAQAADHGFTLLFEDRHPFAGGRDHYAAY +LETADGFEVELVADPA +>PROKKA_00888 +MSGRVLQVEADGGSRGNPGVAGYGALVRDPATGEILRTDAAPLGKASNNVAEYSGLVAGL +RMARDLDPEARVHVLMDSKLVVEQMSGRWKIKHEDMRRLAAEARSVLPPERVSYEWIPRN +RNKDADRLSNEAMDAGARGEQWDAGASEVPVAAPAAAGSTAAEASTTSASAVAESCLDAD +ADVRAVEADGPEAVASPGDATPAPAPTGRLHHVEIWVADLAAAEASLGWLFGELGYVPGE +GWAEGRTYQGAGEYLVLEAGPDVAAGAHERTRPGLNHLAFRAGSRARVDELTAAARDRGF +RLLFEDRHPHAGGPDHYAAYLETADGFEVELVAVED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000814.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000814.fa new file mode 100644 index 0000000000000000000000000000000000000000..6789c7281264960451046456bcf883bc1e55464a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000814.fa @@ -0,0 +1,50 @@ +>PROKKA_00942 +MADTASTQTPEWNTQQKLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR +RVQEAPLSVESTYPLVEAMAAMDLGAATIDLAELAAKHKASGQDVQAFLDAELAEVKGKA +GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR +DSIHGPFDGTIVVDEDRDVITANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDD +EGLSQHLQAKGAAKVLLTAPGKGEMKNIVFGVNSDDITPQDTIVSAASCTTNGITPVLKV +IQDDYGIDHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVLTETGAAKAVAKALPEL +KGKLSGNAIRVPTPDVSMAILNLELTTPTSVEELNARLKQESLTGPLRGQVGYVDSPEVV +STDFVGSDRAGVVDGLATLVNNDGKNAILYVWYDNEYGYSHQVIRVVEKMAGQQVPAFPQ +A +>PROKKA_00661 +MADTASTQTPEWNTQQKLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR +RVQQAPLSVESTYPLVEAMAAMDLGAATIDLAELAAKQKASGQDVQAFLDAELAEVKGKA +GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR +DSIHGPFDGTIVVDEDRDVITANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDD +EGLSQHLQAKGAAKVLLTAPGKGEMKNIVYGVNSDDITPQDTIISAASCTTNGITPVLKV +IQDDYGIDHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVLTETGAAKAVAKALPEL +KGKLSGNAIRVPTPDVSMAILNLELTKPTSVGELNARLKQESLTGPLRGQVGYVDSPEVV +STDFVGSDRAGVVDGLATLVNNDGKNAILYVWYDNEYGYSHQVIRVVEKMAGQQVPAFPQ +A +>PROKKA_01996 +MADTASTQTPEWNTQQELAERMVPLLGSLYRENNVVTSIYGRSLVNRGVIDIIKAHRYAR +RVQDAPLSVAATYPLVEAMAAMDLGAANVDLAELAARHKESGQEVQAFLDAELAEVKGKG +GEGLGEPQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLVKRASLLRR +DSIHGPFDGTIVVDEDRNVITANGTEIQVIYSNDPTTVDYTAHGIKDALVIDNTGRWRDD +EGLSQHLQAKGVKKVLLTAPGKGEMKNIVFGVNSDDITPEDTIVSAASCTTNGITPVLKV +IQDDYGIDHGHVETVHAYTNDQNLTDNFHKGSRRGRSAGLNMVLTETGAAKAVAKALPEL +KGKLSGNAIRVPTPDVSMAILNLELNKATSVEELNARLKQESLTGVLRGQVGYVDSPEVV +STDFVGSDRAGVVDGLATLVNNEGKNAILYVWYDNEYGYSHQVVRVVSGPRPGRDQAPSA +RPWSASGPCCSIASASSSSSCPKGSSSVPGSQVTPGTFMRSARCARFQRRCHLPSRRLT +>PROKKA_01894 +MADTASTQTPEWNTQQKLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR +RVQEAPLSVEATFPLVEAMAGMDLGAANIDLAELAAKQQASGQDVQAFLDAELADVTGKS +GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR +DSIHGPFDGTIVVDEDRNVITANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDV +EGLSQHLQAKGATKVLLTAPGKGDMKNIVFGVNSDDILDEDTIVSAASCTTNGITPVLKV +IQDEYGVQHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVITETGAAKAVAKALPEL +KGKLSGNAIRVPTPDVSMAIINIALEKPTSVEEINARLKQESLTGDLRGQIGYVDSPEVV +STDFVGSDRAGVVDGLATIVNNEGKNAILYVWYDNEYGYSHQVVRVVEKMAGQQVPSFPK +A +>PROKKA_00891 +MADTASTQTPEWNTQQNLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR +RVQEAPLSVESTYPLVEAMAAMDLGAATVDLAELAAKQKASGQDVQAFLDAELAEVKGKA +GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR +DSIHGPFDGTIVVDEDRDVIIANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDD +EGLSQHLQAKGAAKVLLTAPGKGEMKNIVFGVNSDDITPEDTIVSAASCTTNGITPVLKV +IQDDYGIDHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVLTETGAAKAVAKALPEL +KGKLSGNAIRVPTPDVSMAILNLELNTPTSVEELNARLKQESLTGPLRGQVGYVDSPEVV +STDFVGSDRAGVVDGLATLVNNDGKNAILYVWYDNEYGYSHQVIRVVEKMAGQQVPAFPQ +A diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000815.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000815.fa new file mode 100644 index 0000000000000000000000000000000000000000..ab815528a055381b8a9aa45f45d8868b89cb4dfd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000815.fa @@ -0,0 +1,25 @@ +>PROKKA_00943 +MASIRPVTVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQEAAHGVGLAAPQVGVGLRIF +TWTFPDSGDAPNVGHVINPVLTHLDKAPREEPHPDEHTEGCLSVPGLGFPLQRPTRVRLS +GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT +WLPGTDEDPFGHDADDHEDHEHGPDGDHGDDEA +>PROKKA_00662 +MASIRPITVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQDAAHGVGLAAPQVGVGLRIF +TWTFPDSGDAPNVGHVINPVLTHLDKAPREDPHPDEHTEGCLSVPGLGFPLQRPTRVRLS +GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT +WLPGTDEDPFGHDADDHEDHEHGPDGDHGDDEA +>PROKKA_01995 +MASIRPITVYGEPVLHTRAAEVEVIDDEIRRLVEDMYVTQDAARGVGLAAPQVGVGLRVF +TWTYPHSGDAPSVGHVINPVLTVLDKASQEATDPDEHTEGCLSVPGHGYPLQRAPRVRLA +GQRVDGEMFEFVAEGWFARVMQHEYDHLNGTLYVNRLEGRWQRRWKRAQRAERMNVPGVT +WLPGTDEDPFGHDELDEAEAIEQHGPDADHGRADGA +>PROKKA_01892 +MPSIRPITVYGEPVLHTRAAEVEVIDDSIRELVEDMYVTQDVANGVGLAAPQVGVGLRVF +TWTFQDTGDAPNLGHVINPVLTMLSKPSTEEPDRHEDTEGCLSVPGHGFPLKRSAHVRMT +GQRMDGSTVDIEATGWFARILQHEYDHLNGTLYVNRLEGKWARRWKRAQRAERLNVPGVT +WLPGTDPDPFGHDVDVDEDAPAHEHHDHDHEGHDHAQEAR +>PROKKA_00893 +MASIRPITVYGEPVLHRRAAEVEVIDDEIRELIEDMYVTQEAAHGVGLAAPQVGVGLRIF +TWTFPDSGDAPNVGHVINPVLTHLDKAPREDPHPDEHTEGCLSVPGLGFPLQRPTRVRLS +GQRVDGEMFEFEAEGWFARIMQHEYDHLNGTLYVNRLEGKWQRRWKRAQRAERLNVPGVT +WLPGTDEDPFGHEEIEDHEH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000816.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000816.fa new file mode 100644 index 0000000000000000000000000000000000000000..1b4b393df4c6a487db620a97692e5a3691f4e816 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000816.fa @@ -0,0 +1,15 @@ +>PROKKA_00947 +MSVVKINAISVPEGAGPELEKRFAARKHAVDQEPGFEGFQLLRPTAGEDRYFVVTTWASE +EDFRRWRDGRMPAAHAAEQGGRPAPVATGADLLEFEVVDLG +>PROKKA_00666 +MSVVKINAISVPEGAGPELEKRFAARKHAVDQEPGFEGFQLLRPTAGEDRYFVVTTWASE +EDFQRWRDGRMPAAHAAEQGGRPAPVATGADLLEFEVVDLG +>PROKKA_01990 +MSVVKINAITVPEGAGPELEKRFAVRKHAVDAEPGFEGFQLLRPTAGEDRYFVVTTWATE +EDFQNWKGGRMPAAHAAESEGRPAPVATGAELLEFEVVDLD +>PROKKA_01891 +MSVVKINAISVPEGAGPELEKRFAVRKHAVDQEPGFEGFQLLRPTAGEDRYFVVTTWASE +EDFQRWRDGRMPAAHADEQGGRPTPVATGADLLELEVVDLG +>PROKKA_00895 +MSVVKINAISVPEGAGPELEKRFAARKHAVDQEPGFKGFQLLRPTAGEDRYFVVTTWASE +EDFQRWRDGRMPAAHAAEQGGRPAPVATGADLLEFEVVDLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000818.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000818.fa new file mode 100644 index 0000000000000000000000000000000000000000..119e58eaae5b473548d302b58a8110bbe8485ffd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000818.fa @@ -0,0 +1,55 @@ +>PROKKA_00957 +MSVSTPRPSGSTAHRPEYVGVGGLRADPQVAGADWWPILVGTLGSLLLVVGSYSVGWLAS +ASPINRWQWLIPWRTQETGVLAGAALLTLGCWVMFWAWLRLGQTIRPFGRGALRTVNLAT +VLWCLPQVVALPIFSRDIFAYVGQGRLMEAGQDPYVDTISSLSNWFQLGADATWADSETP +YGPIFLWIEQAVVAISGDMNPDLAIFLFRLVAVAGVALIMVFVPLLARRMGVNDAWAQWI +SVANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQRPGQSVAWGVAGVVLVTL +SLGIKPITLVLLPFIGLLWAGPTARWPRRFAFWALTAGISFGLMALVGVLNGFGFGWVAV +MVGTGTGTVPWGPIGMLSLITVGASELLGQGADVQAVEGVYKTAGRVLSVLIVLALMFLG +RQDRVMTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDNWQIKWVVFTVGYFLAFG +ASDQLFTWQFLDIADQVKAVSLIVSAVCLLWILVVDRRTSRFVKDHWHVRPAVRAGLARL +RGAPRPVEPGE +>PROKKA_00670 +MSVSTPRPSGSTAHRPEYVGVGGLRADPQVAGADWWPILVGTLGSLLLVVGSYSVGWLAS +ASPINRWQWLIPWRTQETGVLAGTVLLTLGCWVMFWAWLRLGQTIRPFGRGALRTVNLAT +VLWCLPQVVALPIFSRDIFAYVGQGRLMVAGQDPYVDTISSLSNWFQLGADATWADSETP +YGPIFLWIEQAVVAISGDMNPDLAIFLFRLVAVAGVALIMVFVPLLARRLGVNDAWAQWI +SAANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQRPGQSVAWGVAGVVLVTL +SLGIKPITLVLLPFIGLLWAGPTARWPRRFAFWALTAGISFGLMALVGVLNGFGFGWVAV +MVGTGTGTVPWGPIGMLSLITVGASELLGQGADVQAVEGVYKTAGRVLSVLIVLALMFLG +RQDRVMTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDNWQIKWVVFTVGYFLAFG +ASDQLFTWQFLDIADQVKAVSLIVSAVCLLWILVVDRRTSRFVKDHWHVRPAVRAGLARL +RGAPRPVEPGE +>PROKKA_01930 +MSVTTPRPSGSTAGRPAHIGVGGLRADPKVAGGNTWPILVGTLGSLLLVAGSFSVGWLAS +ASPINRWQWLIPWRTQETGVIVGTILLTLGCWVMFWAWLRLGQTVRPFGRGSLRTVNLAT +ALWCLPQVFALPIFSRDIFAYVGQGRLMVAGQDPYEDTISSLSNWFQLGADATWADSETP +YGPIFLWIEQAVVAVSGDMNPDLAIFLFRLVAVAGVVLIMVFVPLLARRLRVNGAWAQWV +SAANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQSAARSAAWGVAGVVLVTL +SLGIKPITLVLLPFIGLLWAGPTAGWIRRFVLWFLTAGISFGIMAVVGALNGFGFGWVAV +MVGTGTGTVPWGPIGILSLLTVGISELVGQGADQQAVEGVYKTAGRVLSVLIVLALMFLG +RQDRVLTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDDWQIKWVVFTVGYFLAFG +ASDQLFTWQFLAIADQVKAISLIVSAVCLAWILVVDRRTSRFVKDHWHVRPAVRAGLARL +RRAPRTPEPGE +>PROKKA_01882 +MGVPAAGPSGSTAFRPEYIGVGGLRADPQVAGRPLWPILVGLLGSLMLVAGSFSVGWLAS +ASPINRWQWLIPWRTQESGVMTGTVLLTLGCWVMFWAWLRLGQTVRPFGPGALRTVNVAT +ALWCLPMVFALPIFSRDIFAYVGQGRLMVNGQDPYTDAISSLNNWFQLGADATWAGSETP +YGPVFLWIEEVVVRISGDMNPDLAIFLFRLVAVVGVVLTMVFVPLLARRLSVNGAWAQWV +SAANPLFTVSFVASGHNDALMVGLALAGTWCALRAGHPRGGQSTASHVGWGVAAVVLVTA +SLGVKPITLVLLPFIGLLWAGPRAGWSRKFVYWAVTGGLSLALMVLVGRLNGFGFGWLEV +MAGTGSGTSPWAPVGMMSIATRVLMEVLQLGPDLQAIEGFYKSVCRLLSVLIVLALMFLG +RQDRVFTRMTWAFTTLVVLSPIVQPWYLLWLLPFFAVIGLRDNWQIKWVVFTVGYFLAFG +AMDQLFTWQFLDIAEEVRAASLLVSGVSLVWILAVDRKTSRFIKDHWHVRPALREGVRRL +RRRPTGGAAAPHTRPHPVERLGESGSEDAAARGAR +>PROKKA_00903 +MSVSTPRPSGSTAHRPEYVGVGGLRADPQVAGADWWPILVGTLGSLLLVVGSYSVGWLAS +ASPINRWQWLIPWRTQETGVLAGTALLTLGCWVMFWAWLRLGQTIRPFGRGALRTVNLAT +VLWCLPQVVALPIFSRDIFAYVGQGRLMEAGQDPYVDTISSLSNWFQLGADATWADSETP +YGPIFLWIEQAVVAISGDMNPDLAIFLFRLVAVAGVALIMVFVPLLARRLGVNGARAQWI +SAANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQRPGQSVAWGVAGVVLVTL +SLGIKPITLVLLPFIGLLWAGPTARWPRRFAFWALTAGISFGLMALVGVLNGFGFGWVAV +MVGTGTGTVPWGPIGMLSLITVGASELLGQGADVQAVEGVYKTAGRALSVLIVLALMFLG +RQDRVMTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDNWQIKWVVFTVGYFLAFG +ASDQLFTWQFLNIADQVKAVSLIVSAVCLLWILVVDRRTSRFVKDHWHVRPAVRAGLARL +RGAPRPVEPGE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000820.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000820.fa new file mode 100644 index 0000000000000000000000000000000000000000..451c0c19c377d7731b7182a55df9a2eeb072fda3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000820.fa @@ -0,0 +1,50 @@ +>PROKKA_00960 +MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG +VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRAGHGVALA +AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV +TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS +SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN +VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDTLRRLPAVLVSAALAAGLIGTAFFPQVY +PLHRTIAGDMTMTQHARDLDHAVGLIPDGVCVEAADNAVPHLTARTHVGLHGDIGDELAT +WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSAGDVVVLHHPDRAVSPTCTTYLEH +R +>PROKKA_00673 +MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG +VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRTGHGVALA +AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV +TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS +SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN +VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDALRRLPAVLVSTALAAGLIGTAFFPQVY +PLHRTIVGDMTMTQHARDLDHAVALIPDGVCVEAADNAVPHLTARTYVGLHGDIGDELAT +WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSAGDVVVLHHPDRAVSPTCTTYLEH +R +>PROKKA_01928 +MTRREGLHLGILLALASALAIVHSFLRYGIYEAKGYDLGIFDQVVRQYALFNAPLSSVKG +VDFNILGDHFHPILALLAPFYWIWPDPRMLGIVMALALAAAAVPVYLFTRRRTGHAVSLV +AVAALMLSWPFQAMVNWDFHEVTLGVPLMAWLVWALDGQRPWLATVLAAVLLTVREDMGV +TLIAVALVMALRRFWPQAALVAVLGVLGYWFATSVVIPHYSPTGDFGYWQFQALGPDMGS +SILTILTRPWEAAAALVDHPLKAALWLLHLVPLLFLPLLSPLTLMALPILLSRLWNDRLN +VWAPVYQYDAILAPLLLMAALEGAVRLSDLLARRRRPRPAGTGAGSHASPPTRRLPAVVA +STALATGLVGTAFFPQVFPYHRTLTGDMTMTQHARDLDHAVSLIPDGVCVEAADNAVPHL +TARTYVGLHGDIGDELATWMIVDTSVAELGGWDPLTPDQALDRAERLGFETVWERGDVVV +LRHPDRAVSPTCTQYLQHR +>PROKKA_01879 +MPARRFPGQDRVRTWLHAPRPAVPAVAVTRRQGLHLGLVLLAFAALSITHSFLRFATYEA +KGYDLGIFDQVVRQYALFNAPLSSVKGVDFNILGDHFHPILALLAPTYWIWPDPRMLGII +MALALCAAAVAVYLTARRRVSHGWSLAAAGVVLFSWPFQAMVNWDFHEVTLGVPIMAWLV +WALDGERPWLALGLGTALLTVREDMGVTVCALAVVFALRRRWVQAGLALVLGLAGYWFAT +SVAIPHFSPTGGFGYWQFQALGPDMGSSLLTILTRPWEAVAALFDHPLKLALWLLHLVPL +LFLPVLSPLTLLALPILLSRLWNDRLNVWAPVYQYDAILAPILLLAALEAATGLAARFPR +VRRLPQVLLAWAGAVTLAGTAFLPQVFPFHRTLTGQMTTTQHARDLDQAVGMIPDGVCVE +AADNAVPHLTDRTHVGLHGDIGDDLATWMIVDTSVTELGGWDPLTPDQALERARRLGFER +VWSQGDVVVLHHPTRPVSATCTDYLRHR +>PROKKA_00906 +MTRREGVQLAALLVAAAALYVTHSFLRYATYEAKGYDLGIFDQVVRQYALFNAPLSSVKG +VDFHILGDHFHPILALLAPFYWVWPDPRMLGVVMALALAASAVPVYLFARRRTGHGVALA +AVAALLLSWPFQAMVNWDFHEVTLGVPILAWLVWALDGQRAWLATGLAALLLTVREDMGV +TLLAVALVMAIRRFWPQAAVTAVLGVLGYWFATSVVIPHYSPTGAFGYWQFTALGPDMRS +SVLFLLTQPWNAVAVLFDHPLKVALWLLHFVPLLFLPVLSPLTLMALPILLSRLFNDRLN +VWAPVYQYDAILAPLLLMAALEAAHRLAGRRDTLRRLPAVLVSTALAAGLIGTAFFPQVY +PLHRTIVGDMTMTQHARDLDHAVALIPDGVCVEAADNAVPHLTARTHVGLHGDIGDELAT +WMIVDTSVPELGGWDPLTPEQALARAERLGFERVWSARDVVVLHHPDRAVSPTCTTYLEH +R diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000821.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000821.fa new file mode 100644 index 0000000000000000000000000000000000000000..9ac03679f6065e616deae41383e8cea27a655325 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000821.fa @@ -0,0 +1,24 @@ +>PROKKA_00962 +MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDRETAEWVDAHTNWYSISAFGQ +LGSNTAQSVKKGNPVIVTGRLRVRDWSSGERSGTSVDVVADAVGLDLGFGSAAFQRSQRA +AVPRPESAPRDDDASGGRAGAVGDGFSAGLPDGFQGGDAPASPGPDESDAGAPGREPAAA +GVA +>PROKKA_00675 +MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDREAAEWVDAHTNWYSISAFGQ +LGSNTAQSVKKGNPVIVTGRLRVRDWSSGERSGTSVDVVADAVGLDLGFGSAAFQRSQRA +AVPRPESAPRDDASGGRAGAVGDGFNVGLPDGFQGGDAPASPGPGEPDAEAPDREPAAAG +VA +>PROKKA_01926 +MQDIITVRGFVATDPVTRTTASGATVAGFRLATTERRFDREAGAWVDAHTNWYSVSAFGQ +LGSNTAQSVRKGNPVIVTGRLRVRDWSTEERSGTTVDVVADAVGLDLAFGSAAFQRSQRA +ASARPEGADEQDGQGQAGAVASAGPAEADGTAAGTGDGYVTELPPALRGGDAPATPPPPS +SEEGDEADEADDDAHGVRALCGGVSAA +>PROKKA_01877 +MQDTVTIRGFVATDPTTRHTASGAAVVGFRLASTERRFDRDAGMWVDAHTNWYSVSAFGQ +LGSNTAQSVKKGNPVIVTGRLRVRDWSTEDRSGTSVDVVADAVGLDLAYGASAFMRNGRR +ADAVERADAPVDADAGASLDAAPADGFGLALPPAFTGGDAPASSAEDAHEAAGALAVA +>PROKKA_00908 +MQDLITVRGFVATDPATRHTASGAAVTGFRLATTERRFDRETAEWVDAHTNWYSISAFGQ +LGSNTAQSVKKGNPVIVTGRLRVRDWSSGDRSGTSVDVVADAVGLDLGFGSAAFQRSQRA +AVPRPESAPRDDASGGRAGAVGDGFSAGLPDGFQGGDAPASPGPDESDAGAPEREPAAAG +VA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000822.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000822.fa new file mode 100644 index 0000000000000000000000000000000000000000..f7bcf269096f87d555ebfa7d2609abf0978b376b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000822.fa @@ -0,0 +1,55 @@ +>PROKKA_00963 +MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG +EARLSPGYSVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMANPDADFDAL +MGEMGELQSAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP +DLLLLDEPTNHLDAESVLWLEQHLASYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLYPYE +GNYSTYLETKRARLEVQGKKDAKLAKRLAEELDWVRSNTKGRQAKSKARLARYEEMAAEA +EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIDGLSFSLPRNGIVGVIGPNGV +GKTTLFKTIVGLEPLDGGELKIGETVKISYVDQSRSNIDPEKSLWEVVSDGLDYIKVGNV +EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL +TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVD +RLGPEAARPHRMTHRKLTRD +>PROKKA_00676 +MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG +EARLSPGYSVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMANPDADFDAL +MEEMGELQSAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP +DLLLLDEPTNHLDAESVLWLEQHLASYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLYPYE +GNYSTYLETKRARLEVQGKKDAKLAKRLAEELDWVRSNTKGRQAKSKARLARYEEMAAEA +EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIDGLSFSLPRNGIVGVIGPNGV +GKTTLFKTIVGLEPLDGGELKIGETVKISYVDQSRSNIDPEKSLWEVVSDGLDYIKVGNV +EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL +TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVD +RLGPEAARPHRMTHRKLTRD +>PROKKA_01925 +MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG +EARLSPEYTVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMASPDADFDAL +MEEMGELQTAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP +DLLLLDEPTNHLDAESVLWLEQHLAAYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLHAYE +GNYSTYLETKRARLEVQGKKDAKLAKRLAEELDWVRSNTKGRQAKSKARLARYEEMAAEA +EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIEGLSFSLPRNGIVGVIGPNGV +GKSTLFKTIVGLEPLDGGELKIGETVKISYVDQSRANIDPEKSLWEVVSDGLDYIKVGQV +EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL +TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVE +RLGPEAARPHRVTHRKLTRD +>PROKKA_01876 +MSRFPPPPTSLERMAEFIYTMVKARKKVGDKLILDDVTMSFFPGAKIGMVGPNGAGKSTI +LKIMAGLDEPSNGEARLSPGYSVGILLQEPKLDEDKTVLENVQQGVGEIYGKIQRYNAIS +EEMADPDADFDALMEEMGQLQTEIDAADAWDLDSQLDQAMDALRCPPPEAQVSHLSGGEK +RRVALCALLLSKPDLLLLDEPTNHLDAESVLWLEQHLSSYPGAVVAVTHDRYFLDHVAGW +ICEVDRGRLYPYEGNYSTYLETKRQRLEIQGKKDAKLAKRLAEELDWVRSNAKGRQAKSK +ARLARYEEMAAEAEKTRKLDFEEIQIPPGPRLGNVVIEATNLQKGFDGRTLIDGLSFSLP +RNGIVGVIGPNGVGKTTLFKTIVGLEPLDGGDLKIGETVKISYVDQNRTNIDPEKSLWEV +VSDGLDYIKVGNVEMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLL +LDEPTNDLDVETLTSLENALLEFPGCAVVVSHDRWFLDRTATHMLAYEGTEENPANWYWY +EGNFESYEANKVERLGPEAARPHRVTHRKLTRD +>PROKKA_00909 +MAEFIYTMVKARKKVGDKLILDDVTMSFYPGAKIGMVGPNGAGKSTILKIMAGLDEPSNG +EARLSPGYSVGILMQEPKLDESKTVLENVQEGVGEIYGKIQRYNQISEEMANPDADFDAL +MEEMGELQSAIDAADAWDIDSQLEQAMDALRTPPGDEPVTNLSGGEKRRVALCKLLLEKP +DLLLLDEPTNHLDAESVLWLEQHLASYPGAVIAVTHDRYFLDHVAEWIAEVDRGRLYPYE +GNYSTYLETKRARLEVQGKKDAKLAKRLADELDWVRSNTKGRQAKSKARLARYEEMAAEA +EKTRKLDFEEIQIPPGPRLGTVVIEAKDLKKGFGDRVLIDGLSFSLPRNGIVGVIGPNGV +GKTTLFKTIVGLEPLDGGELKIGETVKISYVDQSRSNIDPEKSLWEVVSDGLDYIKVGNV +EMPSRAYVSAFGFKGPDQQKKAGVLSGGERNRLNLALTLKEGGNLLLLDEPTNDLDVETL +TSLENALLEFPGCAVVVSHDRWFLDRVATHMLAYEGTAEDPANWYWYEGNFESYEANKVD +RLGPEAARPHRMTHRKLTRD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000823.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000823.fa new file mode 100644 index 0000000000000000000000000000000000000000..888b27be4c9896c0e77d595a4a2be124ce8dd699 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000823.fa @@ -0,0 +1,35 @@ +>PROKKA_00964 +MLRGILELTPAAPDPVTGQVRFTGTTPRQTRGRVFGGQVLAQALAAASRTVPAARPAHSL +HGYFIRPGDALQPITFTVETLRDGRSFSVRRVLASQNEKAILALTCSFQEPAGSALDHQV +AMPEGVPRPEDLPTTADVLGGINHPVAQEWAWSRPFDIRHVTPAIYVDPAAETENRNMVW +MKTFTPLADDPALHLAALTYASDYTLLEPILRQHGVAWIQPGMSAASLDHAMWFHRPARV +DQWLLYVQDSPSAQGARGLGTGAVFTEDGTLVATVAQEGMVRLPEGAAARRARVRGAAQR +MAMRTVLRRSWRR +>PROKKA_00677 +MPQRHPRPRPGRAPARPASAPKDPTDVLRGILELTPAAPDPVTGQVRFTGTTPRQTHGRV +FGGQVLAQALAAASRTVPAARPAHSLHGYFIRPGDALQPITFTVETLRDGRSFSVRRVLA +SQNEKAILALTCSFQEPAGSALDHQVAMPEGVPRPEDLPTTADVLGGINHPVAQEWAWSR +PFDIRHVTPAIYVDPAAETENRNMVWMKTFTPLADDPALHLAALTYASDYTLLEPILRQH +GVAWIQPGMSAASLDHAMWFHRPARVDQWLLYVQDSPSAQGARGLGTGAVFTEDGTLVAT +VAQEGMVRLPEGAAARRARVRGAAQRMAMRTVLRRSWRR +>PROKKA_01923 +MPQRHPAPRPGRAPARPASAPKDPTDMLRGILELNRADADPLTGQPRFTGTTPRQAHGRV +FGGQVLAQALAAASRTISADRPVHSIHGYFIRPGDALQPITFTVETLRDGRSFSVRRVLA +TQNEKAILALTCSFQEPAEAALDHQVAMPEGVPAPEDLPSTADVLGRINHPIAQEWAWAR +PFDIRHVTPAIYVDPAPEAENRNMVWMKTFTPLADDPALHVAALTYASDYTLLEPVLRQH +GVAWIQPGMSVASLDHAMWFHRPARADEWLLYVQHSPSAQGARGLGTGSVFTRDGTLVAT +VAQEGMIRMPEGAAARRARLQGAAQRFALRTVLRRSWRR +>PROKKA_01872 +MSPKPPARPATAPQDPTEALRGLLDLTDAGPDPVTGEPRFEGRTPAQVGPRVFGGQVLGQ +ALAAASRTVPTARSAHSLHGYFIRPGDALQPITFTVETLRDGRSFSVRRVLASQNEKAIL +ALTCSFQEPTGSALDHQVAMPEGVPRPEDLPTTADVLGGINHPVAQEWAWSRPFDIRHVT +PAIYVDPAAETENRNMVWMKTFTPLADDPALHLAALTYASDYTLLEPILRQHGVAWIQPG +MSVASLDHAMWFHRPARVDEWLLYVQDSPTAQGARGLGRGHVFTRDGELVATVAQEGMIR +LPEGHAATAAKAKNVVQRAAMKTVLRRTWRG +>PROKKA_00910 +MLRGILELTPAAPDPVTGQVRFTGTTPRQTRGRVFGGQVLAQSLAAASRTVPGARPAHSL +HGYFIRPGDALQPITFTVETLRDGRSFSVRRVLASQNEKAILALTCSFQEPAGSALDHQV +AMPEGVPRPEDLPTTADVLGGINHPVAQEWAWARPFDIRHVTPALYVDPAPETENRNMVW +MKTFTPLADDPALHRAALTYASDYTLLEPILRQHGVAWIQPGMSVASLDHAMWFHRPARV +DQWLLYVQDSPSAQGARGLGTGAVFTEDGTLVATVAQEGMIRLPEGAAARRARVRGAAQR +MALRTVLRRSWRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000825.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000825.fa new file mode 100644 index 0000000000000000000000000000000000000000..03c12ea8e366b87cf69e9e5499acf89ad0a68cf2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000825.fa @@ -0,0 +1,80 @@ +>PROKKA_00967 +MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI +DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV +DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN +EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH +LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT +VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTGAWT +TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF +MVGVRAYIAKHAWQNTELPDLMTELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT +ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLIRTERFELDVAGEVTEVV +EAAARRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG +EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA +EAEDGSDNQLQFVKAFALHARTTAQLDRLSALVDGTRTVPGLDLTTDLRWELLTALVAAG +RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAVWDRVMAGELSNTEQRQALIGF +ARVHDAALIAPFADAYFEGVEAMWDSRSHEMAETAATLGYPTAQVTPEIADRATALSERL +ADTRAGLSRVLAEGRDETIRALAAREHATAHVHQVHAGA +>PROKKA_00680 +MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI +DFVAGQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV +DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEDSRRTLGVVAN +EENLQGVDAAVWEFTPTPRISSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH +LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT +VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT +TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF +MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT +ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA +EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG +EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA +EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAG +RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF +ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTSQVSRETADRATALSERL +ADTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA +>PROKKA_01920 +MSSSARLNITREEAAQRAAALTVDAYEVSLDLTRGPERFRTASTVTFAASEDAVGTHTWI +DFVASQAPEVTLNGERVAVEDYDGARLPIGPLAAQNTLVVEGLGDYSNTGEGLHRFVDPV +DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVEN +EDQLSGVDAAVWEFVPTPRISSYITALVAGPYAAVHSELTSADGRTIPLGVYCRASLVEH +LDADNVFELTRQGFEFFEAQYGHPYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT +VPEAMVERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTRYTGSWT +TFSSMEKNWAYRQDQLSSTHPIKAQIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF +MAGVRAYIAKHAWSNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGV +ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA +EAAGRRRPALILPNDDDLAYAKLRLDHASWEAASTRLKDVDSSLARTLLWGAAWDAVRDG +EASAAWFADLILANIGHEQDSSVVQTLLRQLATSLGQYLPEEQSTAARAAVADRLWGLVA +GAEDGSDSQLQFVKAFALHARTAAQLDRLAGVVDGTHTVPGLDLTTDLRWELLTALVAAG +RAGEAEIAAAEREDATATGALAAIQARAAVPTAEAKQAAWDRVMAGELSNTEQRQALIGF +ARAHEAALLAPFADAYFEGVEAMWDSRSHEMAETAAVLGYPAAQVSDETAQRATALSEKT +AGTRAGLSRVLAEGRDETVRALAAREHAAAHVHEVSASA +>PROKKA_01868 +MTTAAAMNITREEAAARAAALTVESYQVALDLTRGAERFGSTTTVTFSAADEAVGTQTWI +DFMATQAPEVTLNGQAVDVADFDGARLPIGPLAAENTLVVDGLADYTTTGEGLHRFVDPV +DDEVYLYSQFEVPDSRRMFAVFEQPDLKATFAFTVTAPAHWAVVSNQPEAAHRTLGVVET +PEAPEGVDAAVWEFTPTPRISSYITALVAGPYKSVHSELTSADGRTVPLGVYCRGSLFEH +LDADEVFDLTRRGFEFFEAQYGHPYPFDKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT +VTDAVRERRAITILHELAHMWFGDLVTMKWWNDLWLNESFAEFMSTLAAAENTRYEGAWT +TFSSMEKNWAYRQDQLSSTHPITAEIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF +MAGVRAYIEKNAWSNTELPDLMTELEAASGRDLSEWTRLWLETSGVNTLAVQVDADYAGT +ITSLRLHQSAPDGSPAAPGDDVLRPHRIAVGFYDLDEATGRLTRTERFELDAAGEVTEVA +EAAGRRRPALILPNDDDLAYAKIRLDDASWETAGARLADVDSSLARTLLWGAAWDTVRDG +EASAAWFVDLILTNIGREQDSTVIQTLLRQLATAISQYLPEERSAQVRADAANRLWMLVE +QAEPGSDAQLQFVKAFALHAREEGQLTALADVWDRSSELPGLDLTTDLRWELLTALVAAG +RAGETEIAAAETEDPTATGALAAALARAAVPTAEAKQTAWDQVVAGTLSNTTQRQVLLGF +QRAHDPALLAPFTDAFFGSIQDVWGSRSHEMAETVAVLGFPSSQVCQEVVDRATALSDEV +RGTNAGLARTLAESRDEMARALKARAAA +>PROKKA_00913 +MTTVAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI +DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV +DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN +EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH +LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT +VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT +TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF +MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT +ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA +EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG +EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA +EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAS +RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF +ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTAQVTREIADRATALSERL +AGTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000826.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000826.fa new file mode 100644 index 0000000000000000000000000000000000000000..2d9f5a417e6267c8b41b03ca58997e4e6fefe5d9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000826.fa @@ -0,0 +1,34 @@ +>PROKKA_00972 +MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG +GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP +PPAATVRLRLRAEHGWADLIGASRCRALTPAEAADVVAGLGPDPLSDDDPAPFYDLARRT +RRPIGVVLMDQAAVSGIGNIFRAEALFRVGIDPWRPARDVSASELESLWADNAALMREGV +RLGRIVTTRPEHRPGIPAEAAWPEHASYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT +CQS +>PROKKA_00685 +MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG +GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP +PPASTVRLRLRAEHGWADLIGANRCRALTRAEAADVVAGLGPDPLNDDDPAPFYDLARRT +RRPIGVVLMDQGAVSGIGNIFRAEALFRAGIDPWRPAREVSAPDLAFLWADNAALMREGV +RLGRIVTTRPEHRPGIPAEAAWPEHANYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT +CQS +>PROKKA_01918 +MPEGHSIHRLARQFTDVFGGWPIRASSPQGRFAEGAARMDGQVLEAARAHGKHFFADLAD +GHVLNVHLGMYGAWSFGGDERFDAASSIGAPRRIGEREVHADGAAAAEPDRDDDGWVLPP +PPVPTVRLRVRAEHGWADLIGASTCRLLTPAEAGDVVAKLGPDPLNDDDPAPFLDLAGRT +RRPIGAVLMDQAAVGGIGNIFRAEALFRAGLDPWRPSNAVPREVLRRLWSDNAELMREGV +RLGRIVTTRPEHRPGVPAEQAWPEHANYVYQRQGSPCLVCGQDAIVVEGMAARKLYRCTV +CQR +>PROKKA_01866 +MPEGHSIHRLARQVQDVFGGQALAASSPQGRFADGAALLDGRVLERAWAHGKHFFADIEG +GLTLNVHLGMYGAMTFGGDEAFAAASSIGAPRRIGETEDHGALAAAEPPPARPTVRLRLR +SAHGWADLIGAGTCRVLTPQELAEVTSKLGPDPLNDDDPAAFVARAARTGRPVGVVLMDQ +SMVGGIGNIYRAEVLFRAGLDPWTPARDVGADVLAALYADAQALMRDGVRLGRIVTTAPE +HRPGVAAEDAWPEHANYVYRRQGMPCRVCGQDAIVREEMAARNLFRCTDCQR +>PROKKA_00915 +MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG +GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP +PPAATVRLRLRAEHGWADLIGASRCRALTPAEAADVVAGLGPDPLSDDDPAPFYDLARRT +RRPIGVVLMDQAAVSGIGNIFRAEALFRAGIDPWRPAREVSASDLAFLWADNAALMREGV +RLGRIVTTRPEHRPGIPAESAWPEHANYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT +CQS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000828.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000828.fa new file mode 100644 index 0000000000000000000000000000000000000000..460ceb95006e5921c0eea0e604be20d150dc20d6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000828.fa @@ -0,0 +1,47 @@ +>PROKKA_00976 +MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRQGKIPARLIEQRFG +REIVVDQAVNEGLNTWFSAAIAEAEVTPISRPEVDVTATPDAENAEGPVAFTAEFDVRPT +IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG +EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV +KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP +VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD +QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK +AVDLTAFVTPGGQEALDAEAEGAEAEGADEAEEKPAEKAPAKKKSTAKKAPAEQADDAEA +AEQA +>PROKKA_00690 +MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRQGKIPARLIEQRFG +REVVVDQAVNEGLNTWFSAAIAEAELTPISRPEVDVTATPDAENAEGPVVFTAEFDVRPT +IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG +EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV +KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP +VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD +QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK +AVDLTAFVTPGGQEALDAEAEGADEAAEQA +>PROKKA_01914 +MVKSTAENLSPTRVKLNVEVPFEEVKPSLDKAYKDIANQVQIPGFRKGKIPARLIEQRFG +REAVVDQAVNEGLNTWFSAAISEAELTPISRPEVDVTATPDSENAEGPVVFTAEFDVRPT +IELPDYKGLKVTVEPAKATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTASVDG +EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFESTLNGGEHDGKTAVVKLELTAV +KERELPEADDEFAQLASEFDTIDELKEDLKKQAAEDAVNRQGVEARDKVLAELAKLVEVP +VPDGVITEQVEQHFSAGGHAAGDDHDTPEHRAELEANTREAFANEVILDEVAEAEEVTVD +QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEFAEVTDTDGK +AVDLKAFVTPGGQEALDAEAEGADPAEAEEKPAKKAAAKKPAAKKAPAKKKAEEKADDAE +ASEQA +>PROKKA_01861 +MVKSTAENLSPTRVKLTVEVPFEEVKPVLDKAYKDIAMQVQVPGFRQGKVPARLIEQRFG +REAVVDQAVNDGLNTWFGQALAEAEVTPISTPEVDVTATPAAAEGPVEFTAEFDVRPTIE +LPDYKGIEVTVEPAQATDEDEQAQLDALRSRFGTLKDVDRPAAKDDFVTMDLTATVGEEQ +VDQAQGLSYQVGAGTMLDGIDEALEGLSAGEDATFETTLNGGEHDGETATVKLVLQAVKE +RELPEADDDFAQLASEFDTIAELKEDLKKKAAEAAETRQGVEARDKVLAELGKLVEVPVP +ENVIAEQLEQHFSQGGHSAGDEHDTPEHREELEKNTREAFANEVILDEVAEAESVTVDQG +ELIEYIFATSAEYGMDPNQFAMMLDQAGQIPMIMGEVRRRKALAKVLEHAVVTDTDGNAV +DLTAFVTPAAAEEEKAEEKPAKKAPAKKAAAKKAAAKKPAAKKAEAEESEEA +>PROKKA_00919 +MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRKGKIPARLIEQRFG +REIVVDQAVNEGLNTWFSAAIAEAELTPISRPEVDVTATPDAENAEGPVAFTAEFDVRPT +IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG +EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV +KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP +VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD +QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK +AVDLTAFVTPGGQEALDAEAEGAEAEGADEAAEQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000829.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000829.fa new file mode 100644 index 0000000000000000000000000000000000000000..916c3b3189388c49369d8a48745fc92c9bec2929 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000829.fa @@ -0,0 +1,25 @@ +>PROKKA_00977 +MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDPEKDI +YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV +LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAQEA +LEYGFIDHIADRAASVTGGGGVRG +>PROKKA_00691 +MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDTEKDI +YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV +LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAQEA +LEYGFIDHIADRAASVTGGGGVRG +>PROKKA_01913 +MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDPEKDI +YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV +LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAKEA +LEYGFIDHIADRAASVTGGGGVQG +>PROKKA_01860 +MTDLTPRMTSVEPTQREDYLYNQLLKNRIIWLGSDVRDDNANAICSQLLLLSAEDPEKDI +YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGAPGKRYATPHARI +LMHQPSGGIGGTESDIRIQAQLILHMKQIMAELTAAQTGQSVETILEDNARDKWFTAQEA +LEYGFIDRIAQSAASVTGGGGVEG +>PROKKA_00920 +MTDITPSMRSVDPAQREDFLYTQLLKSRIVWLGEDVRDDNANAICSQLLLLSAEDTEKDI +YLYINSPGGSVTAGMAIYDTMQYIPNDVVTVATGLAASMGQFLLASGTKGKRYATPHARV +LMHQPSGGIGGTESDIRIQAQLILHMKQVMAELTAEQTGQSVETILEDNARDKWFTAQEA +LEYGFIDHIADRAASVTGGGGVRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000830.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000830.fa new file mode 100644 index 0000000000000000000000000000000000000000..1102fcc9b242eda4b37f2a4db43d879ad19b5bbe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000830.fa @@ -0,0 +1,25 @@ +>PROKKA_00978 +MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS +ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA +AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLQIHAQEINRMRVWMEETLASLTN +RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA +>PROKKA_00692 +MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS +ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA +AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHAQEINRMRVWMEETLASLTN +RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA +>PROKKA_01912 +MTQFPAGLPTGTPSMPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGSQVDDAS +ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA +AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIQAQEINRMRVWMEQTLASLTN +RTPEEVSRDIDRDKFLSAEQALEYGLVDEVLASRKITRPAG +>PROKKA_01859 +MTQFPAGLPVGTPSQAAPSARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGSQVDDAS +ADDIMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA +AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHANEINRMRVWMEQTLASLSN +RTPEDVSRDIDRDKFLSAEGAKEYGLVDEVLAPRKITRTGA +>PROKKA_00921 +MTQFPAGLPTGMPSLPTPDARYILPQFEERTPYGFKRQDPYAKLFEDRIVFLGAQVDDAS +ADDVMAQLLVLEAMDSERDITLYINSPGGSFTAMTAIYDTMQFIRPEVQTVCLGQAASAA +AVLLAAGAPGKRLALPNARVLIHQPAMQGDRGTATDLEIHAQEINRMRVWMEETLASLTN +RTPEEVSQDIDRDKFLSAEQALEYGLVDEVLASRKITRPSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000831.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000831.fa new file mode 100644 index 0000000000000000000000000000000000000000..c57ef370f3d61b529b4b462b8579a5e2d6e49771 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000831.fa @@ -0,0 +1,45 @@ +>PROKKA_00979 +MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV +LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE +VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA +DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK +HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE +DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD +ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP +AEVERRRRGRSA +>PROKKA_00693 +MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV +LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE +VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA +DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK +HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE +DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD +ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP +AEVERRRRGRSA +>PROKKA_01911 +MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAADSDEMV +LPTPQEIFDHLEGYVIGQEVAKRSLAVAVYNHYKRVRGPQGRGGDLADRLTERDDLADVE +VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA +DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK +HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGEVSYADVRPE +DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPNNALLKQYQKLFLMDGAELEFEPE +ALDAVVELAEARGTGARGLRSIMEDVLKPVMFELPSRTDVGTVVISGEAVRGEAEPVLIP +AEVERRRRGRSA +>PROKKA_01858 +MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAETDELE +LPTPREIFEHLERYVIGQEAAKRSLAVAVYNHYKRVRGPQGRGGDLAERLEERDDLADVE +VGKSNILMVGPTGSGKTYLAQTLARMLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA +DHDVKRAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK +HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGSGEVSYADVRPE +DLLKFGLIPEFIGRLPVITTVEDLTHDQLVRVLTEPKNALLKQYQKMFLMDGVELEFEPE +ALDAVVELAQARGTGARGLRSIMEDVLKPVMFELPSRTDVGTVVISGDVVTGQAEPLLIP +AEVERKRRRRTA +>PROKKA_00922 +MARIGESADLLKCSFCGKSQKQVRKLIAGPGVYICDECIELCNEIIEEELGEAAEADETV +LPTPQEIFDHLESFVIGQEAAKRSLAVAVYNHYKRVRGPQARGGDLADRLTERDDLADVE +VGKSNILMVGPTGSGKTYLAQTLARRLNVPFAVADATSLTEAGYVGEDVENILLKLIQAA +DYDVKKAEQGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRK +HPHQEFLQIDTSNVLFIVAGAFAGLDEIIGSRAGRKGIGFGAPLNHLGAGDVTYADVRPE +DLLKFGLIPEFIGRLPVITTVEDLTHEQLVRVLTEPRNALLKQYQKMFLMDGVELEFEQD +ALDAVVAQAEARGTGARGLRSIMENVLKPVMFELPSRSDVGTVVISGDVVRGEAEPTLIP +AEVERRRRGRSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000832.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000832.fa new file mode 100644 index 0000000000000000000000000000000000000000..8c1177382f10cc30be89428b015a4c152b92b15a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000832.fa @@ -0,0 +1,25 @@ +>PROKKA_00980 +MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL +ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD +ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD +GAVALADFPYFYEIKRARTTDPQFD +>PROKKA_00694 +MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL +ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD +ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD +GAVALADFPYFYEIKRARTTDPQFD +>PROKKA_01910 +MSENTQPVVDFYFDPTCPFAWITSRWILEVEKVRDIQVKFHQMSLYMLNEGRDLPEDYRR +STDRGLIPGRGTQHVGAEHPERLAEWYTALGTRIHNEGQKDYEAALTGAAVDLGLDPAPI +LAATETDAEDERLREKQRAAEELVGNDVGTPVVSFNGTAFFGPVLTRIPRGEEAGRIFDG +AVALAEYPYFYEIKRARTTDPQFD +>PROKKA_01857 +MSENTAPVVDFYFDPTCPFAWITSRWILEVEKVRDLSVTFHQMSLYMLNEGRELPEDYRR +HTDRGLMPGRATLHVGEHHPELLSDWYTAVGTRIHNEGNQDYEAVVTGAAAELGLDAAPI +LEATRTDAADDDLRAKQRAAEELVGNDVGTPVVSFDGTAFFGPVMTRIPRGEEAGEIFDA +AVRLAQFPYFYEIKRARTTDPQFD +>PROKKA_00923 +MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL +ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHDAD +ILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIFD +GAVALADFPYFYEIKRARTTDPQFD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000834.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000834.fa new file mode 100644 index 0000000000000000000000000000000000000000..d5b515f07309e0e1793e56dd339aa672ffa1db9e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000834.fa @@ -0,0 +1,80 @@ +>PROKKA_00982 +MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ +VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY +YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL +SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP +GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV +FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR +QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI +RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL +DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ +IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP +DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA +AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLTRLAATVEQATRAFEAYDYARALNVTE +QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW +RAGSVHTAAWPGAADEVASLSFAASAGDAEVLPTVAQVLGGIRKAKSEAKVKQRTEVRSA +VVTGPADWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPVDDD +>PROKKA_00696 +MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ +VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY +YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL +SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP +GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV +FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR +QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI +RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL +DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ +IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP +DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA +AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLTRLAATVEQATRAFEAYDYARALNVTE +QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW +RAGSVHTAAWPGAADEVAALSFAASAGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA +VVTGPTEWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPVEDD +>PROKKA_01907 +MAENTQGTDTPIDASTASTPAAGAVAVPDKPGLEGLEEKLTARWAQEGTYAFDPRTTREQ +VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMTGKNVFYPMGWDDNGLPTERRVQNY +YGVRCDPTKPYIEGYTPPAQPAKNQRDWDVVSRKNFIELCEELAVEDEKVFEDLFTRLGL +SVDWSMTYRTIDDVSRAVSQRAFLRNVAAGDAYLSEAPTMWDVTFRTAVAQAELEDREVP +GAYHRYPFTAADGTQVFIETTRPELLASCSALVAHPEDERYQPLFGTMVRSPLFDVEVEV +KAHELAKPDKGSGIAMVCTFGDLTDVTWWRELQLPTRTLIGRDGRFAAETPEWISSEAGR +AFYAESIAGKTVFSAKEAVVTALTEAGLMDGEPKKVQHAVNFYEKGDKPLEIVTSRQWYI +RNGGRDADRREQLIARGRELDWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYRL +DAEGEPVYDEPIVPEDAALPVDPVAETAPGFTEDQRDQPGGFTGDPDVLDTWATSSLTPQ +IVGRWSRDEEFFANVFPFDLRPQGHDIIRTWLFSTVVRADALNGSVPWTDTALSGWILDP +DRKKMSKSKGNVVVPTDILEEFGSDAVRYWASSARLGADTAYEVAQMKIGRRLAIKLLNA +AKFVLNLGATRDAVVRTPDDAARVTNALDASLLARLATTVEQATAAFDAYDYARALNVTE +SFFWQFTDDYVELIKDRAYGGHGEAEQASVVAALATTLDSLLRLLAPFQPFATEEVWSWW +RTGSVHRAPWPGLESEAAGLRAAAEGGDPQVLAVVAQVLGRVRKAKSEAKVKQRTQVRTA +TVRAAAAQLDALRGGLADLKGAGNVADVTLTEADGELEVTDIELAPAEEA +>PROKKA_01854 +MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ +VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY +YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL +SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP +GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV +FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR +QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI +RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL +DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ +IVGRWSRDDAFFSSVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP +DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA +AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLARLAVSVEQATRAFEAYDYARALNVTE +QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW +RAGSVHTAAWPGAADEVASLSFAASSGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA +VVTGPAEWLEKLRGGLADLKAAGNIADLSLTQGEAGEAAPLTVSDVQLAPVEDD +>PROKKA_00925 +MAENTQGTDTPIDASTPSTPAAGAVAVPDKPALEGLEEKLTARWADERTYAFDTQTTREQ +VYSIDTPPPTASGSLHVGHVFSYTQTDVLARYQRMNGKNVFYPMGWDDNGLPTERRVQNY +YGVRCDPAKPYVEGYRPPEKPAKNQRDWDVISRKNFIELCEELAVEDEKVFEDLFTRLGL +SVDWDMTYRTIDDVSRAVSQRAFLAGIASGDAYLAEAPTMWDVTFRTAVAQAELEDREVP +GAYHRYAFTAADGEQVFIETTRPELLASCSGLVAHPDDERYQHLFGTTVTSPLYGVEVEV +FPHPLAKPDKGSGIAMVCTFGDLNDVTWWRELQLPTRTLIGRDGRFAADTPEWITTDAGR +QAYADTVAGKTVFSAKQGVVDALTAAGLLDGEPKKIMHAVNFYEKGDKPLEVVTSRQWYI +RNGGRDADRRAELIERGRELSWHPEHMRHRYENWVEGLNGDWLVSRQRFFGVPIPVWYPL +DAEGEPDYENPILPADEQLPVDPAAEAAPGYSEDQRDVPGGFTGDPDVLDTWATSSLTPQ +IVGRWSRDEAFFNNVFPFDLRPQGHDIIRTWLFSTVVRAHALNGSVPWTDTALSGWILDP +DRKKMSKSKGNVVVPTDILDQFGSDAVRYWAASARLGADTAYEVAQMKIGRRLAIKLLNA +AKFVLNLGATQDAVIRTADDAAAVTNPLDASLLARLAATVEQATRAFEAYDYARALNVTE +QFFWAFTDDYVELVKDRAYGGHGEAEQASVVTTLATTLDALLRLLAPFQPFATEEVWSWW +RAGSVHTAAWPGAADEVAALSFAASGGDAEVLPTVAQVLGGVRKAKSEAKVKQRTEVRSA +VVTGPADWLEKLRGGLADLKAAGNIADLSLTQGEAGESAPLTVSDVQLAPAEDD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000841.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000841.fa new file mode 100644 index 0000000000000000000000000000000000000000..b44c5065676577404acb335144f6c3e4c24c061d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000841.fa @@ -0,0 +1,30 @@ +>PROKKA_00989 +MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLVARLEAPTAGVV +KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVAAGERRERAGELLRLVHLDDAADLR +PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHGELERVWRQTGRTVVFV +THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA +H +>PROKKA_00703 +MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNIIARLEAPTAGVV +KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVAAGERRERAGELLRLVHLDDAADLR +PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHGELERVWRQTGRTVVFV +THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA +H +>PROKKA_01900 +MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLIARLEAPTAGVV +KAPRQGAAFMFQDAALFPWLTARGNIELALRFAGVPAAERRGRAGELLRLVHLGDAADLR +PHQLSGGMRQRVALARALAQDRPLLLMDEPFGALDAITRDLLHVELERVWRQTGRTVVFV +THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA +H +>PROKKA_01847 +MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLIARLEAPTAGVV +KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVPAAGRRERAGELLRLVHLGDAADLR +PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHVELERVWRQTGRTVVFV +THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAAHHDAPAAAALTAAITARLGQEIRRHA +H +>PROKKA_00932 +MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLVARLEAPTAGVV +KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVAAGERRERAGELLRLVHLDDAADLR +PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHGELERVWRQTGRTVVFV +THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA +H diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000842.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000842.fa new file mode 100644 index 0000000000000000000000000000000000000000..c223dac7dfd86f17dd8f71e50695d6c8077c73d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000842.fa @@ -0,0 +1,35 @@ +>PROKKA_00990 +MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV +LLVAIWQAFAWLAGARGEPITGPGDVVGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV +GVGLGLLLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV +VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA +EIIAVGGPMGVGLGTLLHEGRAESDLAVVLCAVLAILAVGVLVELTAFGPAERRMLRRRG +LLEGSTR +>PROKKA_00704 +MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV +LLVAIWQAFAWLAGARGEPITGPGDVVGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV +GVGLGLVLGQVGVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV +VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA +EIIAVGGPMGVGLGTLLHEGRAASDLAVVLCAVLTILAVGVLVELAAFGPVERRMLRRRG +LLEGSTR +>PROKKA_01899 +MRTDTPTLDAPGRAPGAAADDELRELDSGLDALQAVDSARRTGLAGWDWSRVLLPVAAVV +LLVAIWQVAAWLAGARGEPITGPGDVLGAFGALWAQGLVQQAVATSVGRAVVGFALAVVA +GVGLGLLLAQVGVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVILTGAVPAV +VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA +EIIAVGAPMGVGLGTLLHQGRTESDLAVVLCAVLAILAVGVLVELTAFGPVERRMLRRQG +LLEGSTR +>PROKKA_01846 +MRTDTPTLDAPGRAPGAAADDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV +LLVAIWQVAAWLAAARGEPITGPGDVLRAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV +GVGLGLLLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV +VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA +EIIAVGGPMGVGLGTLLHQGRAESDLAVVLCAVLAILAVGVLVELTAFGPVERRMLRRQG +LLEGSTR +>PROKKA_00933 +MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV +LLVAIWQAFAWLAGARGEPITGPGDVLGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV +GVGLGLVLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV +VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA +EIIAVGGPMGVGLGTLLHEGRAASDLAVVLCAVLTILAVGVLVELAAFGPVERRMLRRRG +LLEGSTR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000843.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000843.fa new file mode 100644 index 0000000000000000000000000000000000000000..2f56f46374d081390e47eaa33e13f1b707466d67 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000843.fa @@ -0,0 +1,45 @@ +>PROKKA_00991 +MTASDLYPTSLRLLGRPVLIVGGGRVAGRRVGALLDAGALVSVVAPEPGEEVERLAAAGL +LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV +RAGDVTVAVNAGGDPRRARALKDAIALALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL +ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA +RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA +TGFTLVTGHEELAEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD +QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGIPAPISTLNPTSEGA +RA +>PROKKA_00705 +MTASDLYPTSLRLLGRPVLMVGGGRVAGRRMGALLDAGALVTVVAPEPGEEVERLAAAGL +LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV +RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL +ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA +RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA +TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD +QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGVPAPISTLNSTSEGA +RA +>PROKKA_01898 +MTASDLYPTSLRLLGRPVLMVGGGRVAGRRVGALLDAGALVTVVAPEPGEEVERLAAAGL +LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV +RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL +ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA +RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA +TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD +QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGARAAGVPAPILTLNPTSEGA +RA +>PROKKA_01845 +MTASDLYPTSLCLLGRPVLIVGGGRVAGRRVGALLDAGALVTVVAPEPGEEVERLAAAGL +LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVA +RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL +ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA +RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA +TGFTLVTGHEELAEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD +QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGVPAPISTLNPTSEGA +RA +>PROKKA_00934 +MTTSDLYPTSLRLLGRPVLVVGGGRVAGRRMGALLDAGALVTVVAPKPGEEVERLAAAGL +LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV +RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL +ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA +RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSVVSVPAAAGIPVTHRGVA +TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD +QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGIPAPILTLNPTSEGA +RA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000844.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000844.fa new file mode 100644 index 0000000000000000000000000000000000000000..f62bb241a45a8aa8b70f30f30e831b5b46279305 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000844.fa @@ -0,0 +1,100 @@ +>PROKKA_00994 +MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPTRNEDGSQNEFVFYDG +PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS +EIEAMGIDTFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL +HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP +DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL +AVDLVGAHARELGYADADAARAAVTETIPGARLGGLAYAPLFTDVFDAHRGETFTVNGRD +LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVMLSVDSGARFLPLFA +REDVGRGDLREIAGVQVFEANRTIIRALRALGRVAREASYEHSYPHCWRCRTPLIYRAVT +SWYVKVTQIKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD +HPDFPRQEVYGSLAEIEEAFGRLPRNAEGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV +EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD +RPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLIV +TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPEGYRAQERHTAEDPLDQYILAAA +GRMLREVKAGLDAYEVSDATDALRGFMDTLTNWYIRRSRERFFDEDTVAFDVLYTVLEAF +TRAAAPLMPLIAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS +ALRKGAGRRVRLPLPRLSVVVPDAAGLEGTYARIVADELNLKDVELTELSEEAIARYGIG +TELKLNFRELGKAFGRQVPLVKQAVDAGAYEETAEGLAVTLADGETVTLAPALYELRTVS +TGAPEGTAVGVLPGTAGFLVLDTEVSAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR +IEGPTAVVAALEAHRGLVAEETLTVDLELVDSGAADPRKDPADDAMKTVAVSVAKADA +>PROKKA_00708 +MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPAFNEDGSQNEFVFYDG +PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS +EIEAMGIDKFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL +HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP +DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL +AVDLVGAHARELGYADADAARAAVTETIPGARLGGLAYAPLFTDVFDAHRGETFTVNGRD +LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDSGARFLPLFA +REDVGRGDLREIAGVQVFEANRTIIRALRALGRVAREASYEHSYPHCWRCRTPLIYRAVT +SWYVKVTQIKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD +HPDFPRQEVYGSLAEIEEAFGRLPRNAQGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV +EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD +RPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLIV +TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPEGYRAQERHTAEDPLDQYILAAT +GRMLREVKTGLDAYEVSDATDALRGFMDTLTNWYIRRSRERFFDEDTVAFDVLYTVLEAF +TRAAAPLMPLIAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS +ALRKGAGRRVRLPLPRLSVVVPDAAGLEGTYARIVADELNLKDVELTELSEEAIARYGIG +TELKLNFRELGKAFGRQVPLVKQAVDAGAYEETAEGLAVTLADGETVTLAPALYELRTVS +TGAPEGTTVGVLPGTAGFLVLDTEVSAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR +IEGPTAVVAALEAHRGLVAEETLTVDLELVDSGAADPRKDPADDAMKTVAVTVAKADA +>PROKKA_01895 +MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPALNEDGSQNEFVFYDG +PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS +EIEAMGIDTFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL +HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP +DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL +AVDLVGAHATELGYADADAARAAVTETIPGARLGGLAYEPLFTDVFDAHADETFTVNGRD +LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDSGARFLPLFA +REDVGRGDLREIAGVQVFEANRTIVRALRGLGRVAREASYEHSYPHCWRCRTPLIYRAVT +SWYVKVTQVKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD +HPDYPLQEVYGSLAEIEEAFGRLPRNAEGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV +EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD +RPAFSNVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLVV +TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPDGYRAQERHTAEDPLDQYILAAT +GRMLREVKTGLDAYEVSDATDALRGFMDTLTNWYIRRSRQRFFDEDTAAMDVLYTALEAF +ARAAAPLMPLVAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS +ALRKGAGRRVRLPLPRLSVVVPDAEGLEGTYARIVADELNLKDVSLTELSDEAIARYGIG +TELKLNFRELGKVYGKQVPLVKKAVDAGSYEETADGLAVTLADGATVTLDPALYELRTVS +TGAPEGTAVGVLPGAAGFLVLDTEVSAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR +IDGPAAVVAALEAHRDLVAEETLTVELELVDSGEADPRKDPADDAMKTVAVTVAKADA +>PROKKA_01842 +MYPLASTDPAGATPASPLLPEIEQRILRYWDEDGTFQASIDARPAVNEDGSQNEFVFYDG +PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS +EIEAMGIDRFNDACRSSVLKYTEEWRRYVTRQARWVDFDNDYKTLTPDFMESVIWAFSEL +HRKGLTYRGFRVLPYCWHDETPLSNHELRMDDDVYKMRQDPSVTVSFPILGLPDDAALVP +AGGADAALADELAGVHVLAWTTTPWTLPTNAALAVGPEIEYAVVPAGPEGATVAAAERFL +LAVDLVGAHAKELGYADADAARAAVERTVLGARLGGLRYEPLFTDVFEAHAGETFPVGAR +TLTLDGVHRILVDDYVSTDDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDEGARFLPLF +AREGQGRGDLKDIAGVQVFEANRTIIRALRALGRIAREASYEHSYPHCWRCRTPLIYRAI +TSWYVSVTKVKDRMLELNEDITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWES +DHPDYPLQEVYGSLAELEEAFGRLPRNADGEVDLHRPWIDDLTRPHPDPEAAAAGATMRR +VEDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALF +DRPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGSDAMRWFLMASPILRGGNLI +VTEEGIREATRQVILPLWNAWHFFTLYANTAHDGGARPEGYRASERHTAEDPLDQYVLAA +CGTMLRQVKAALDAYEVSDAADALRAFMDTLTNWYIRRSRERFFAEDTAAMDVLSTVLEA +FTRAAAPLLPLVAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADALVARMDLVRSITSAG +SALRKGAKRRVRLPLAAMSVVVPDAAALEGTFTRIVADELNLKEVRLTELSEEAISRYGI +GTELKLNFRELGKHFGRQVPLIKKAVDAGAYAEGEQGLDVTLADGAVVTLAPELYELRTV +STGAPEGTAVGVLPGGGFLVLETAVSAELAAEGVARDVIRAVQAARKDAGLDVADRVRTR +IEGPAPVVAALESHRDLVAQETLTVELDLVDSGAADPRRDPADDAMKTVAVAVAKAQA +>PROKKA_00937 +MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPTRNEDGSQNEFVFYDG +PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS +EIEAMGIDTFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL +HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP +DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL +AVDLVGAHARELGYADADAARAAVTETIPGARLGGLAYAPLFTDVFDAHRGETFTVNGRD +LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDSGARFLPLFA +REDVGRGDLREIAGVQVFEANRTIIRALRALGRVAREASYEHSYPHCWRCRTPLIYRAVT +SWYVKVTQIKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD +HPDFPRQEVYGSLAEIEEAFGRLPRNAQGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV +EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD +RPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLIV +TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPDGYRAQERHTAEDPLDQYILAAT +GRMLREVKTGLDAYEVSDATDALRGFMDTLTNWYIRRSRERFFDEDTVAFDVLYTVLEAF +TRAAAPLMPLIAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS +ALRKGAGRRVRLPLPGLSVVVPDAAGLEGTYARIVADELNLKDVELTELSEEAIARYGIG +TELKLNFRELGKAFGRQVPLVKQAVDAGAYEETAEGLAVTLADGETVTLAPALYELRTVS +TGAPEGTTVGVLPGTAGFLVLDTQVTAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR +IEGPTAVVAALEAHRGLVAEETLTVDLELVDSGAADPRKDPADDAMKTVAVTVAKADA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000846.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000846.fa new file mode 100644 index 0000000000000000000000000000000000000000..b2fe25dca63a581863f7613ae3f25ed8f86aecb3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000846.fa @@ -0,0 +1,20 @@ +>PROKKA_00997 +MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP +FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN +LVHGSDSTLSAERELAIWFG +>PROKKA_00711 +MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP +FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN +LVHGSDSTLSAERELAIWFG +>PROKKA_01893 +MAQHIEETLVLVKPDGVERNLVGEILARIERKGYVIADLKMLTPTRSMLERHYEEHQGKP +FFDPLVDFMASGPVVAVRVTGNSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGESVQKN +LVHGSDSSLSAERELGIWFG +>PROKKA_01839 +MTHHPEETLVLVKPDGVERRLTGEIIARIERKGYEVVDLKMLVPTREMLAAHYEEHEGKP +FYEPLLEFMGSGPVVALRLAGDRVIEGFRSLAGATDPTVAAPGTIRGDYARDWGAGVQKN +LVHGSDSTLSAERELAIWFA +>PROKKA_00940 +MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP +FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN +LVHGSDSTLSAERELAIWFG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000850.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000850.fa new file mode 100644 index 0000000000000000000000000000000000000000..f6295b8c6e1f6eb726ed0a477b6c4df304e46d38 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000850.fa @@ -0,0 +1,15 @@ +>PROKKA_01001 +MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF +ALSAGSVAFGQRRGRKVVDIVPAAE +>PROKKA_00715 +MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF +ALSAGSVAFGQRRGRKVVDIVPAAE +>PROKKA_01889 +MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF +ALSAGSVAFGQRRGRKVVDIVPAAE +>PROKKA_01817 +MAHKKAGSSSKNGRDSNPQYLGVKRFGGQDVNAGEILIRQRGTKFHPGRNVGRGKDDTLF +ALSAGTVSFGQRRGRKVVDIVAAGE +>PROKKA_00944 +MAHKKAGSSSKNGRDSNPQYLGVKRYGGEDVNAGEIIVRQRGTKFHPGRNVGRGKDDTLF +ALSAGSVAFGQRRGRKVVDIVPAAE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000851.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000851.fa new file mode 100644 index 0000000000000000000000000000000000000000..e72012f1dc95670e9ebc1088aebee7438a6c92af --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000851.fa @@ -0,0 +1,50 @@ +>PROKKA_01002 +MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGDGGDGGDITLVVDSQTTTLLDY +HHAPHRSAENGQPGMGDHREGKNGQSLVLPVPDGTVVKDEQGNIVADLVGEGATYVAAAG +GQGGLGNAALASVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAALS +AARPKIADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL +VHVLDCGSLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLIALNKTDLP +DGAAMADMVRDELEGRGLRVFDISALAREGLDALKYAMAELVAEARSRVVEPAPAAPVEV +PRRHRRRGERAEFTIRREERNLEPLFRVRGEKPERWVAQTDFQNDEAIGYLADRLQRAGV +EDGLFKAGARPGDAVVIGDDVTGVVFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK +RAEQDARRAARAATRAEMEAERRSGLWTDTDDREG +>PROKKA_00716 +MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGDGGDGGDITLVVDSQTTTLLDY +HHAPHRSAENGQPGMGDHREGKNGQSLVLPVPDGTVVKDEQGNIVADLVGEGATYVAAAG +GQGGLGNAALASVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAALS +AARPKIADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL +VHVLDCGSLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLIALNKTDLP +DGAAMADMVRDELEGRGLRVFDISALAREGLDALKYAMAELVAEARSRVVEPAPAAPVEV +PRRHRRRGERAEFTIRREERNLEPLFRVRGEKPERWVAQTDFQNDEAIGYLADRLQRAGV +EDGLFKAGARPGDAVVIGDDVTGVVFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK +RAEQDARRAARAATRAEMEAERRSGLWTDTDDREG +>PROKKA_01888 +MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGNGGNGGDITLVVDSQTTTLLDY +HHAPHRSAENGQPGMGDHRAGKHGESLVIPVPDGTVVKDEQGNIVADLVGEGASYTAAAG +GQGGLGNAALSSVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAAIS +AARPKIADYPFTTLVPNLGVVQAGEVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL +VHVLDCGTLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLVALNKTDLP +DGAAMAEMVRAELEGRGLRVFDISALARDGLEALKYAMAGLVTEARERVPEPEPAAPVEV +PRRHRRKGEHAEFTVRREERNLEPLFRIRGEKPERWVAQTDFQNDEAVGYLADRLQRVGV +EDALFKAGATPGDAVVIGDDASGVLFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK +RAEQDQRRAARAATRAEMEAERRSGLWTETYDRED +>PROKKA_01816 +MAAFVDRVVLHLTAGNGGHGCVSVKREKFKPLGGPDGGNGGNGGDITLVVDHQTTTLLNY +HHAPHRSADNGQPGMGDHRAGRHGEDVVLPVPAGTVVKDADGNILADLVGEGASFVAAAG +GQGGLGNAALSSVKRKAPGFALLGLPGEERELILEVKSVADIALVGYPSAGKSSLIAAIS +AARPKVADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGKGLGLEFLRHVERCAAL +VHVLDCATLDPERDPLSDFEAIEAELEAYAVEPVFSQGGAGVVPLNERPRLVALNKTDLP +DGREMADLVRAQLEERGLRVFDISALAHDGLESLKFAMAGLVEEARAREPEPEEAPVVEV +PRRRRRGDQADFTVRREERNLEPLFRIRGDKPEKWVAQTDFQNDEAIGYLADRLQRAGVE +DALFKAGARPGDAVVIGDDATGVVFDWEPTLSAGAELLAGPRGSDLRLEERTRATRAEKR +AEQDQRRAARAATRAEMEAERRSGLWTGDPVEEEELD +>PROKKA_00945 +MAAFVDRVVLHLTAGNGGHGCVSVHREKFKPLGGPDGGDGGDGGDITLVVDSQTTTLLDY +HHAPHRSAENGQPGMGDHREGKNGQSLVLPVPDGTVVKDEQGNIVADLVGEGATYVAAAG +GQGGLGNAALASVKRKAPGFALLGLPGESRDLTLEIKTVADVALVGFPSAGKSSLIAALS +AARPKIADYPFTTLVPNLGVVQAGDVRFTVADVPGLIPGASEGRGLGLEFLRHVERCAAL +VHVLDCGSLESDRDPIADFEAIEAELEAYAVEPVFSQGGEGVVPLNERPRLIALNKTDLP +DGAAMADMVRDELEGRGLRVFDISALAREGLDALKYAMAELVAEARSRVVEPAPAAPVEV +PRRHRRRGERAEFTIRREERNLEPLFRVRGEKPERWVAQTDFQNDEAIGYLADRLQRAGV +EDGLFKAGARPGDAVVIGDDVTGVVFDWEPTLSAGAELLAGPRGTDLRLDERTRATRAEK +RAEQDARRAARAATRAEMEAERRSGLWTDTDDREG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000855.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000855.fa new file mode 100644 index 0000000000000000000000000000000000000000..1208058dfbacdb2e78199ecfa48ce6e3f2ffff0a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000855.fa @@ -0,0 +1,25 @@ +>PROKKA_01006 +MTVASRTPVPAPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP +WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF +FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC +RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS +>PROKKA_00720 +MTVASRTPVPAPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP +WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF +FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC +RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS +>PROKKA_01884 +MAVSSRTTASEPTAGGARRRRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVIFVPTGQP +WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGMTYTVDTLRDLRRLHPDAELF +FITGADAMGQILTWKDVDELWDLAHFVGVTRPGHDLTDMGLKDDVSLMEIPAMAISSTDC +RERVARGRPVWYLVPDGVVQYIAKHHLYVSDEETP +>PROKKA_01812 +MTSATRDPAPPPTSRRHRLGVMGGTFDPIHHGHLVAASEVAAEFGLDEVVFVPTGQPWQK +SDTRVSPAEHRYLMTVIATASNPRFTVSRVDIERPGNTYTVDTLRDIRAKRPDSELFFIT +GADALNQILTWKDVEELWDLAHFVGVTRPGYQLEDYGLSEDISLMEIPAMAISSTDCRRR +VERGRPVWYLVPDGVVQYINKHHLYTPEGDRP +>PROKKA_00949 +MTVASRTPVTAPTAGRARRPRLGIMGGTFDPIHHGHLVAASEVAAEFELDEVVFVPTGQP +WQKSDRQVSPAEDRYLMTVVATASNPRFTVSRVDIDRPGVTYTVDTLRDLRRLHPDAELF +FITGADAMGQILTWKDVDELWGLAHFVGVTRPGHDLSDMGLGADVSLMEIPAMAISSTDC +RERVRRGRPVWYLVPDGVVQYIAKHHLYVSEEETS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000856.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000856.fa new file mode 100644 index 0000000000000000000000000000000000000000..9af4c1c3b620b34cf8ad655a0b6aaaf9d810d3d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000856.fa @@ -0,0 +1,20 @@ +>PROKKA_01007 +MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE +EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP +EESTRPDAATQDDGASASHAS +>PROKKA_00721 +MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE +EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP +EESTRPDAATQDDGASASHAS +>PROKKA_01883 +MTVPQTTLDALTVAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE +EALLKEEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLA +EEHTRPDAAGEGAADDAAPHAS +>PROKKA_01810 +MTVPQTTLDALQVAAAAAAEKVATHIVAVDVAERLGLTDAFLIASGASERQVNAIVDGIE +EDLLVKEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDSPAIDLGLP +EEATRPDDALDAAAQD +>PROKKA_00950 +MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE +EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP +EESTRPDAAAQDDDASASHAS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000857.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000857.fa new file mode 100644 index 0000000000000000000000000000000000000000..7c14b4209e1ba67c87bf4f93eb337010cdb505e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000857.fa @@ -0,0 +1,24 @@ +>PROKKA_01008 +MRLILLRHGETDWNVLDRYQGHTDIELNAEGERQARRAAGGPVGDLVEDAEELVAVCSPL +ARARRTAEIVLEARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAEPALD +AGPVGGETLRGGGERALRALRGHVPPHWADTPRDGGAHTLLVVAHGALIRAATGLLLRHE +GEAFAAMERIGNARAAVLQGAFTADTGAEGWGDWTLEGYGI +>PROKKA_00722 +MRLILLRHGETDWNVLDRYQGHTDIELNAEGERQARRAAGGPVGDLVEDAEELVAVCSPL +ARARRTAEIVLEARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAEPALD +AGPVGGETLRGGGERALRALRGHVPPHWADTPRDGGAHTLLVVAHGALIRAATGLLLRHE +GEAFAAMERIGNARAAVLQGAFTADTGAEGWGDWTLEGYGI +>PROKKA_01882 +MRLILLRHGETDWNAGDRYQGRTDVELNAVGERQARRAAVGPVGDLLEEAAELVAVASPL +ARARRTAEILLEARVGAADLALDEQLMELHGGDWEGLGLTAIAQRWPEEHRSWRAVPALD +AGPVGGETLRAAGERALGALRGRVPQHWAVYAAAL +>PROKKA_01809 +MRLVLLRHGETDWNALDRYQGRTDVPLNALGERQAAAAAAGPVGELLRSAEDLVAVSSPL +IRARRTAEIVLEDAVGAVELAVDSRLVELGGGEWEGLDFTEIGARWPHEHHAWRTVPDLD +GGPVGGEVLRAGGERVLAAAAAHVPEDWSTPRPARVPDARTLLIVAHGAVIRAAAGLALA +LEGADFAHLARVSNARAVILDGTFAGEGPGAWSLLGYDV +>PROKKA_00951 +MRLILLRHGETDWNALDRYQGHTDIELNAEGERQARRAAGGPVGDLLEDAEELVAVCSPL +ARARRTAEIVLQARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAVPALD +AGPVGGETLRGGGERALRALRGHVPPHWADTPRDGGAHTLLAVAHGALIRAATGLLLRHE +GEAFAAMERIGNARAAVLQGAFAPATEGWGDWTLEGYGI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000858.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000858.fa new file mode 100644 index 0000000000000000000000000000000000000000..7ff51185ef33123c574104a042a32ff36ca0bd3c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000858.fa @@ -0,0 +1,49 @@ +>PROKKA_01014 +MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG +ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP +VAEKTDREMDRLIAKIDELTAEIDAAAPWEHPRAAELDKISFRHWLEQQSDDPEAIDNVS +IYIASGMLTKPSHTFSLLQALLMSASAGSFRNLVDEDFILDKRVEGGMQSVSLAMAAELG +DDVVLGQPVRTLRWAEPDPSTADEKNGVAADVRNGVAHDGAAGDVVALTDDYEVHARYAV +LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL +VQEIYDNTNRGENLAGGAPGKEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL +GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY +QHVDGAIRMGEAAALAIAEREATDAGQPTG +>PROKKA_00728 +MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG +ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP +VAEKTDREMDRLIAKIDELTAEIDAAAPWEHPRAAELDKISFRHWLEQQSDDPEAIDNVS +IYIASGMLTKPSHTFSLLQALLMSASAGSFRNLVDEDFILDKRVEGGMQSVSLAMAAELG +DDVVLGQPVRTLRWAEPDPSTADEKNGVAADVRNGVAHDGAAGDVVALTDDYEVHARYAV +LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL +VQEIYDNTNRGENPAGGAPGEEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL +GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY +QHVDGAIRMGEAAALAIAEREATDAGQPTG +>PROKKA_01874 +MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG +ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP +VAEKTDREMDRLIGNIDELTAEIDAAAPWEHPRAAELDTISFRHWLEQESDDPEAIDNVS +IYIASGMLTKPSHTFSMLQALLMAASAGSFRNLVDEDFILDQRVEGGMQSVSLAMAAELG +DDVVLGQPVRTLRWTEPDPSTADEKNGVAADVRNGVAHDGDAGDVVALTDDYEVHARYAV +LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL +VQEIYDNTNRGENLAGGAPGEEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL +GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY +QHVDGAIRMGEAAALAIAEREATDAGQPTG +>PROKKA_01230 +METPSDVIVVGAGLAGLVAARTLAEAGLSVRVLEREAEVGGRQRTRTVDGFVLDRGFQLV +NPAYPELPRHADVDALGLRPFGAGVRVRTRRGLALLADPRREPRLAARTLRDGVRHGLLD +ARELAALSRWAAPALAAPRVAKHRMDAPLIEAWDRAGVRGPLRDAVLEPFLRGVLADPDL +TTSSRFTELLVRMFVLGTPGVPARGVAALPEQLAARVRAAGTRVTTGASVTAVRPAADGV +VVDVAGGAPLHARAAVLAVGPEAFTGLLPEAATDRLPVPSRGLTTWWFRAPSAPARERFL +AVDGTGSGPLVHTAVMTAAAPGLSPDGTPLVEATALLDPSAPAVTDAQARAHAARIWGVD +ASDWDLLARDDVPHALPVQAAPLRLRAEARVAERVYAAGDHRDTASIQGALVSGRRVAER +LLHELPR +>PROKKA_00957 +MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG +ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP +VAEKTDREMDRLIAKIDELTAEIDAAAPWEHPRAAELDKISFRHWLEQQSDDPEAIDNVS +IYIASGMLTKPSHTFSLLQALLMSASAGSFRNLVDEDFILDKRVEGGMQSVSLAMAAELG +DDVVLGQPVRTLRWAEPDPSTADEKNGVAADVRNGVAHDGAAGDVVALTDDYEVHARYAV +LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL +VQEIYDNTNRGENLAGGAPGKEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL +GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY +QHVDGAIRMGEAAALAIAEREATDAGQPTG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000861.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000861.fa new file mode 100644 index 0000000000000000000000000000000000000000..b555162b5caa574f15e6c34c9ec4f9dd38ae99fc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000861.fa @@ -0,0 +1,33 @@ +>PROKKA_01019 +MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRLELTTA +GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP +RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD +DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALTEANSGRVAQALVAAGAGVAVVTEDP +AFGLTPVRVIAQGRTLTVRLHAAWRGDHFAAETLEAIARRLQAFVRDRYAEPGDDAPGRG +RSA +>PROKKA_00733 +MDEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRFELTTA +GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP +RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD +DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP +AFGLTPVRVIAQGRTLAVRLHAAWREDHFAAETLQALARRLQAFVRDRYAEPGDDAPR +>PROKKA_01868 +MEERLLRAFVTVAEAGTVSAAAQRLDLVQSALSRQLQRLQRELRLPLFARVGSRLELTTA +GEAFLPVARRVLAAHRQAEQAARTLASGSLAEVAIAAPGTTLIDVVLPFVATLDEDDPRP +RVAETQLDDSLQDAVARHDLVVMPMAPGPTVQALHLIDLPVWAYVAPGHPWADRADVALE +ELVDVRVVAPSRSFMARRVLDGAVAVAGLTAPELSEANSGRVAQALVATGAGVAVVTEDP +AFGLVPLRVLLDGRALSVGLHAAWRADHFAAATLARIAASLQDFVRTRYPQPGPADDIPV +TTRASPLSAAPSQ +>PROKKA_01760 +MDSIAAGGRALDLDHLLDPALLRTFVAVVDEGTVTAAARELGLGQSALTRHLQRLQRDLG +LALFAPEGARLRITPAGQAWLPVARSLLAAHAHARQAARILAAGRLTELSLGAPGTTLID +VVIPFLTVLGEGDPAVRVTETQLDDSLQDSVARLDLVVLPSTPPDDVAALPLQSMPVWAC +VAPGHPWADRDELDAAELAGARLVLPSRSFKARRVFDAALEVAGAAPRQVVEANSGRVAQ +ALAANGTAVAVVTEDPAFGLRPLPIRAGGRRLEVHLHAVWRRDHFAAEEIAGVAAQLRVF +VRRRYDVAEAQDDADGSLSRAVSVD +>PROKKA_00963 +MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVGGRLELTTA +GEAFLPVAREVLVAHRRAEQAARTLASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP +RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD +DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP +AFGLTPVRVIAQGRALAVRLHAAWREDHFATATLEKIARRLQAFVRDRYAEPGDDAPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000866.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000866.fa new file mode 100644 index 0000000000000000000000000000000000000000..1c5d17f901d3b18851514659cbb5a22a0d07e417 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000866.fa @@ -0,0 +1,15 @@ +>PROKKA_01024 +MTVTVYTKPACVQCNATYRALDKKGIAYEVVDMSQDPAALERVRALGFMQAPVVVTETDS +WSGFRPDKIAELAESAAASVA +>PROKKA_00739 +MTVTVYTKPACVQCNATYRALDKKGIAYEVVDMSQDPAALERVRALGFMQAPVVVTETDS +WSGFRPDKIAELAESAAASVA +>PROKKA_01861 +MTVTVYTKPACVQCNATYRALDKKGIAYEIVDMSQDPAALERVRGLGFMQAPVVVTETDS +WSGFRPDKIAELAEAAAASVA +>PROKKA_01751 +MTVTVYTKPACVQCNATYRALDKKGIAYETVDMSQDPEALDRVRALGFMQAPVVITDTDS +WSGFRPDKIAELAESAATQVA +>PROKKA_00968 +MTVTVYTKPACVQCNATYRALDKKGIAYEVVDMSQDPAALERVRALGFMQAPVVVTETDS +WSGFRPDKIAELAESAAASVA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000868.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000868.fa new file mode 100644 index 0000000000000000000000000000000000000000..cbd5a2591e867a1e1e7e49b10b32b49d1f4e12a8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000868.fa @@ -0,0 +1,70 @@ +>PROKKA_01026 +MTTTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV +NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY +TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK +KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS +GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG +VVIPDITFQLAKKNEDMYLFSPYDVERVYGVPFSEISVTEKYYEMVDDARIKKTKINARE +FFQTIAEIQFESGYPYVVFEDTVNAANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHV +GQDISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNAASHAIGL +GQMNLHGYLARERVHYGSEEGIDFTNMYFYAVLFHALRASNRIAIETGQRFGGFEDSKYA +SGEFFDKYTDQEWAPATERVAELFAEAGIALPTQDDWRELKASVMEHGIFNRNLQAVPPT +GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT +YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWTKGIKTIYYIRLRQLALEGTEVEGC +VSCML +>PROKKA_00741 +MTTTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV +NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY +TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK +KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS +GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG +VVIPDITFQLAKKNEDMYLFSPYDVERVYGVPFSEISVTEKYYEMVDDARIKKTKINARE +FFQTIAEIQFESGYPYVVFEDTVNAANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHV +GQDISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNAASHAIGL +GQMNLHGYLARERVHYGSEEGIDFTNMYFYAVLFHALRASNRIAIETGQRFGGFEDSKYA +SGEFFDKYTDQEWAPATERVAELFAEAGIALPTQDDWRELKASVMEHGIFNRNLQAVPPT +GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT +YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWTKGIKTIYYIRLRQLALEGTEVEGC +VSCML +>PROKKA_01859 +MTLTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV +NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY +TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK +KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS +GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG +VVIPDITFQLAKKNEDMYLFSPYDVQRVYGVPFSEISVTEKYYEMVDDARIKKTKINARE +FFQTLAEIQFESGYPYIVFEDTVNRANPIKGRITMSNLCSEILQVSEASEYNEDLTYSHI +GQDISCNLGSMNIAKTMDSPDFGQSVETAIRALTAVSVMSDIQSVPSIAKGNSASHAIGL +GQMNLHGYLARERVHYGSEEGVDFTNMYFYAVLFHALRASNKIAIETGERFGGFEDSKYA +SGEFFDKYTDQEWTPATERVAGLFSDAGITLPTQEDWRELKASVMEHGIFNRNLQAVPPT +GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT +YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWRKGIKTIYYIRLRQLALEGTEVEGC +VSCML +>PROKKA_01749 +MTVTEADLIQQAKHMPEAWQDLGYHELNAMLNLYGSDGKIQFEADHAAARQYFLQHVNTN +TVFFHDLEEKLEYLQEKHYYEPETFAQYAPEFVKATFDRAYKAKFRFPTFLGAFKFYTSY +ALKTFDGKRYLERYEDRVAVVALHLAAGDEALATHLVDEMISGRFQPATPTFLNAGKAQR +GELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNVREQGAPIKHIQNQSSGVL +PVMKLLEDSFSYANQLGARQGAGAVYLHAHHPDIHRFLDTKRENADEKIRIKTLSLGVVI +PDITFELAKRNEDMYLFSPYDVERVYGKAFSEISVTEKYYEMVDDARIKKTKINAREFFQ +TLAEIQFESGYPYIVFEDTVNRANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHVGQD +ISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNSASHAIGLGQM +NLHGYLAREHVHYGSEEGVDFTNIYFYTVLFHALRASNLIAQETGQKFGGFEDSTYASGE +FFAKYTEQEWTPATARVAELFETAGIDIPTQDDWRELQAKVMEHGLFNRNLQAVPPTGSI +SYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDTYAA +ATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWTKGIKTIYYIRLRQLALEGTEVEGCVSC +ML +>PROKKA_00970 +MTTTAPTEADLIRQAKNMPAEWQNLGYHELNAMLNLYGADGRIQFEADHAAARQYFLQHV +NTNTVFFHDLEEKLDYLQKNDYYETETFEQYPFEFIRGLFDRAYKAKFRFPTFLGAFKFY +TSYALKTFDGKRYLERYEDRVAVVALHLARGDQELATHLVDEMIAGRFQPATPTFLNSGK +KQRGELVSCFLLRIEDNMESIARGINSALQLSKRGGGVALSLTNIREHGAPIKQIENQSS +GVIPVMKLLEDSFSYANQLGARQGAGAVYLNAHHPDIHRFLDTKRENADEKIRIKTLSLG +VVIPDITFQLAKKNEDMYLFSPYDVERVYGVPFSEISVTEKYYEMVDDARIKKTKISARE +FFQTIAEIQFESGYPYVVFEDTVNAANPIKGRITMSNLCSEILQVSEASEYNEDLSYAHV +GQDISCNLGSMNIAKTMDSPDFGRSVETAIRALTAVSVMSDIQSVPSIAKGNAASHAIGL +GQMNLHGYLARERVHYGSEEGIDFTNMYFYAVLFHALRASNRIAIETGQRFGGFEDSKYA +SGEFFDKYTDQEWAPATERVAELFAEAGIALPTQDDWRELKASVMEYGIFNRNLQAVPPT +GSISYINNSTSSIHPVASKIEIRKEGKLGRVYYPAPYLTNENLEYYEDAYEIGYEKIIDT +YAAATQHVDQGLSLTLFFKDTATTRDLNRAQIYAWRKGIKTIYYIRLRQLALEGTEVEGC +VSCML diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000870.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000870.fa new file mode 100644 index 0000000000000000000000000000000000000000..d600a0cee6d26cfa5c0b2f480b43544cd67e0c1a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000870.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000872.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000872.fa new file mode 100644 index 0000000000000000000000000000000000000000..e7c7a69014c68a677068e6665f44419fbd740e6c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000872.fa @@ -0,0 +1,25 @@ +>PROKKA_01035 +MTILPASPPPSVILLGGASGSGKSYLARQHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT +PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPDGVIVAE +GIFAERMPAALDRAEVHYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD +AARRAAAMAAGFTPRRKREIIADLT +>PROKKA_00748 +MILLGGASGSGKSYLARQHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRTPYGEIDWDHPG +TWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAEGIFAERMPAAL +DRAGVRYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTDAARRAAAVAAG +FTPRRKREIIADLTA +>PROKKA_01849 +MILLGGASGSGKSYLARRHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRTPYGEIDWDHPG +TWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAEGIFAERMPAAL +DRAGVGYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTDAARRAAAVAAG +FTPRRKREIIADLTA +>PROKKA_01739 +MTILPASPPPSVILLGGASGSGKSYLARRHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT +PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAE +GIFAERMPAALDRAGVGYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD +AARRAAAVAAGFTPRRKREIIADLTA +>PROKKA_00977 +MTILPASPPPSVILLGGASGSGKSYLARRHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT +PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAE +GIFAERMPAALDRAGVRYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD +AARRAAAVAAGFTPRRKREIIADLTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000874.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000874.fa new file mode 100644 index 0000000000000000000000000000000000000000..d009a5350a24df5a7a80185d8a6148406d3313d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000874.fa @@ -0,0 +1,40 @@ +>PROKKA_01037 +MSQKVRGVVAMAKDAPVTVETIVIPDPGPGEAVVDIKTCGVCHTDLHYQQGGIGDEYPYL +LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE +DGTELSPALGIGAFADKTLVHAKQCTQVDGVDTPKEQAAVGLLGCGIMAGIGAAINTGEV +KLGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV +EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELKLPLLEVFGR +GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS +VVVL +>PROKKA_00750 +MSQKVRGVVAMAKDAPVTVETIVIPDPGPGEAVVDIKTCGVCHTDLHYQQGGIGDEYPYL +LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE +DGTELSPALGIGAFADKTLVHAKQCTQVDGVDTPKEQAAVGLLGCGIMAGIGAAINTGEV +KLGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV +EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELKLPLPEVFGR +GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS +VVVL +>PROKKA_01847 +MPQKVRGVVARAKDAPVTLETIVIPDPGPGEAVVDVKTCGVCHTDLHYVQGGIGDEYPYL +LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE +DGTELSPALGIGAFADKTLVHAKQCTKVDGVDTPEEQAAVGLLGCGIMAGIGAAINTGEV +KRGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAQELGATHTVNSKDEDPV +EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELKLPLLEVFGR +GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETVALDEVNEAFETMKAGDVLRS +VVVL +>PROKKA_01737 +MSQKVRGVVAMAKDAPVSIETIVIPDPGPGEAVVDIKTCGVCHTDLHYVQGGIGDDYPYL +LGHEATGVVSAIGEGVTHVEVGDTVILNWRAVCGECRACKKGEPKYCFNTHNASQKMTLE +DGTELSPALGIGAFAEKTLVHAKQCTKVDGVDSTEEQAAVGLLGCGIMAGIGAAINTGEV +KRGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV +EAIRALTGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELQLPLLEVFGR +GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS +VVVL +>PROKKA_00979 +MSQKVRGVVAMAKDAPVTVETIVIPDPGPGEAVVDIKTCGVCHTDLHYQQGGIGDEYPYL +LGHEATGVVSAIGEGVDHVKVGDTVILNWRAVCGECRACRKGEPKYCFNTHNATQKMTLE +DGTELSPALGIGAFADKTLVHAKQCTKVDGVDTPEEQAAVGLLGCGIMAGIGAAINTGEV +KRGESVAVIGCGGVGVAAIAGAKLAGATTIIAVDIDAKKLAKAEELGATHTVNSKDEDPV +EAIRAATGGFGADVVIEAVGRPETYEQAFYARDLAGRVVLVGVPTPGMELQLPLLEVFGR +GGALKSSWYGDCLPERDFPMLVDQYRLGRLPLDEFVTETIALDEVNEAFETMKSGDVLRS +VVVL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000875.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000875.fa new file mode 100644 index 0000000000000000000000000000000000000000..52dbcc0c2d8b733b6560aca4bd2d12208e7d672e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000875.fa @@ -0,0 +1,30 @@ +>PROKKA_01039 +MCGRYVMARATSDLVALGDAEANEDLVLRQSWNVAPTAEVPILVAHADDVGAGGTRGGDG +GAGVTRRIHVARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYY +EWKTPEPGAKGPDGRIAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAWV +LSTTILTMAAPDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVGQ +VCAGAYDVAAGWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL +>PROKKA_00752 +MCGRYVMARATSDLVALGDAEANEDLVLRQSWNVAPTAEVPILVAHADDVGAGGARGGDG +GAGVTRRIHVARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYY +EWKAPEPGAKGPDGRAAKKQSYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAWV +LSTTILTMAAPDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVGQ +VCAGAYDVAAGWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL +>PROKKA_01846 +MCGRYVMARAAGDLVALGGGELPDERLELRRSWNVAPTSDVPILLEREADGAVRRELHVA +RWGLVPSWAKELAVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYYEWKAPAPGAKG +PDGKAAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAEAAGRDPWVLSTTILTMAAP +DADDEDEVLGSLGDLHDRLPVPLDAETMDAWLTPGRLGSAEEADALVGQVCAGAYDVAAG +WVLRPVGTAVGNVRNDGPELIQAEEPAQGTLL +>PROKKA_01736 +MARAAGDLVALGGGLLPEEGLELRPNWNVAPTADVPILLEREDAGVVRRELHVARWGLVP +TWAKELSVGSRAFNARSETVTSKPTFRSAVRARRCAVPVEGYYEWKAPEPGSTGPDGKAA +VKQPFYVHPAGGGDGEGPVIWFAGLYEWWKDAGAEARGDDPWVLSTTILTMPSPADDEPG +VLGELADLHDRLPMPMGPAAMDSWLSPDKLGSADEAAALVDEMTAQAYDVARGWELRPVG +RAVGNVRNNGPELIAPPAEVQDALL +>PROKKA_00981 +MCGRYVMARATSDLVALGDAETNEELVLRQSWNVAPTAEVPILVAHADDVGAGVTRRIHV +ARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYYEWKTPEPGAK +GPDGRAAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAWVLSTTILTMAA +PDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVGQVCAGAYDVAA +GWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000877.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000877.fa new file mode 100644 index 0000000000000000000000000000000000000000..40562bacd883952202d4732c86443a45310843e4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000877.fa @@ -0,0 +1,15 @@ +>PROKKA_01044 +MGVLTQSVAVECGADGTPQGLRWNGRDYVLAERPVRWFERRRWWAEEVRAEKGRGAGLVD +HEMWRLQVRLARAGAAPLQTLDVAHHLDSGRWRLVRVHEHAQDLRRSA +>PROKKA_00757 +MGVLTQSVAVECGADGTPQGLRWNGRDYVLAERPMRWFERRRWWAEEVRAEKGRGAGLVD +HEMWRLQVRLARAGAAPLQTLDVAHHLDSGRWRLVRVHEHAQDLRRSA +>PROKKA_01845 +MGVLTQSVAVERAADGTPQGLRWNGRDYVLAEPPVRWFERRRWWAEEVRAEKGRGAGLVD +HEIWRLQVRLARAGSAPVQTVDVAHHLDSGRWRLVRVHEQARDLRRSA +>PROKKA_01732 +MGTFTQSVAVERDRQGAPARLHWEGREYVLAERPLRWFERRRWWAEEARAEKGRGPGLVD +HEIWRLQVRLARAGNAPVRTVDLAHHLDSGRWRLVRVHAPAQERTLSRTA +>PROKKA_00985 +MGVLTQSVAVECGADGTPQGLRWNGRDYVLAERPVRWFERRRWWAEEVRAKKGRGAGLVD +HEMWRLQVRLARAGAAPLQTLDVAHHLDSGRWRLVRVHEHAQDLRRSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000878.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000878.fa new file mode 100644 index 0000000000000000000000000000000000000000..ba7d3795e727224ee855118f69a02086eb1fe638 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000878.fa @@ -0,0 +1,109 @@ +>PROKKA_01045 +MSQAAAAGRTAAPFAHLHVASAFSAHHGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK +HVGACLRHGITPIVGVDLAVRWSEDGDAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG +GAAGGSPWASVAELAAAAAGRVPTAANRDNPSTPELFVLLGPDSDVGRHLARRRYAAGLA +ALHRWKAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD +GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVAFAADDRPAPLLEATR +RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRERTRTGLLARYPHLHTGGGLPG +TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL +RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYHAVVERFGAERTTLMSMQN +AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE +GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDATLLHRTPVQPSGMGLPMSQFDKHDMD +PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQI +ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV +LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSLD +VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM +VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEIDDGAPGRWGIRLPLTSLSGLSEAETD +RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR +GTAPGRTAPRSRSARPRQVEGQLALDLPDTELTALAPLFPDPGPAARVRTELELTALDVT +AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT +GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGDRAVSVQAVRAWDLHRPETLPDPDY +LDATRQQWRDWLAADRRAAAARRSSRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR +PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR +>PROKKA_00758 +MSRAAAAGRTVAPFAHLHVASAFSAHYGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK +HVGACLRHGITPIVGVDLAVRWSEDEDAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG +GAAGGSPWASVAELAAAAAGRVPTAANRDNPPTPELFVLLGPDSDVGRHLARRRYAAGLA +ALHRWKAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD +GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVASAADDRPAPLLEATR +RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRARTRTGLLARYPHLHTGGGLPG +TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL +RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYHAVVERFGAERTTLMSMQN +AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE +GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDAALLHRTPVQPSGMGLPMSQFDKHDMD +PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDDATYAMIRTTHTLGCFQI +ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV +LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSPE +VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM +VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEVDDGAPGRWGIRLPLTSLSGLSEAETD +RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR +GTAPGRTAPRSRSARPRQVEGQMALDLPDTELTALAPLFPDPAPAARVRTELELTALDVT +AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT +GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGGRAVSVQAVRAWDLHRPQTLPDPDY +LDATRQQWRDWLAADRRAAAARRSGRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR +PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR +>PROKKA_01844 +MGLRRRARRRRGSSRVPTAANRDNPPTPELFVLVGPDADVGRHLARRRSAAGLAALRRWK +EALPAGSLHADVVTHLSTPGRRLDAGHAVKALRTARRAGVPAVLTNAVRYAGPDGAATAD +VLDAVRALSSLDAVHDLQPNGQGWLKPTAAMHRVAHEVASAADERAAPLLEATRRLAEAC +VLDPEADLGWGVPRVPEAAVIGIEGPPERVLRERTYAGLAARYPRLHAGGRLTSAAEARD +LEARAEHELGIITRLGFSSYFLTVAAVVDLIEGMGVRVAARGSGASSLVNHALRISNVDP +VANGLIMERFLSDARSTLPDIDIDVESARRHEIYRAVFERFGAERTTLMSMQNAYRARGA +VRDAGLALGMPEPEVDGIAKQLWRFSASSFREALERMPELGGLSRRIESGRAEGSRQLDL +LVDLTERLDRLPRHISMHPCGVILGDAALLHRTPVQPSGMGLPMSQFDKHDMDPMGFLKL +DILGVRMQSAIAYTLAEVERTTGERVDLEQVPLDDPATYAMIRTTHTLGCFQIESPGQRE +LVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPARYPHPDLRPVLAETHGV +TVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHRVEEAFRAGALARGYSLDVIDEVWA +TLAAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPEAFMAAILEHDPGMYPARLMVAEARRM +GIPVLPVDVNASSRHVRVEWVPWHPELDGPPAEDAGAGGGEPGDVVARPHAEGGAEADLA +EGAGRGPGRWGIRLPLTGLSGLSEAETERLDAGRPYRSLADVRDRARPTARNLERLAQLG +ALDCLLPAGGASRTDLVHHLELQHSATRGSGPGRAAARSRSARPRQVDGQLALDLPDTEL +AALTPLFPDPSVAARVRTELELTALDVTAHLMDSHAPYLDALGVTRAADLLGLRTQSRVL +VAGVRVATQTPPMRSGKRVVFLSVDDGTGCVDASFFTEAQHASGEMLFSARLLLIEGTVR +RTGPRAVSVQAVRAWDLHRPESLPDPDYLDATRRQWREWLAADRRAAAARRRGQEDAGAP +RLPDIPHHGTGGWPVKVALGGAGAPSPSSDARAPAGRGVSAGAGPGAAGQGAAARVGAGG +VPADRRPIPVPHPDTWELLPTPER +>PROKKA_01731 +MSAFPHLHVASAFSAHHGVSWPADLAAAAAAADMDLLACTDRDGLYGTVKHVGACLARRI +TPIVGVDLAVRWDEDEPAGRVVVLARGGCHGTGYRALCRLVSAAHARTAGGAAGGAPWVL +VAEVAAAAAGPIPTGANPGNPPTPELFVLVGPDSDVGRHLARRRTAAGLAALRRWRAALP +AGATRAEVVSHLSAPGRRLDTGHAVKMLRTARTARVAPILTNAVRYAAPDGAATADVLDA +VRALSALDAVHDLQPNGQGWLKPTAAMEALAAEIAHAADEHPAALLESTRALAEACALDP +ETDLGWGRPRVPEASVVGTVGDPRQVLRERTRAGLAARYPHLHTGAGLPGTTQAARDLQD +RAEQELGIIDRLGFAGYFLTVAAVVELIEGMGVRVAARGSGASSLVNHALRISHVDPMAN +GLIMERFLSDARSTLPDIDIDVESARRHEIYRAVVDRFGAERTTLMSMQNAYRARGAVRD +AGLVLGMEEDEVDGIAKQLWRFSASSFRDALDRMPELSSLAARIDAGRAAGRHQLDLLVD +LTERLDRLPRHISMHPCGVILSDAALLDRTPVQPSGMGLPMSQFDKHDMDPMGFLKLDIL +GVRMQSAIAYTLQEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQIESPGQRELIG +KLEPREFNDLTVDISLFRPGPMQSDMVRPFLEHRHGWAPAHYPHPHLEPVLAETHGVTVF +HEQVLRTLDVMTGCGLARADELRRLVGGPEEHRVETFFRTAALENGYSLDVVDEVWHTLH +AFGSFGFCKAHGAAFAVPTYHSAWLKTHHPEAFMAAVLEHDPGMYPARLMVAEARRMGIP +VLPVDVNASTRHVHVEWVPSHPEVDGADPTTDPATGAPGRWGIRLPLTSLSGLSAAEVDR +LDAGRPYATLADVRDRARPTARSLERLAQLGALDSLLPAGGASRTDLVHHLELQHSATRS +TDPGRTARRSRTARPRQVDGQLALDVPDTELTALTPLFPEPSRDAAVRTELDLTALDVTA +HLMDSHAPYLDALGVTRAEDLLSLRSQSRVLVAGVRVATQTPPMRSGKRVVFVSVDDGTG +CVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGARAVSVQGVRAWDLHRPERLPDPDYL +DATREQWRAWLAADRRAAAARRRGETPVGAVPDIPHHSTGGWPVKVRADVAVGRERAAVE +RPAPAPSSRPIPVPHPETWELLPTPES +>PROKKA_00986 +MSQAAAAGRTAAPFAHLHVASAFSAHYGVSWPEDLVAAAAAADMDLLACTDRDGLYGMAK +HVGACLRHGITPIVGVDLAVRWSEDENAGRVVVLARGGCHGSGYRSLCELVSAAHARTTG +GAAGGSPWASVAELAAAAAGRVPTAANRDNPPTPELFVLLGPDSDVGRHLARRRYAAGLA +ALRRWEAALPAGSPHADVVTHLSAPGRRLDTGHAVKTLRAARQARIPAVLTNAVRYAAPD +GAATADVLDAVRALSSLDALHDLQPNGQGWLKSTAAMHRIAHEVAFAADDRPAPLLEATR +RLAEACALDPETDLGWGVPRVPEAAVIGIDGPPEHVLRERTRTGLLARYPHLHTGGGLPG +TSQAARDLQDRAEHELGIITRLGFSSYFLTVAAVVDLIEGMGIRVAARGSGASSLVNHAL +RISHVDPMANGLIMERFLSTDRSTLPDIDIDVESARRHEIYRAVVDRFGAERTTLMSMQN +AYRARGAVRDAGLALGMPEPEVDAIAKQLWRFSASNFREALQRMPELGGLSRRIESGRAE +GDRQLDLLVDLTERLDRLPRHISMHPCGVILGDATLLHRTPVQPSGMGLPMSQFDKHDMD +PMGFLKLDILGVRMQSAIAYTIAEVERTTGERIDLEQVPLDDPATYAMIRTTHTLGCFQI +ESPGQRELVGKLAPREFNDLTVDISLFRPGPMQSDMVRPFLEQRHGWAPAHYPHPDLRPV +LAETHGVTVFHEQVLRTMDVMTGCGLARADEHRRLLGGPQEHLVEEAFRTGALARGYSLE +VIDEVWATLSAFGSFGFCKAHGAAFAVPTYHSAWLKTHHPAAFMAAILEHDPGMYPARLM +VAEARRMGIPVLPVDVNASSRHVHVEWVPAHPEIDDGAPGRWGIRLPLTSLSGLSEAETD +RLDAGRPYRSLADVRDRARPTARNLERLAQLGALDCLLPPGGASRTDLVHHLELQHSTTR +GTAPGRTAPRSRSARPRQVEGQLALDLPDTELTALAPLFPDPGPAARVRTELELTALDVT +AHLMDSHAPYLDALGVTRAKDLLGLRTQSRVLVAGVRVATQTPPMRSGKRVVFLSVDDGT +GCVDASFFTEAQHASGEMLFSARLLLIEGTVRRTGDRAVSVQAVRAWDLHRPETLPDPDY +LDATRQQWRDWLAADRRAAAARRSGRAGTGAQPLPDIPHHGTGGWPVKVRTDVGPAGGAR +PGRTAPDRPAPEHTPIPVPHPETWELLPTPDR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000880.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000880.fa new file mode 100644 index 0000000000000000000000000000000000000000..5325af273c58d3265de789f196895eab7e1ed1a7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000880.fa @@ -0,0 +1,25 @@ +>PROKKA_01047 +MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT +CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA +ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN +MSQTLGETRQILADVWDRAAQDHAARQAANARAAGEHPRPGAGGPA +>PROKKA_00760 +MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT +CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA +ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN +MSQTLGETRQILADVWDRAARDHAARQAANARAAGEHPRPGAGGPA +>PROKKA_01841 +MTRPEASDADARDLARASADASATDGFALPGAPDAFERFWNAHRMAYVTQGSDQVKDEHT +CPFCAAPQRSDEASLIVHRGRAAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTAEEAAEMA +ELTQTAMLALGHATRAAGYNLGMNQGSVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN +MSQTLGETREILAGVWDEAAADHARLQEANARAAAERAGRRDEDRP +>PROKKA_01729 +MTTTPHDDAAEVSADGAPAGERPYGDPAADAAALDGFELPGTPDAFDRLWNPHRLAYIQK +GPEQVKDEDTCPFCAAPGRDDASALIVHRGATCFVILNLFPYNPGHLLICPYRHIPMYTD +ATAEETAELADLAQTAMIAFELATRPKGYNLGMNQGVAGGAGIAAHLHQHVVPRWTGDGN +FLPIIAQTKNMSQTLGQTREILADVWPQALAEHAERRARNAAAAAQAPRADA +>PROKKA_00988 +MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT +CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA +ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN +MSQTLGETRQILAGVWDRAARDHAARRAANARAAAEHPRPGAGDPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000882.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000882.fa new file mode 100644 index 0000000000000000000000000000000000000000..0460be27544a6f1f3228df655a6d9a4d50006afb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000882.fa @@ -0,0 +1,20 @@ +>PROKKA_01049 +MGQRKKDRGARHGAATPAVAALEAAGVPYRLHTFDVALDAGGERFGVQVARALSVPADRL +FKTLMVADPDGALAACVVPVSGQLDLRAAAAVLGVKRLALADLAVVERRTGYVRGGVSPL +GQRRPHPVVLDSSALDAELMYVSGGQRGLDVEIAPADLVRVTGAVVAEIAAG +>PROKKA_00762 +MGQRKKDRGARHGAATPAVAALEAAGVPYRLHTFDVALDAGGERFGVQVARALSVPADRL +FKTLMVADPDGALAACVVPVSGQLDLRAAAAVLGVKRLALADLAVVERRTGYVRGGVSPL +GQRRPHPVVLDSSALDAELMYVSGGQRGLDVEIAPADLVQVTGAVVAEIAAD +>PROKKA_01837 +MAKTGRGRGRAHGAATPAVAALETAGVPYTLHTFEVDLDAGGERFGVQVARAMGVPPERM +FKTLMVAAPDGGLAACVVPVSGQLDLRAAAAVLGVKRLALADLALVERRTGYVRGGVSPL +GQRHRHPVLLDSSALDAPVMYVSGGQRGLDLELAPADLAAATDAVVAPIAAR +>PROKKA_01727 +MGRRKAADAAHGAATPAIRALVDAGVPHRVLSFDVHLDAVGERFGVQAAKALGVPPERTF +KTLMVALPDGSLAACCVPVSGQLDLRAAATALGVKKVAMADLAVAERRTGYVRGGISPLG +QRQRHPVVVDSSALDGDVLYVSAGQRGRDLELAPADLVAVTDAVVAPIAAR +>PROKKA_00990 +MGQRKKDRSARHGAATPAVAALEAAGVPYRLHTFDVALDAGGERFGVQVARALSVPADRL +FKTLMVADPDGALAACVVPVSGQLDLRAAAAVLGVKRLALADLAVVERRTGYVRGGVSPL +GQRRPHPVVLDSSALDAELMYVSGGQRGLDVEIAPADLVQVTGAVVAEIAAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000883.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000883.fa new file mode 100644 index 0000000000000000000000000000000000000000..74a45f6a4c640cdd18075e5eb355cf9efbbb7933 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000883.fa @@ -0,0 +1,20 @@ +>PROKKA_01050 +MTENHAVPAALAEIIDDFAGVPDPEKLELLLEFSDELPALPERYDGHEAEMEQVVECQTP +LFLAVELEGEPGPQAPVRLFITAPPEAPTTRGFASVLTQGLDGLSALEVVDVPEDIPTRL +GLAKALTPLRLRGMSAMLGRIKRNVREQAGIA +>PROKKA_00763 +MTENHAVPAALAEIIDDFAGVPDPEKLELLLEFSDELPALPERYDGHEAEMEQVVECQTP +LFLAVELEGEPGPQAPVRLFITAPPEAPTTRGFASVLTQGLDGLSALEVVDVPEDIPTRL +GLAKALTPLRLRGMSAMLGRIKRNVREQAGIA +>PROKKA_01836 +MTQNHAVPAALAEIVDDFAGVPDAEKLELLLEFADELPALPERYDGHEAEMEQVVECQSP +LFLAVELEGEDEPGPESVVRLFITAPPEAPTTRGFASVLSQGLDGLTARQIVDVPEDIPS +RLGLAKALTPLRLRGMSAMLGRIKRNVREQTGVA +>PROKKA_01726 +MTDTAVPANLAEIVDDFAGVPDPQKLELLLEFSDELPALPERYAGHEDEMEQVVECQSPL +FLAVELEDGATGDDAVVRLFISSPPEAPTTRGFASVLTQGLDGCTARQVLAVPEDIPSRL +GLQKALTPLRLRGMSAMLGRIKRNVREQAGIA +>PROKKA_00991 +MTENHAVPAALAEIIDDFAGVPDPEKLELLLEFSDELPALPERYDGHEAEMEQVVECQTP +LFLAVELEGEPGPQAPVRLFITAPPEAPTTRGFASVLTQGLDGLSALEVLDVPEDIPTRL +GLAKALTPLRLRGMSAMLGRIKRNVREQAGIA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000885.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000885.fa new file mode 100644 index 0000000000000000000000000000000000000000..7d0351964765ec0b588f3ba79a3f36abadd408be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000885.fa @@ -0,0 +1,35 @@ +>PROKKA_01052 +MAQIVHLADRSPQVTPDQLLAGFHPSYRFGTVSFDTYIPDPAHPTQAQAVERLRRFAADL +GRGGSGGGFLGGLFGGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVEYT +NLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSNTLPG +SLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAAVEATAQENFPD +AGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFADRLYD +KDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK +>PROKKA_00765 +MAQIVHLADRSPQVTPDQLLAGFHPSYRFGTVSFDTYIPDPAHPSQAQAVERLRRFAADL +GRGGSGGGFLGGLFGGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVEYT +NLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSNTLPG +SLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAVVEATAQENFPD +AGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFADRLYD +KDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK +>PROKKA_01834 +MAQIVHLADRSPQVTPDQLLAGFHPSYRFGEVSFDTYIPDPAHPSQAQAVERLRRFAAAL +GRGSGSGGGFLSGLFGGGRKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVE +YTNLVGALSFRKAVDVLKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVHLVATSNTL +PGSLGEGRFAAQDFQREIQVLAEQFEVIRVDGEDYRHRGLSAAPDPLPDDQVVSTAEANF +PDSGVLAVDDFDALTAMLSRVHPSRYRELVKDVDVIALHDVKTITEQATALRFVVFADRL +YDKDVPVVASGVPFDDLFTQEMMHGGYMKKYFRTVSRMTALVREGQLGIAEEK +>PROKKA_01724 +MPQTVHLADRSPQVSADQLLAGLHPSYRFGEVSFDSYIPDPAHPSQAQAVERLRRFAASL +GGPRGGSGGGGFLGGLFGGGRKRGPEPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTF +VEYTNLVGALSFRQAVDVLKGYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSN +TLPGSLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPEPLADDAVESTAQA +NFPHADVVSVDDFAALTAMLSRVHPSRYRELVKDVDVAAFHDVQTITEQATALRFVVFAD +RLYDKDVPVVASGVPFDQLFTSEMMHGGYMKKYFRTVSRMTALVREGQTGETVEK +>PROKKA_00993 +MAQIVHLADRSPQVTPDQLLSGFHPSYRFGTVSFDTYIPDPAHPSQAQAVERLRRFAADL +GRGGSGGGFLGGLFGGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVEYT +NLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSNTLPG +SLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAAVEATAQENFPD +AGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFADRLYD +KDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000888.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000888.fa new file mode 100644 index 0000000000000000000000000000000000000000..3bf558416153b2e9692a848f13700791cecc7738 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000888.fa @@ -0,0 +1,40 @@ +>PROKKA_01059 +MTAPTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPVGRRRVLTPSPVAVVAEE +ARLPVLKADRLRGPEGADALQAIRALEADVAVVVAYGALVPAEALQTPRHGWLNLHFSAL +PAYRGAAPVQRAVMAGETEIAADVFQLEEGLDTGPVFARLTRPVAADETAGTVLTDLAER +GGPLVIDVLDRLADGTATATPQRGEPTHAPKLTAADGLVDPARPAAEVAARINGVTPEPG +AWGWLTADDGAAPARFKLDGVAPVRAGDDGWPSVLDAAVPGQILVAAKAAWLRTAGGAVR +LSRVQPAGRKLMPAADWARGAAAGAALLAGEALAHHEEQARRDAAARAAARQAARNATEQ +DEEARA +>PROKKA_00778 +MTAPTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPVGRRRVLTPSPVAVVAEE +ARLPVLKADRLRGPEGADALQAIRALEADVAVVVAYGALVPAEALQTPRHGWLNLHFSAL +PAYRGAAPVQRAVMAGETEIAADVFQLEEGLDTGPVFARLTRPVAADETAGAVLTDLAER +GGPLVIDVLDRLADGTATATPQRGEPTHAPKLTAADGLVDPARPAAEVAARINGVTPEPG +AWGWLTADDGAAPARFKIDGVAPVRPGDDGWPTALDAAAPGQILVAAKAAWLRTTDGAVR +LSRVQPAGRKLMPAADWARGAAPGAALLAGEALAHHEDQARQEAAARAAARQAARNATAQ +DEEARA +>PROKKA_01827 +MTATTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPIGRRRVLTPSPVAVVAEE +AGVPVVKADRLRGPAGEPALEAVRALEPDVAVVVAYGALVPAEALALPRHGWLNLHFSAL +PAYRGAAPVQRAVMAGEPEIAADVFQLEEGLDTGPVHARLTRAVAPDETAGQILADLAER +GGPLVLELLGRIADGTAAPRPQEGEPSHAPKLTAADGLVDPARPAAEVAARINGVTPEPG +AWGWLTVGEGGEPARFKLDGVAPATPADADWPADLDAAPPGALRTAGRAAWLRTADGAVR +LGRVQPAGKKLMPAADWARGAADGAALLAGEALAAHTARLGQEAAARAARREAARETEAH +A +>PROKKA_01717 +MSIPETALSPDAGSAPARSLRVLFAGTPEAAVPVLRALVGSAHEVAGVLTRTDAPVGRKR +VLTPSAVARAAAESAPDVPVLKADRLRGPEAAEVLEAIRALEADVAVVVAYGALVPAEAL +TIPAHGWLNLHFSHLPAYRGAAPVQRALMDGVERTGADVFQLEEGLDTGPVFARIGRDVA +PEDTAGDLLAALAEDGGPLVLEVLDALAAGEARSVPQTGEPTHAPKLTAADGLVDAAAGT +REVAARINGTTPEPGAWGWLVPAGEADAAPARLKLGGVVPTHPGEDGWPEAAEAAAPGAI +VAAGGTAWLRTAGGAVRLDQVQPAGKKPMSAADWARGLTAPVRLLAGDELAAHLAALDAE +AARRAAQQAAARAAQAGEGA +>PROKKA_01006 +MTAPTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPVGRRRVLTPSPVAVVAEE +AGLPVLKADRLRGPEGADALQAIRVLEADVAVVVAYGALVPVEALQIPRHGWLNLHFSAL +PAYRGAAPVQRAVMAGETEIAADVFQLEEGLDTGPVFARLTRPVAADETAGAVLTDLAER +GGPLVIDVLDRLADGTATATPQRGEPTHAPKLTAADGLVDPARPAAEVAARINGVTPEPG +AWGWLTADDGAAPARFKLDGVAPVSAGDDGWPSALDAAAPGQILVAAKAAWLRTAGGAVR +LSRVQPAGRKLMPAADWARGAAAGAALLAGEALAHHEEQARREAAARAAAREAARNATAQ +DEEARA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000889.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000889.fa new file mode 100644 index 0000000000000000000000000000000000000000..d2ef198005f9ef50db3f40976c5a631aa4fc15b5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000889.fa @@ -0,0 +1,55 @@ +>PROKKA_01060 +MSREGQAGQGRGERGARGERGRAPRPDPQDRRDAQGRTRNRGRSGAGRKYSAQAPSQRSR +TADPARRVAFGVVRSVHAEDAYANLVLPARIRQARLDRRDAGFATELAYGTLRGLGLYDA +ILTRCVDRPLEQIDPPVLDALRLGAHQLLGMRVPAHAALDATVSLVRAEIGAGASGFVNA +VLRRVAERPLEEWLADVAPADGGDAALAVRASHPVWIVRALRQALAAHRGTRHIADRDAE +LAALLEADNAPPVVNLVALPVAGGAEALAAALDDGAEPGPLAPDSALHSGGDAGRLPGVR +EGVLRVQDAGSQLTARALAQAPVPAAEGRAERWLDLCAGPGGKAALLAALAAERGATLVA +NEVAPHRADLVRQALAAVPADAWTVRTGDGRTIADAPEAAPAFDRVLVDAPCTGLGALRR +RPESRWRRTPADLAELTGLQAELLDAAVSVLAPGGVLAYVTCSPHVAETVVQVQDLVRRH +PELELLDARTALDTVALDDLRLDEAEPAGAPKPGDVVARTAQLWPHRHGTDAMFLALLRA +PGA +>PROKKA_00779 +MSRERQPGQGRGERGARGERGRAPRPDAQDRRDAQGRTRNRGRSGAGRKYSAQAPSQRSR +TADPARRVAFGVVRSVHAEDAYANLVLPARIRQARLDRRDAGFATELAYGTLRGLGLYDA +ILTRCVDRPLEKIDPPVLDALRLGAHQLLGMRVPAHAALDATVSLVRAEIGAGASGFVNA +VLRRVAERPLEEWLADVAPADGGDAALAVRASHPVWIVRALRQALAAHRGTRHTADRDAE +LAALLEADNAPPVVNLVALPVAGGAEALAAALDDGAEPGPLAPDSALHSGGDAGRLPGVR +EGVLRVQDAGSQLTARALAQAPVPAAEGRAERWLDLCAGPGGKAALLAALAAERGATLVA +NEVAPHRADLVRQALAAVPAGAWTVRTGDGRTIADAPEAAPAFDRVLVDAPCTGLGALRR +RPESRWRRTPADLAELTGLQAELLDAAVAVLAPGGVLAYVTCSPHVAETVVQVQDLVRRH +PELELLDARTALDAVALDDLRLDEAEPAGAPEPGDVVARTAQLWPHRHGTDAMFLALLRA +PGA +>PROKKA_01826 +MSGEGQGRQGRGRGGSGGGSRGGAGGGSRGGSRNGSGGGPRGGSHGGPRGGSGGARRESG +GEERRDAQGRTRSRGRSGAGRRYSAQAPAQRSRTADPARRVAFEVIRAVHAEDAYANLVL +PGRIRQARLDRRDAGFATELAYGTLRGIGLYDAVLARCVDRPLEKIDPPVLDALRLGAHQ +LLAMRVPAHAALDATVALVRAEIGAGPSGFVNAVLRRVAERPLEDWLADVAPAEGGDAAL +AVRASHPVWIVRALRQALAAHRGTRHVADRDAELGALLEADNASPVVNLVALPVPGGREG +LSAALEDGAEPGPLAPDSALHAGGDAGRLTGVREGVLRVQDAGSQLTARALAAAPAAAAE +GRPERWLDLCAGPGGKAALLAALAAERGATLVANEVAEHRAELVRQALGAVPAAAWTVRA +GDGRAIADAPEAAGGFDRVLVDAPCTGLGALRRRPESRWRRTPADLAELTGLQSELLDAA +AAVLAPGGVLAYVTCSPHVAETTVQVQDLLRRRPELELLDAGAVLSEVALGDLRLDEGEP +GGDEAAGAAAPDDVAARTAQLWPHRHGTDAMFLALLRAPSDTPESPERTRG +>PROKKA_01716 +MSAGQDGSTGRGAGQGGRGRGGAEGRQGPGGRQGAGGQDRRDAQGRQLNRGASGTGRHRT +TLAPKERARRADPARRVAFEVVRAVHAEDAYANLVLPARIRQGRLDRRDAGFATELTYGT +LREQGLYDAVLARCVDRALDALDAPVLDALRLGAHQLLGMRVPAHAALDATVALVRAEVG +AGPAGFVNAVLRRVSERPREDWLAEVAPADGGDTARAVRHSHPAWIVRALRQALAGHPGT +ADVEDRDAELEALLVADNAAPVVNLVGLPVPGGREALASALGDGAEPHPLTPDAALHAGG +DAGRLPGVREGVLRVQDAGSQLTARALAAVPAASGRDAGGRKAERWLDLCAGPGGKAALL +AALASERGATVLANEVAPHRADLVRSALAGVPASAWEVRTGDGRTIAEDAPAGGFDRILV +DAPCTGLGALRRRPESRWRRTPADLAELTGLQAELLDAAVGVLAPGGVLAYVTCSPHVAE +TLVQVQDLLRRHPVLEQLDAPAALQDVAVADLGLAAPEDADPVLARTAQLWPHRHGTDAM +FLALFRAPVA +>PROKKA_01007 +MSRERQPGQGRGERGARGERGRAPRPDPQDRRDAQGRTRNRGRSGAGRKYSAQAPSQRSR +TADPARRVAFGVVRSVHAEDAYANLVLPARIRQARLDRRDAGFATELAYGTLRGLGLYDA +ILTRCVDRPLEKIDPPVLDALRLGAHQLLGMRVPAHAALDATVSLVRAEIGAGASGFVNA +VLRRVAERPLEEWLADVAPADGGDAALAVRASHPVWIVRALRQALAAHRGTRHIADRDAE +LAALLEADNAPPVVNLVALPVAGGAEALAAALDDGAEPGPLAPDSALHSGGDAGRLPGVR +EGVLRVQDAGSQLTARALAQAPVPAAEGRAERWLDLCAGPGGKAALLAALAAERGATLVA +NEVAPHRADLVRQALAAVPADAWTVRAGDGRTIADAPEAAPAFDRVLVDAPCTGLGALRR +RPESRWRRTPADLAELTGLQAELLDAAVAVLAPGGVLAYVTCSPHVAETVVQVQDLVRRH +PELELLDARTALDAVALDDLRLDEAEPAGAPKPGDVVARTAQLWPHRHGTDAMFLALLRA +PGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000896.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000896.fa new file mode 100644 index 0000000000000000000000000000000000000000..e3e8394b7842e601d167c2c6df6bc737020ddcfd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000896.fa @@ -0,0 +1,29 @@ +>PROKKA_01080 +MSLAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELARRYNAAGADELTFLDVTASTSDR +ATTYEVVTRTAEEVFIPLTVGGGVRTVEDVDRLLRTGADKVSVNTAAVARPEVITEITRR +FGSQVLVLSLDARRTEDPGCASGYEVTTHGGRRGTGIDAVAWCREASERGVGEILLNSID +ADGTREGFDLEMIRDVRAVTRVPLIASGGAGEPEHFPPAVAAGADAVLAASLFHFGPDDM +LARVKDALRQAGHTVR +>PROKKA_00799 +MSLAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELARRYNAAGADEITFLDVTASTSDR +ATTYDVVTRTAEEVFIPLTVGGGVRTVEDVDRLLRTGADKVSVNTAAVARPEVITEITRR +FGSQVLVLSLDARRTEDPGCASGYEVTTHGGRRGTGIDTVAWCREASERGVGEILLNSID +ADGTREGFDLEMIRDVRAVTRVPLIASGGAGEPEHFPPAVAAGADAVLAASLFHFGPDDM +LARVKDALRQAGHTVR +>PROKKA_01818 +MVKGVNFENLRDAGDPVELARRYNAAGADEITFLDVTASTADRATTYDVVTRTAEEVFIP +LTVGGGVRTEEDVDRLLRVGADKASVNTAAVARPELITEITRRFGSQVLVLSLDARRTQD +PGCASGYEVTTHGGRRGTGIDAVAWCREASERGAGEILLNSIDADGTRNGFDLEMIRDVR +AVTRVPLIASGGAGVPEHFPPAVEAGADAVLAASMFHFGPDDMLARVKDALRQAGHTVR +>PROKKA_01705 +MTVAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELAARYGAQGADELTFLDVTATTGDR +ATMFDVVTRAAEQIFIPLTVGGGVRSVEDVDRLLRTGADKASVNSAAVARPELIGEIARR +FGNQVLVLSLDARRTRDPGCASGYEVTTHGGRKGTGIDAVAWCREATERGVGEILLNSID +ADGTRDGFDLEMIRDVRAVTTVPLIASGGAGLPEHFPPAVDAGADAVLAASMFHFGPDDM +IGQVKDALRAAGHVVR +>PROKKA_01029 +MSLAVRVIPCLDVDAGRVVKGVNFENLRDAGDPVELARRYNAAGADEITFLDVTASTSDR +ATTYDVVTRTAEEVFIPLTVGGGVRTVEDVDRLLRTGADKVSVNTAAVARPEVITEITRR +FGSQVLVLSLDARRTEDPGCASGYEVTTHGGRRGTGIDTVAWCREASERGVGEILLNSID +ADGTREGFDLEMIRDVRAVTRVPLIASGGAGEPEHFPPAVAAGADAVLAASLFHFGPDDM +LARVKDALRQAGHTVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000898.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000898.fa new file mode 100644 index 0000000000000000000000000000000000000000..7d13bd4000ca32d1001c7f66106ea6d4798d3e73 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000898.fa @@ -0,0 +1,50 @@ +>PROKKA_01082 +MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA +WSRYSFIGAGSSVTLTSRNGEAHWQGTPPEGLPTQGRALDVLAACLRLLRTDVRAEVGGV +LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA +VNGNGLATGADRAYDDALARLDAMVERLAAPAADPVSDVPRRWLEADADEVAAQAEDRWG +AEGFREAVAKAQRAIRDGDVFQAVVSRRLSVTTDATGLDVYRVLRTVNPSPYMYLFSFET +PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATEKDDRLLGKDLLEDEKERAEHL +MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA +GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG +AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA +>PROKKA_00801 +MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA +WSRYSFIGAGSAVTLTSRDGEAHWQGTPPEGLPTQGRALDVLAACLRLLSTDVRAEVGGV +LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA +VNGNGLATGADRAYDDALARLDAMVERLTAPAADPVSDVPRRWLEADADEVAAQAEDRWG +AEGFREAVGKAQRAIRDGEVFQAVVSRRLSVTTDATGLDVYRVLRMVNPSPYMYLFSFET +PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATAEDDRLLGKDLLEDEKERAEHL +MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA +GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG +AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA +>PROKKA_01815 +MSAATTPSREEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESAAPGAV +WSRYSFVGAGSAVTLTSRDGQAHWQGVPPEGLPTEGRALDVLAACLRLLRTDARTHLDGA +LPHLVSGMAGFLGWNTVRAWERLPNPPQDDLGLPDLAMNLVTDLAVHDALDGTVTLIANA +VNGNGLATGAEGAYEDALARLDAMVDQLAAPAAEPVSTVPRRWLDADADEVAAQAEDRWG +AAGFREAVGKAQEAIRDGEVFQAVVSRRLSVTTGATGADVYRVLRMVNPSPYMYLFSFET +PDGEPYEIVGSSPEALVTVQDRRVVTHPIAGSRRRGATLEDDRLLGKDLMEDEKERAEHL +MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMREDVDALDVLRAAFPA +GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG +AGVVADSDPDAETAETVTKATAPLRSVLTAGEMGRA +>PROKKA_01703 +MSGVVPSREEFLAVAPTSRVIPVVRRVLADGLTPLAIHRRLADSRPGTFLLESATPGAAW +SRYSFIGAGSAATLTARGEDAVWLGEPPEGLPTEGRALDVLAESLRLLSTDARTRVDAAL +PHLVSGMAGFLGWPAVRAWERLPHPPEDHLGLPLLAMNLISDLAVHDAQDGTVTLIALAI +NGDGLATGAERAYDDAVARLEDMVARLRAGAEDPVDEVPRRWLDATAEEVAAEAEDRWGA +AGFRDAVGRAQQAITDGEVFQIVVSRRFSVDTAASGVDVYRVLRMVNPSPYMYLFSFQTP +DGEPYEIVGSSPEALVTVQDRRVVTHPIAGSRRRGATPEDDRLLGKELAEDEKERAEHLM +LVDLSRNDLSRVCEAGTVEVTQFMELEAFSHILHLVSHVEGRLRDDVTSLDALRSAFPAG +TLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSVTLAGRQAHVQAGA +GIVADSDADAETAETVTKATAPLRAVLTAAELRGA +>PROKKA_01031 +MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA +WSRYSFIGAGSAVTLTSRDGEAHWQGTPPEGLPTQGRALDVLAACLRLLSTDVRAEVGGV +LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA +VNGNGLATGADRAYDDALARLDAMVERLTAPAADPVSDVPRRWLEADADEVAAQAEDRWG +AEGFREAVGKAQRAIRDGEVFQAVVSRRLSVTTDATGLDVYRVLRMVNPSPYMYLFSFET +PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATAEDDRLLGKDLLEDEKERAEHL +MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA +GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG +AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000900.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000900.fa new file mode 100644 index 0000000000000000000000000000000000000000..223d703be8e3289b074ea9f7319cd97101bc6882 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000900.fa @@ -0,0 +1,15 @@ +>PROKKA_01084 +MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL +VGFVAGCVGLLADWSVVVWIGVALMAVGVVVGIVAGKAGAGRGQHGH +>PROKKA_00803 +MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL +VGFVAGCVGLLADWSVVVWIGLALMAVGVVVGIVAGKAGAGRGQHGH +>PROKKA_01813 +MSHTANTEHTTRRAARNGAVEDVVVTEDGRVLNDPTHLELPDHGNTPGGWAMVALVLVGF +VAGCIGLLADWMIVVWIGVALIVVGVLVGIVAGRGGSARSGHRAH +>PROKKA_01701 +MSHTEATVNHTAQAGAHAAGHTTGHTASREVVVTEDGRVLNDPTHAKVPGHGNSPAAWAM +AGLVVLGFLAGCIGLLNDALVIVWIGVAVIVVGVLVGIVGGKAAGRSDH +>PROKKA_01033 +MSHTANTAHTEPTTRRAARRGAVEDVVVTEDGLVLNDPTHLELPGHGNSPGAWAMVALVL +VGFVAGCVGLLADWSVVVWIGLALMAVGVVVGIVAGKAGAGRGQHGH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000901.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000901.fa new file mode 100644 index 0000000000000000000000000000000000000000..153e3a749257744517cfb153c82b9b4a712f8d93 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000901.fa @@ -0,0 +1,30 @@ +>PROKKA_01085 +MSVLQEIIDGVREDLEPRRRALPEARLSELVAATPAPRDAHAALHGGRTDPAGIRVISEV +KRASPSKGALAEIPEPATLARAYERGGASAVSVLTEARRFGGSLADLDAVRAAVDLPVLR +KDFTVTEYQIHEARAHGADLVLLIVAALDDAELAGFLQLTESLGMHALVEAHTPEEIERG +VAAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESEEQIKAYAAAGADV +VLVGEALVRHGAPEEALRAFRAASLTVR +>PROKKA_00804 +MSVLQEIIDGVREDLEPRRRALPEARLAELVAAAPAPRDAHAALHGGRTDPAGIRVISEV +KRASPSKGALAEIPEPATLARAYERGGASAVSVLTEARRFGGSLADLDAVRAAVDLPVLR +KDFTVTEYQIHEARAHGADLVLLIVAALDDAELAGFLQLTESLGMHALVEAHTPEEIERG +VAAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESEEQIKAYAAAGADV +VLVGEALVRHGAPEEALRAFRAASLTVR +>PROKKA_01812 +MSVLQEIIDGVREDLAPRRRDVPEARLAELVAAAPAPRDAHAALLGGRTDPAGIRVISEV +KRSSPSKGALAEIPEPAALARAYERGGASAVSVLTEARRFGGSLADLDAVRGAVDLPVLR +KDFTVTEYQIHEARAPGADLVLLIVAALDDAELTGFLQLTESLGMHALVEAHTPEEIERG +VTAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESDEQIKAYAAAGADA +VLVGEALVRHGAPEEALRAFRAASLTVR +>PROKKA_01700 +MPETVLDSIVAGVLEDLAPRREAVPEARLQELIAQAPAPRDAYAALRDGRSDPAGIHVIA +EVKRRSPSKGALAEITEPAALAASYADGGAGAISVLTEQRRFGGSLADLDAVRAAVARPV +LRKDFTVTEYQILEARAHGADLVLLIVASLDDARLRGFRELAESLGMHALVEAHTSEEIA +RGVDSGARILGVNVRNLKTLDVDPDRYAALAGDLPEDVVRVAESGVESEAQVRQYAAAGA +DAILVGEALVRHGAPADALRAFRAASLTVR +>PROKKA_01034 +MSVLQEIIDGVREDLEPRRRALPEARLAELVAAAPAPRDAHAALHGGRTDPAGIRVISEV +KRASPSKGALAEIPEPATLARAYERGGASAVSVLTEARRFGGSLADLDAVRAAVDLPVLR +KDFTVTEYQIHEARAHGADLVLLIVAALDDAELAGFLQLTESLGMHALVEAHTPEEIERG +VAAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESEEQIKAYAAAGADV +VLVGEALVRHGAPEEALRAFRAASLTVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000903.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000903.fa new file mode 100644 index 0000000000000000000000000000000000000000..7ec0e939effac0707ee7571d63f4baf6b08d4bdf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000903.fa @@ -0,0 +1,30 @@ +>PROKKA_01087 +MTVNSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAADNGADVIELGLPYTDP +VMDGPVIQAATQAALQAGFHVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL +AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS +VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR +ALTDGGPQAVGALARELAAGAVREG +>PROKKA_00806 +MTVHSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP +VMDGPVIQAATQTALQAGFRVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL +AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS +VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR +ALTDGGPQAVGTLTRELAAGTVREG +>PROKKA_01810 +MTVHSKTAAALDAARRAGRTGLVAYLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP +VMDGPVIQAATQASLRAGFRVADVFEIIRRVTQRVDAAVLVMTYWNLVDRMGVDEFARRL +AEAGGAGLVTPDLVPEEAGAWLEASDRHGLDRVFLTAPSSTDERVRLAVESSRGFVYAVS +VMGVTGARDAVSTAAETVVRRAEEAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR +ALGEGGPQAVGALARELAAGAVREG +>PROKKA_01698 +MSTPDQQHEATAEKPSTAGDAIERARAAGRTALIGYLPAGYPSIDESVEAAVQLGENGVD +VIEIGLPYSDPVMDGPVIQAATSHALANGFHTRDVFEVVRRITERTEAAVVVMTYWNLVD +RMGVDEFARRLAEAGGAGLVTPDLVPEEAGEWFEASEEHGLDRIFLTAPSSSDERVRLAV +ESSRGFVYGVSVMGVTGARGKVSDAAERVVARAKAAGARNVCVGLGISSADHVREIGSYA +DGAIVGTALVKALRDGGPEAVGALARELAAGTAKES +>PROKKA_01036 +MTVHSKTAAALDAAKAAGRTGLVAFLPAGYPSVDECVEAVVAAAENGADVIELGLPYTDP +VMDGPVIQAATQTALQAGFRVADVFDIIRRVTQRTDAAVLVMTYWNLVDRMGVDEFARRL +AEAGGAGLVTPDLVPEEAGAWMEASDRHGLDRVFLTAPSSTDERVRLTVDSSRGFVYAVS +VMGVTGTRDAVSTVAETVVRRAQDAGAEHVCVGLGVSQAAHVREIGAYADGAIVGTALVR +ALTDGGPQAVGTLTRELAAGTVREG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000904.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000904.fa new file mode 100644 index 0000000000000000000000000000000000000000..eea1095d1c0a898f61e224e84c7312fa0434a94a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000904.fa @@ -0,0 +1,35 @@ +>PROKKA_01088 +MTALASLASPAALAPLAAFPAPGWDGFQLGPVKIHAYALCIILGIVLALWLAERRWRARG +GPEDRVLDIALWAIPFGFVGGRLYHVFSSPDRYFGPGFDGTGDPIQILYVWNGGLGIWGA +IALGAVGAWIACRRYGLRLTAFGDVVAPGILLAQAIGRWGNWFNQELFGGPTTLPWGLEV +DPASPNFPAGYAPDTLFHPTFLYECLWNLAGVALLLLVDRALHLRHGLMLWSYVAWYTAG +RTWIEMLRIDDAEMVTLFGVTQRLNVWTSLLVFVIALAFIVGILLRHRGAAAGPHAHQSV +WRAGHAPEGDDGVAVAAGRSGSHAVGAAEDDAVRR +>PROKKA_00807 +MTAALAPLAAFPAPGWDGFQLGPVKIHAYALCIILGIVLALWLAERRWRARGGPEDRVLD +IALWAIPFGFVGGRLYHVFSSPDRYFGPGFDGTGDPIQILYVWNGGLGIWGAIALGAVGA +WIACRRYGLRLTAFGDVVAPGILLAQAIGRWGNWFNQELFGGPTTLPWGLEVDPASPNFP +AGYAPDTLFHPTFLYECLWNLAGVALLLLVDRALHLRHGLMLWSYVAWYTAGRTWIEMLR +IDDAEMVTLFGVTQRLNVWTSLLVFVIALAFIVGILLRHRGAAAGPHAHQSVWRAGHAPE +GDDGAAVAAGRSGSHAVGAAEDDAVRR +>PROKKA_01808 +MKIYAYALSIILGIVLALWLAERRWKARGGPEGRVLDVALWAIPFGFVGGRLYHVFSSPD +RYFGPGFDGTGDPVQILHVWNGGLGIWGAIALGAVGAWIACRRYGLRLSAFGDVVAPGIL +LAQAVGRWGNWFNQELFGRPTTAPWGLRVDADHPNFPDGVAPDTLFHPTFLYESLWCLLG +VAVLLLADRRWRLRRGAMVWAYVAWYTAGRVWIETLRIDDAELVTLFGLTQRLNVWTSIV +MLLLALVMLAVILVKHGPAAAGPRSDDSVWLPGRGPALEAGAGAPVDAAVAGQGPDDGAG +STAAGVREDR +>PROKKA_01697 +MGSGALTPLAAFPAPVWDGFELGPMKIHAYALCIIAGIVVALWLSGRRWADRGGPEGRVL +DIALWAIPFGFVGGRLYHVFSSPDLYFGPGYDGTGDPIKILYVWNGGLGIWGAIALGAVG +AWIACRRYGLRLTAFADVVAPGVLLAQAIGRWGNWFNQELFGGPTTLPWGLTVDPASPNF +PAQYAPGTLFHPTFLYESLWNLLGVAVLLLVDRRLHLRHGAMLWSYVAWYTAGRTWIEMM +RIDDAELVTLFGVTQRLNVWTSLLMFAIALAFLIGILLRHRGAAAGPHARQSVWRDGHGP +VGEDVEGAGPAAAPAVRTTQGGSGSHAWDDVGA +>PROKKA_01037 +MTAALAPLAAFPAPGWDGFQLGPVKIHAYALCIILGIVLALWLAERRWRARGGPEDRVLD +IALWAIPFGFVGGRLYHVFSSPDRYFGPGFDGTGDPIQILYVWNGGLGIWGAIALGAVGA +WIACRRYGLRLTAFGDVVAPGILLAQAIGRWGNWFNQELFGGPTTLPWGLEVDPASPNFP +AGYAPDTLFHPTFLYECLWNLAGVALLLLVDRALHLRHGLMLWSYVAWYTAGRTWIEMLR +IDDAEMVTLFGVTQRLNVWTSLLVFVIALAFIVGILLRHRGAAAGPHAHQSVWRAGHAPE +GDDGAAVAAGRSGSHAVGAAEDDAVRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000905.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000905.fa new file mode 100644 index 0000000000000000000000000000000000000000..e029805eda12f39d3d6f774927bf17991678ec37 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000905.fa @@ -0,0 +1,135 @@ +>PROKKA_01089 +MPVASSPASAPRAGGPVDPFVRYADVPAAQGLYDPSRETENCGLAVIATLRGTPGHDIVQ +HALTALRALEHRGAVGADEGTGDGAGLLTQIPDELFRAVVDAELPPVGEYVAGTAFLPPV +DGERAEAKEAVERLAEEEGLQVLAWREVPTDPSALGVGSRAAMPAFEQLFLSLADGQDGT +EPGQSLDVRAWRVRRRAQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDERFTTRL +GVVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEDLF +PLISPIGSDSASFDEVAELLMLSGRPLTQAIMMMIPEAWENHATMDPARRAFYQYHSMLM +EPWDGPAAVAFSDGTQVGAVLDRNGLRPARWWVTDDGLVVLASEVGVVPIEPSAVVRKGR +VAPGRMFLVDTEQGRIIGDDEIKAEVASAQPWEDWVRQNLLDLESLPEREHVRHTSESIL +QRQRIFGYTSEELRILVGPMAQTGAEPLGAMGTDTPIAVLAKRPRLLFDYFVQSFAQVTN +PPLDAIREEQVTSMRTAIGPQGNVLSLEQVRTRQVDVPFPVIDNDQLARIQHLRDADGTR +LTLKVNGVYRVAGGVEELRAQLKAICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT +SAVHHHLLASANRTKSSLIVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEV +SGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFVGTTS +PLDGVGIDVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL +QHSTRERRYDVFKDYTRRVDDQAEELMTLRGLMRLRTGERPPVPVSEVEPVESIVRRFST +GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS +LYLATATDLQIKMAQGAKPGEGGQLMGTKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED +LAQLIHDLKRANPTARVHVKLVSESGVGTVAAGVAKARADVVLISGHDGGTGASPLNSLK +HAGTPWEIGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVV +SGCIMMRVCHLDTCPVGVATQNPELRARFTGKPEFVVNFFEFIAQEVRELLSQLGFRTLD +EAIGHRELLDVDAALHHWKSEGLDLSGILADPSVGRRPGHEDAPMRRTTEQDHDLASHID +HRFIARLGDTLTTGTPVVMDEAVVNTDRSVGTLLGYHVTSTRLADELDDDTITVRLTGEA +GQSLGAFLPAGVTLRLSGDANDYVGKGLSGGRVIVRPDAEAPFVAEENTVAGNVIGYGAT +SGQLFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALILGETGRNLAAGMSGGRA +WVLDLDREDLNPLAVREDALILEAPSAQDRLRIAELLELHRAETGSAVAAALLADLRAGG +DAADAAWDRFTTVLPRQYDLVLRTRQAATAEGLDPDGEAVWDRLLEVTRG +>PROKKA_00808 +MPVASSPASAPRAGGPVDPFVRYADVPAAQGLYDPSRETENCGLAVIATLRGTPGHDIVQ +HALTALRALEHRGAVGADEGTGDGAGLLTQIPDELFRAVVDAELPPVGEYVAGTAFLPPV +DGERAEAKEAVERLAEEEGLQVLAWREVPTDPSALGVGSRAAMPAFEQLFLSLADGQDGT +EPGQSLDVRAWRVRRRAQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDERFTTRL +GVVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEDLF +PLISPIGSDSASFDEVAELLMLSGRPLTQAIMMMIPEAWENHATMDPARRAFYQYHSMLM +EPWDGPAAVAFSDGTQVGAVLDRNGLRPARWWVTDDGLVVLASEVGVVPIEPSAVVRKGR +VAPGRMFLVDTEQGRIIGDDEIKAEVASAQPWEDWVRQNLLDLESLPEREHVRHTSESIL +QRQRIFGYTSEELRILVGPMAQTGAEPLGAMGTDTPIAVLAKRPRLLFDYFVQSFAQVTN +PPLDAIREEQVTSMRTAIGPQGNVLSLEQVRTRQVDVPFPVIDNDQLARIQHLRDADGTR +LTLKVNGVYRVAGGVEELRAQLKAICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT +SAVHHHLLASANRTKSSLIVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEV +SGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFVGTTS +PLDGVGIDVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL +QHSTRERRYDVFKDYTRRVDDQAEELMTLRGLMRLRTGERPPVPVSEVEPVESIVRRFST +GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS +LYLATATDLQIKMAQGAKPGEGGQLMGTKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED +LAQLIHDLKRANPTARVHVKLVSESGVGTVAAGVAKARADVVLISGHDGGTGASPLNSLK +HAGTPWEIGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVV +SGCIMMRVCHLDTCPVGVATQNPELRARFTGKPEFVVNFFEFIAQEVRELLSQLGFRTLD +EAIGHRELLDVDAALHHWKSEGLDLSGILADPSVGRRPGHEDAPMRRTTEQDHDLASHID +HRFIARLGDTLTTGTPVVMDEAVVNTDRSVGTLLGYHVTSTRLADELDDDTITVRLTGEA +GQSLGAFLPAGVTLRLSGDANDYVGKGLSGGRVIVRPDAEAPFVAEENTVAGNVIGYGAT +SGQLFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALILGETGRNLAAGMSGGRA +WVLDLDREDLNPLAVREDALILEAPSAQDRLRIAELLELHRAETGSAVAAALLADLRAGG +DAADAAWDRFTTVLPRQYDLVLRTRQAATAEGLDPDGEAVWDRLLEVTRG +>PROKKA_01807 +MQHPSKTPHADPFRAFAAQPEAAGLYDPEQEKDACGLAAVATLRGPATHKIVQDALTALR +ALEHRGAVGADEGTGDGAGIITQVPDALLRATVSFELPAAGEYAVGTAFLPQDEAARTAA +QEAIAEAAVVEGLDLLGWRPVPTDESVLGPGSRAVVPVFEQLFLAVSAGEDVEAPGQSLD +ARAWRLRRRAQRSGVYFPSLSSRTLVYKGMLSTAQVEPFYPDLSDERYVTRLAVVHSRFS +TNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGELRHPLLGEVPEEMFPIVSASGS +DSASFDEVAELIHLAGRPLSHAIMMMVPEAWENHTTMDEDRRAFYQYHSMLMEPWDGPAA +IAFTDGVQLGSVLDRNGLRPARYWETRDGLVVLASEVGVLDIDPATVVRKGRVKPGRMFL +LDTEQGRIIEDEEVKAEIAASAPWKDWVADSLRRIEDLPEREPVRYHGDSVRLRQRLFGY +TDEEVRTIIEPMARHGAEPLGAMGTDTPIAALSPRPRLLFDYFTQNFAQVTNPPLDSIRE +EQVTSMRTCIGPQASLLAAGKVTTDAVEIPFPVLDNEQLARIAAVRAEDGTRRALKVKGL +YLVAGGAEEMRSRLKEICEQVSAAVQRGVQYVVLSDRDANAQWAPIPSLLLTSAVHHHLL +ASASRTRTSLLVEAGDVREVHHVAVLIGYGASAVNPYLSMETAEELVRTGTLTGVTEQEA +TRNLIHGLGKGVQKIMSKMGISTVASYCGAQTFEALGLSRSFVDRYFTGTRSPMDGVGLD +VIAAESAARHATAFPVDGSSASTVGPRGTSGLPVGGEYKWRREGPPHLFNPETVFRLQHA +TRERRYDIFKDYTRRVDEQSADLMTLRGLLGLATKGRERVPVSEVESVESIVKRFSTGAM +SYGSISQEAHETLAVAMNRLGARSNSGEGGEDPERLLDPERNSRVKQIASGRFGVTSLYL +STATDLQIKMAQGAKPGEGGQLMGAKVYPWVARTRHSTPGVSLVSPPPHHDIYSIEDLAQ +LIHDLKRANPQARVHVKLVSETGVGTVAAGVTKAKADVVLISGHDGGTGASPLNSLKHAG +TPWELGLSEAQQTLRLNGLRDRVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVVSGC +IMMRVCHLDTCPVGVATQNPELRARFTGRPEFVVTFFEYIAQEVRELLAELGLRSLDEAI +GRQDLLHKDAAIGHFKTEGLDLSGVLSDAGVPEEAPRRRLTEQDHRLQDQADQRWLDQVA +DAVVTETPVTVTDRLVNTDRSVGTLLGHRVTAARLDDELPRDTIRIELTGEAGQSLGAFL +PAGVSITLSGDANDYVGKGLSGGTVALRPAPEAPFAAEENMIAGNVVGYGATSGRLFLNG +RVGERFLVRNSGAVAVVEGIGDHGLEYMTGGTALVLGNTGRNLAAGMSGGVGFFLDLDPA +QLNPLAVKDDELLLGRPEGADRALIRELLEEHRAATGSDLAARLLAELDGPAESAEALWE +RFTTVLPRRYAAVQEIRTDSRDAGTDPDGDAAWARILEVTRG +>PROKKA_01696 +MTVAPLSAPTPRSGRSDDPFVRYAAFPEPQGLYDPARETENCGLAVIATLRGTPGHDIVE +HALTALRALEHRGAVGADEGTGDGAGLLTQLPDELFRAVLDVELPPVGEYAAGIAFLPPL +EGERAEAKAAVEELAQAEGLDVLAWRVVPTDPSALGTGSRAAMPSFEQVFLALAEGEDGT +EPGQSLDVRAWRLRRRTQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDPRFTTRL +GIVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEELF +PLISPIGSDSASFDEVAELLMLSGRPLTQAVMMMIPEAWENHATMDPARRAFYQYHSMLM +EPWDGPAAVAFSDGTQVGAVLDRNGLRPARYWETRDGLVVLASEVGVVSIDPADVVRKGR +VAPGRMFLVDTEQGRIVEDEEIKAEVAAAAPWEEWVSQNLLDLDALPEREHLRPSSESIQ +QRQRIFGYTAEELRVLVGPMARDGAEPLGAMGTDTPIAVLSKRPRLLFDYFVQSFAQVTN +PPLDAIREEQVTSMRTGIGPQGNVLSAERVHTRQVDVPFPVIDNDQLARIQHLRDGDGGR +LALKVTGTYRVAGGAEELRTRLKEICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT +SAVHHHLLASANRTRTSLVVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEI +EGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFAGTTS +PLDGVGLEVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL +QHSTRERRYDVFKDYTRRVDGQAEELMTLRGLMRLRSEDRTPVPISEVEPVESIVRRFST +GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS +LYLTTATDLQIKMAQGAKPGEGGQLMGAKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED +LAQLIHDLKRSNPAARVHVKLVSESGVGTVAAGVAKAKADVVLISGHDGGTGASPLNSLK +HAGTPWELGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVVAALLGAEEFGFATAPLVV +SGCIMMRVCHLDTCPVGVATQNPELRSRFTGKPEFVVNFFEFVAQEVRELLAELGFRTLD +EAIGHRELLDVDAALHHWKTEGLDLSGILADPSVGRRAGAADAPMRRMVDQDHDLAAHID +NRLIARLGDTLATGAPVVMDESVVNTDRSIGTMLGHHVTSTRLADELPADTITVRLTGEA +GQSLGAFLPAGVTLRLDGDANDYVGKGLSGGRVVVRPDATAPFAAEDNTVAGNVIGYGAT +SGELFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALVLGETGRNLAAGMSGGRA +WILDLDRADLNPLAVREGDLLLSTPSAADRERIAALLRTHRAETGSAVAERLLADLDAGG +DAAQGVWDRFTTILPRRYDLVLRTRAEAVAEGLDPDGEAVWDRLLEVTRG +>PROKKA_01038 +MPVASSPASAPRAGGPVDPFVRYADVPAAQGLYDPSRETENCGLAVIATLRGTPGHDIVQ +HALTALRALEHRGAVGADEGTGDGAGLLTQIPDELFRAVVDAELPPVGEYVAGTAFLPPV +DGERAEAKEAVERLAEEEGLQVLAWREVPTDPSALGVGSRAAMPAFEQLFLSLADGQDGT +EPGQSLDVRAWRVRRRAQSRAGVYFPSLSSQTIVYKGMLTTAQLEPFYPDLSDERFTTRL +GVVHSRFSTNTFPSWPLAQPFRTIAHNGEINTVKGNRNWMRARQGQLKHPMLGEVPEDLF +PLISPIGSDSASFDEVAELLMLSGRPLTQAIMMMIPEAWENHATMDPARRAFYQYHSMLM +EPWDGPAAVAFSDGTQVGAVLDRNGLRPARWWVTDDGLVVLASEVGVVPIEPSAVVRKGR +VAPGRMFLVDTEQGRIIGDDEIKAEVASAQPWEDWVRQNLLDLESLPEREHVRHTSESIL +QRQRIFGYTSEELRILVGPMAQTGAEPLGAMGTDTPIAVLAKRPRLLFDYFVQSFAQVTN +PPLDAIREEQVTSMRTAIGPQGNVLSLEQVRTRQVDVPFPVIDNDQLARIQHLRDADGTR +LTLKVNGVYRVAGGVEELRAQLKAICEQVSAAVNRGVEYVVLSDRGATAQWAPIPSLLLT +SAVHHHLLASANRTKSSLIVEAGDVREVHHVAVLLGYGASAVNPYLAMESAEELVRTGEV +SGVTAEQAVANLIKALGKGVQKIMSKMGISTVASYTGAQTFEALGLSRRFVDRYFVGTTS +PLDGVGIDVVAAEIQARHEFAYPPDGNDINPYRELEVGGEYQWRREGAPHLFNPETVFRL +QHSTRERRYDVFKDYTRRVDDQAEELMTLRGLMRLRTGERPPVPVSEVEPVESIVRRFST +GAMSYGSISQEAHETLAIAMNRLGARSNSGEGGEDPERLLDPERRSKIKQIASGRFGVTS +LYLATATDLQIKMAQGAKPGEGGQLMGTKVYPWVARTRHSTPGVSLVSPPPHHDIYSIED +LAQLIHDLKRANPTARVHVKLVSESGVGTVAAGVAKARADVVLISGHDGGTGASPLNSLK +HAGTPWEIGLAEAQQTLMLNGLRERVTVQVDGQLKTGRDVVIAALLGAEEFGFATAPLVV +SGCIMMRVCHLDTCPVGVATQNPELRARFTGKPEFVVNFFEFIAQEVRELLSQLGFRTLD +EAIGHRELLDVDAALHHWKSEGLDLSGILADPSVGRRPGHEDAPMRRTTEQDHDLASHID +HRFIARLGDTLTTGTPVVMDEAVVNTDRSVGTLLGYHVTSTRLADELDDDTITVRLTGEA +GQSLGAFLPAGVTLRLSGDANDYVGKGLSGGRVIVRPDAEAPFVAEENTVAGNVIGYGAT +SGQLFLRGRVGERFLVRNSGATAVAEGIGDHGLEYMTGGEALILGETGRNLAAGMSGGRA +WVLDLDREDLNPLAVREDALILEAPSAQDRLRIAELLELHRAETGSAVAAALLADLRAGG +DAADAAWDRFTTVLPRQYDLVLRTRQAATAEGLDPDGEAVWDRLLEVTRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000907.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000907.fa new file mode 100644 index 0000000000000000000000000000000000000000..7777c2bb6e3392444c11e3b3b621c4e8c2c025fa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000907.fa @@ -0,0 +1,50 @@ +>PROKKA_01091 +MRHAKIIATFGPATDSDETTRAIIRAGADVVRLNMSHGDHAVHETSYERVRRLSVEESRP +VAIFADLQGPKIRLGRFTDGPHLLERGDRITITTRDVPGTRELVGTTHKGLPGDVAPGDV +LLVDDGKVRLRAVEVTDTDVLAEVEVPGTVSDNKGINLPGVAVNVPALSEKDERDLRWAL +RTGVDMVALSFVRDAADVDRVHEIMDEEERRVPVIAKIEKPQAVENLEAIVDAFDAVMVA +RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIDSPRPTRAEASDCANAVL +DGADAVMLSGETSVGAYPVETVQTMARIIESTETHGLELIHPLGSRPRTRGGAITRAAVE +VANQLEIPFLATFTESGDSARRLSRLRPRQPIYAFTHHEHTHNILCLTWGVYPKMVPFQD +STDKMTLQVEQSLTSEGIAQHGDLVVIAAGSPPGAVGSTNTLRVHRVGDDAAGGSSAASP +QTREPLGFWPARSPL +>PROKKA_00810 +MRHAKIIATFGPATDSDETTRAIIRAGADVVRLNMSHGDHAVHETSYERVRRLSVEERRP +VAIFADLQGPKIRLGRFTDGPHLLERGDRITITTRDVPGTRELVGTTHKGLPGDVAPGDV +LLVDDGKVRLRAVEVTDTDVLAEVEVPGMVSDNKGINLPGVAVNVPALSEKDERDLRWAL +RTGVDMVALSFVRDAADVDRVHEIMDEEERRVPVIAKIEKPQAVENLEAIVDAFDAIMVA +RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIDSPRPTRAEASDCANAVL +DGADAVMLSGETSVGAYPVETVQTMARIIESTETHGLELIHPLGSRPRTRGGAITRAAVE +VANQLEIPFLATFTESGDSARRLSRLRPRQPIYAFTHHEHTHNILCLTWGVYPKMVPFQD +STDKMTLQVEQSLTSEGIAQHGDLVVIAAGSPPGAVGSTNTLRVHRVGGDAAGGSSAASP +QTREPVGFWPARSPL +>PROKKA_01805 +MRHAKIIATFGPATASDETTRSIIRAGADVVRLNMSHGDHEVHAASFERVRRLSVEERRP +VAIFADLQGPKIRLGRFADGPHHLETGDRFTITTRDVEGTAELVGTTHAGLPGDVRPGDT +LLVDDGKVRLRAVEVTDTDVVTEVEVGGDVSDSKGINLPGVAVDVPALSEKDEEDLRWAL +RTGVDMVALSFVRDAADIERVHAIMDEEERRIPVIAKIEKPQAVDNLEAIVDAFDAVMVA +RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIENPRPTRAEASDCANAVL +DGADAVMLSGETSVGRYPVETVQTMARIIESTETHGLEMIHPLGSRPRTRGGAITRAAVE +VADQLDIPFLATFTESGDSARRLSRLRPRQPIYAFTHREHTHNILCLTWGVYPKMVSFQD +STDKMTLQVEESLTSEGIAERGDLVVIAAGSPPGMVGSTNTLRVHRVGDDAGGGSSPARP +VQKEPVGFWPARSPL +>PROKKA_01694 +MRHAKIIATFGPATQTDETTRALIRAGADVVRLNMSHGDHEVHASSYERVRRLSVEEKRP +VAIFADLQGPKIRLARFSDGPHELAVGDRFTITTREVTGSREIVGTTHKGLPGDVSVGDP +LLVDDGKVRLRAVEVTDTDVVTEVVVPGKVSDNKGINLPGVAVNVPALSEKDEEDLRWAL +ETGVDMVALSFVRDAADVTRVHEVMDEVGRRIPVIAKIEKPQAVDNLEAIVDAFDAIMVA +RGDLGVELPLEDVPIVQKRAIELARRWAKPVIVATQVLESMIENPRPTRAEASDCANAVL +DGADAVMLSGETSVGAYPVQTVETMARIIESTETHGLDMIHPLGSRPRTRGGAITRAAVE +VAGQLDIPFLATFTESGDTARRLSRLRPSQPIYAFTHEEHTHNILCLTWGVYPKMVPFAD +STDKMTMQVEESLTSEGIAEQGDLVVIAAGSPPGKVGSTNTLRVHRVGDGVAADSSPVAP +EDREPVGFWAAHSPM +>PROKKA_01040 +MRHAKIIATFGPATDSDETTRAIIRAGADVVRLNMSHGDHAVHETSYERVRRLSVEERRP +VAIFADLQGPKIRLGRFTDGPHLLERGDRITITTRDVPGTRELVGTTHKGLPGDVAPGDV +LLVDDGKVRLRAVEVTDTDVLAEVEVPGMVSNNKGINLPGVAVNVPALSEKDERDLRWAL +RTGVDMVALSFVRDAADVDRVHEIMDEEERRVPVIAKIEKPQAVENLEAIVDAFDAVMVA +RGDLGVELPLEDVPVVQKRAVDLARRWAKPVIVATQVLESMIDSPRPTRAEASDCANAVL +DGADAVMLSGETSVGAYPVETVQTMARIIESTETHGLELIHPLGSRPRTRGGAITRAAVE +VANQLEIPFLATFTESGDSARRLSRLRPRQPIYAFTHHEHTHNILCLTWGVYPKMVPFQD +STDKMTLQVEQSLTSEGIAQHGDLVVIAAGSPPGAVGSTNTLRVHRVGDDAAGGSSAASP +QTREPVGFWPARSPL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000910.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000910.fa new file mode 100644 index 0000000000000000000000000000000000000000..ace343090ac9082e0e62309bac7449bc3178e7b8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000910.fa @@ -0,0 +1,20 @@ +>PROKKA_01095 +MTVALTVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGTSDV +EVQADALPQAFVLTAIVIAFAITVLLLALAVTGRADDAVASPGETRDSLEQAAADARFPR +EERHAAAGRIAQHYAGQGPEVRR +>PROKKA_00814 +MTVALTVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGTSDV +EVQADALPQAFVLTAIVIAFAITVLLLALAVTGRADDAVASPGETRDSLEQAAADARFPR +EERHAAAGRIAQHYAGQGPEVRR +>PROKKA_01800 +MTIAITVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGRGDV +ETQADALPQAFVLTAIVIAFAITVLLLTLAVTGRDDDAVADGHEAPDPLEQSAADARFPR +EELRAAAARLGREAEARDGGRA +>PROKKA_01690 +MTVALTVGLLMAGAVYLFSKRELLRVILGMVLLGHAANLAILATGGTDRRALPFVDGGPA +PAGAADPLPQAFVLTAIVISFAVTVLLLVLAVTGRADDAVAAPGERPDVREAAAADARFP +LAERHAAARTLTGSLPAAPEAGATPEREERA +>PROKKA_01044 +MTVALTVGLLTFGAFYLFSKRELLRVILGMVLLGHAANLAIIAAGGTDRRGLPFAGTSDV +EVQADALPQAFVLTAIVIAFAITVLLLALAVTGRADDAVASPGETRDSLEQAAADARFPR +EERHAAAGRIAQHYAGQGPEVRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000912.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000912.fa new file mode 100644 index 0000000000000000000000000000000000000000..9a41be477aa39d6fc240154b7094ee0016f6b224 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000912.fa @@ -0,0 +1,20 @@ +>PROKKA_01097 +MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI +ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA +DALRAEIHDMEARMLHAMRKTGVA +>PROKKA_00816 +MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI +ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA +DALRAEIHDMEARMLHAMRKTGVA +>PROKKA_01798 +MHADPSSDRPVPADGTVVLAPGRASALSWPWRWLVFWCWYAWALVTSSEAVLKDLVTPGD +QARSGIARIRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGARGEEPGDPGATRLLYVHG +LYADDADALRGEIHDMERRLLHAMRKQGVA +>PROKKA_01688 +MTVHHPDGGVDLTPGTASAASWPLRWLLFWCWYAWALVTSSGAVLHDLLTPGDQARSGIA +RVRSNCRTDAEVTLFSALITLTPGTLTLGTRREGAQGQEPGDPEARRLLYVHGLYADDAD +ALRAEIHDMEARMLHAMRRTGVAR +>PROKKA_01046 +MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI +ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA +DALRAEIHDMEARMLHAMRKTGVA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000913.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000913.fa new file mode 100644 index 0000000000000000000000000000000000000000..abbda480baa1dddc4a2572a14a7ad4b85a0e6aca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000913.fa @@ -0,0 +1,15 @@ +>PROKKA_01098 +MMPFAYDWSLVGIDLAIALLTVSALVSAYRIVVGPLDADRAVSGDLLTFSVLGMLVLFGV +RADNPWTFDLVLIAAVVAFLSGMSLARALTRGKR +>PROKKA_00817 +MMPFAYDWSLVGIDLAIALLTVSALVSAYRIVVGPLDADRAVSGDLLTFSVLGMLVLFGV +RADNPWTFDLVLIAAVVAFLSGMSLARALTRGKR +>PROKKA_01797 +MPVDYDWSHLGIDVAVALLAVAALVSAYRIVKGPLDADRAVSGDLLTFSILGMLVLFGVR +MDNPFTFDLVLVAAIVAFLSGMSLARALTRGKR +>PROKKA_01687 +MSGLLQDYDWSLAGIDLAIALLLVAALVSAVRILRGPLDADRAVSGDLLTFSVLGMVVMF +GVRAQNPFTFDLVLVAAIVAFLSGMSLARALTRGKR +>PROKKA_01047 +MMPFAYDWSLVGIDLAIALLTVSALVSAYRIVVGPLDADRAVSGDLLTFSVLGMLVLFGV +RADNPWTFDLVLIAAVVAFLSGMSLARALTRGKR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000915.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000915.fa new file mode 100644 index 0000000000000000000000000000000000000000..05eac6010601c2ee166497cdd5debded8e38958d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000915.fa @@ -0,0 +1,20 @@ +>PROKKA_01100 +MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAVISPLAQKMGL +RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA +THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP +>PROKKA_00819 +MSEHTATTPAASDRVYRPGVTPELSPAELAAACAEAGLTPELVAALGGAAISPLAQKMGL +RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA +THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP +>PROKKA_01795 +MTDHAERADAAPAPTSDLVYRPGVTPELTDAQREAACAAAGLTPELVAALGGATVSPLAQ +KMGIRFLELTPERAVATMPVAGNEQPAGLLHGGAHLVLAESLGSMAAKLHAGPERGVVGI +EIGATHHRAARSGLVTGTATAIHLGGTLTTHEVVMTDEQGRRLSTARITNMVLRGRG +>PROKKA_01685 +MTDTTTAPERAQALLAGLTFHAGIRPELTDEERAALATAAGMTPAVQEALGGPAVSHLAL +KMGIRFLELSAERSVATMPVAGNEQPVGLLHGGAHLVLAESLGSLSAKVHAGPHRGAVGT +EIGATHHRSVRSGLVTGTATAIHLGRTLTTHEIVMTDEEGRRLSTVRMTNMLLDPR +>PROKKA_01049 +MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAAISPLAQKMGL +RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDHNVVGVEISA +THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLDAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000919.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000919.fa new file mode 100644 index 0000000000000000000000000000000000000000..d5618f62a5994d1163033a26fe51c663e08591e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000919.fa @@ -0,0 +1,25 @@ +>PROKKA_01105 +MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRLEDEAQAREMVAVLRRR +HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV +RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV +SVLEASYGAAGVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE +>PROKKA_00824 +MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRVEDEAQAREMVAVLRRR +HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV +RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV +SVLEASYGAAAVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE +>PROKKA_01789 +MSAPPARCTVLPRLAAGEDGWIVHELEVRRSRFLTVLGRVADEAQARAMIAALRRRHHDA +RHVCSAFVLGPERSVARSSDDGEPAGTAGTPMLEALTARETAPGRTDLTDVCAVVVRWFG +GVKLGAGGLVRAYSESVSAALDTTPLVTRSRRAILAVDAPHAQAGRWENELRAAGVAVLD +AGYGAAGVRLRVGVPDSDAQRADFAARLADITAGAGRAEPIGTEWIDHD +>PROKKA_01680 +MDSPAPPAGGPVACTVLAAGALAEDGWVVHEEEVRRSRFLAVLARTPDEEAARAVVATLR +RRHHDARHVCSAWILGPGRRRMRSNDDGEPAGTAGVPMLEALSLRDTGGGATDLTDVTAV +VVRWFGGVKLGAGGLVRAYSDAVSRALDAAPLVRRTRRARYELAAPHGEAGRWAHELELT +GASLEGVRWDGPQAVIDLAVPDVPDGHSALASAVARITSGSAVAAPAGHVWVDGALA +>PROKKA_01054 +MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRVEDEAQAREMVAVLRRR +HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV +RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV +SVLEASYGAAAVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000920.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000920.fa new file mode 100644 index 0000000000000000000000000000000000000000..c43cef8bd2ba46b5a2fec61ffb1428273089fb57 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000920.fa @@ -0,0 +1,25 @@ +>PROKKA_01107 +MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV +QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV +QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA +DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD +>PROKKA_00826 +MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV +QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV +QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA +DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD +>PROKKA_01786 +MTESVPVADRPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV +QDEFGDRVLTSDGELDRVALAHIVFSDPQARQRLNRIVHPRIRAAARRIVAAAGPDAVVV +QDVPLLVETGQQDAFDLVIVVEAPLEERLRRMVEDRGMTPEDAQARIDAQATDDQRRAAA +DVVIVNDADLERLASVANQVWDRFLAPDAAEPSAD +>PROKKA_01678 +MTDAVTDVTLRPRLHVGLTGGIAAGKSAVAAELERCGALLVDSDALARLVLEPGTEGLAA +VQDAFGDRVIAADGSLDRAALAQIVFADPAARQRLNGIVHPRVRRMAREIVAQAGPDAVV +VQDVPLLVETGQADAFDLVIVVEAPAEERIRRMVEDRGMSREDALARMAAQATDEERAAV +ADVVIVNDGDLDRLREITRRVWEGMAA +>PROKKA_01056 +MTETDPVAERPRVHVGLTGGIAAGKSAVARVLQERGALLVDSDALARLVLEKGTDGLAAV +QDEFGDRVITADGELDRVEMARIVFGDEGARQRLNRIVHPRIRAAARRIVAEAGPDAVVV +QDVPLLVETGQADAFDLVIVVEAPLEERLRRMVEDRGMSRADAEARIAAQATDEQRRAVA +DVVIVNDADLERLASVANQVWDRFLAPGAAEPSAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000923.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000923.fa new file mode 100644 index 0000000000000000000000000000000000000000..75f819ca27dfbcd3f5c2e97d96fff7d94987f668 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000923.fa @@ -0,0 +1,30 @@ +>PROKKA_01110 +MTALALLALGLHDLLDAVLPGAWPTPRRRWLARAGAAVAAVLAAVLVAVLAPTGISVAVG +GGLVALGLLMGWTWLHPDRPLGVVAVAAAVGLVAVLESTLAPAGLRSAPPALTLLAVTVA +LTETGNRVTRAVLALAGRSADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME +RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV +VVWLALGLTAPGAA +>PROKKA_00829 +MTALALLALGLHDLLDAVLPGAWPAPRRRWLARAGAAVAAVLAAVLVAVLAPTGVAVAVG +GGLVSLGLLMGWTWLHPDRPLGVVAVVAVVGLVAVLESTLAPAGLRSAPPALTLLAVALA +LTETGNRVTRAVLALAGRPADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME +RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV +VVWLALGLTAPGAA +>PROKKA_01782 +MTALTLIALGVHDLAAALLPRAWAARRREVLALAAGTAAAVLAAVLLVVLVPGAPALAIG +GVLVALALLAAWWRLGAGAPLGTLGVAAVVALVAVAEIGLARTAGPAVPIAFTVVAVGLA +LGETANRITRAVLLLAGRRADAAPAPESDAPAEAVLAPETSADDAEAPPLRGGRYIGPME +RVLMVVLGLAHAWPVVAALMAAKGLVRFPEISADRGEGSRAEEFLVGSLASWGIAAAGGA +LVWVGLGAPALS +>PROKKA_01675 +MTALTLLALGLRDLLAVTPGRTSRHPWLALLAAVGAVLIGGVVLAGGAASAAETLSAVAL +ALGAVLAWHALARAGSPHLRVGALGGVVGLAVAEHTGALTVAHGPVGMALLGAGLVLVET +ANVVTRDVLRLAGRPSTDDVHDADDVHDADDDGEGLRGGRFIGPMERLLMAVLGLMAAWQ +AVAAIMAAKGIVRFPEISKDARAGDAKGGPMGASAEEFLVGSLASWTLAAGAGLVVHLAL +AGG +>PROKKA_01059 +MTALALLALGLHDLLDAVLPGAWPAPRRRWLARAGAAVAAVLAAVLVAVLAPTGVAVAVG +GGLVSLGLLMGWTWLHPDRPLGVVAVVAVVGLVAVLESTLAPAGLRSAPPALTLLAVALA +LTETGNRVTRAVLALAGRPADGGDEEAEDPAAEPTTVPSAAPTDPAADGLRGGRYIGPME +RLLMVVLGLAQAYPVIAALMAAKGIVRFPEISADRGAGSRAEEFLIGSLASWGLAAAGAV +VVWLALGLTAPGAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000930.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000930.fa new file mode 100644 index 0000000000000000000000000000000000000000..1b2c4a8672e5afe771f26753b778856aeb4edb40 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000930.fa @@ -0,0 +1,35 @@ +>PROKKA_01121 +MTSPLTGQLPLPPGMGSEGRGVGAGMSRPTARVTALGGGHGLSASLAALRHVAGHLTAIV +TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAHVMQHRFHSTEVPADQAT +LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGR +LRTRCVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALSAIEMADWVVLGPGSLYTSVLP +HLLMPDVRAALAATTARRLMVLNLRTGDQETTGLTHADHLKVLRSYAPDLRLDVVIADVD +AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVSIGEAMTH +>PROKKA_00840 +MTSPLTGQLPLPPGMGSEGRGVGAGMSRPTARVTALGGGHGLSASLAALRHVAGHLTAVV +TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAHVMQHRFRSTEVPADQAT +LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGR +LRTRCVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALSAIELADWVVLGPGSLYTSVLP +HLLMPEVRSALAATAARRLMVLNLRTGDQETTGLAHADHLKVLRSYAPDLRLDVVIADVD +AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVAIDEAMTH +>PROKKA_01772 +MTSPLTGQLPLPPGVGTAVRGPAGGMARPAIRVTALGGGHGLSASLTALRHVAGHLTAIV +TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAQVMQHRFRSTEVDAEEAT +LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGG +LRTRRVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALAAIELADWVVLGPGSLYTSVLP +HLLMPEVCQALDATAARRLMVLNLRTGDQETTGLTHADHLRVLHSHAPDLRLDVVIADVD +AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVAIDEAMTD +>PROKKA_01665 +MTGPVTGPSTSSLPLPPAAARGAWATTSGTVRPQVRVTALGGGHGLSASLAALRLVAGHL +TAVVTVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAQVMQHRFRSTEVPE +AEATLDGHALGNLLIVALWELIGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDLLAED +DAGRLVRRHVEGQVALAQAAHDGRVVDVRLSPADAPATPEALAAIELADWVVIGPGSLYT +SVLPHLLMPEVRGALEVTTARRIFVLNIDTGTQETTGMTHADHLKVLREHAPGLQLDVVI +ADADAVADRAAVVQEARRLGARVAFSRVAHAANRLAHDPLRLAVAIDEAMSS +>PROKKA_01071 +MTSPLTGQLPLPPGMGSEGRGVGAGMSRPTARVTALGGGHGLSASLAALRHVAGHLTAIV +TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAHVMQHRFRSTEVPADQAT +LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGR +LRTRCVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALSAIELADWVVLGPGSLYTSVLP +HLLMPDVRAALAATTARRLMVLNLRTGDQETTGLTHADHLKVLRSYAPDLRLDVVIADVD +AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVAIDEAMTH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000931.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000931.fa new file mode 100644 index 0000000000000000000000000000000000000000..53e4f290b2515a602fddce4ac3d56c498eced7b1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000931.fa @@ -0,0 +1,35 @@ +>PROKKA_01122 +MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVAGRVVVEVELDHGASARRLRA +AITELYGLAPEIVVVSGGNLRRGQRYVLRVVRGGEDLARQTGLIDQRGRPVRGLAPVLVS +GTTAATAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLRVAAKAREVRQ +SDRVVVRDGEAIATLLAAVGAEQTATLWRERRERKEVRATANRLANFDDANLRRSAQAAV +TAGAKVERALEILGDEVPDHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL +AMADKRAAERGIPGTDAASEG +>PROKKA_00841 +MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVAGRVVVEAELDHGASVRRLRA +AITELYGLAPEIVVVSGGNLRRGQRYVLRVVRGGEDLARQTGLIDQRGRPVRGLAPVLVS +GTTAATAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLRVAAKAREVRQ +SDRVVVRDGEAIATLLAAVGAEQTATLWRERRERKEVRATANRLANFDDANLRRSAQAAV +TAGAKVERALEILGDEVPDHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL +AMADKRAAERGIPGTDAASEG +>PROKKA_01771 +MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVSGRVVVEAELDHGASARRLRA +SITELYGLATEIVVVSGGNLRRGQRYVIRVVRGGEDLARRTGLIDQRGRPVRGLASALVT +GTTADTAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLDVAAKAREVRQ +ADRVVVRDGEAIATLLTAVGAEQTAALWRERRERKEVRATANRLANFDDANLRRSAQAAV +AAGAKVERALEILGDEVPEHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL +AMADKRAAERGVPGTDTPAED +>PROKKA_01664 +MALTMTLKEELARVPVGAVPERRAETATMLRFAGGLHLVSGRVVIEAELDHGASARRLRA +AITELYGHATEIVVISGGNLRRGQRYVIRVVRGGEDLARQTGLLDLRGRPVRGLPPALVQ +GSAADTAAVWRGALLAHGSLTEPGRSSCLEVTTPGPEAALALVGAARRLGVAAKAREVRQ +ADRVVVRDGEAIAALLTAVGADQTAALWQERRERKEVRATANRLANFDDANLRRSAQAAV +AAGARVERALEILGDDVPDHLGYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL +SMADKRAAAEGIPGTAVDGA +>PROKKA_01072 +MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVAGRVVVEVELDHGASARRLRA +AITELYGLAPEIVVVSGGNLRRGQRYVLRVVRGGEDLARQTGLIDQRGRPVRGLAPVLVS +GTTAATAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLRVAAKAREVRQ +SDRVVVRDGEAIATLLAAVGAEQTATLWRERRERKEVRATANRLANFDDANLRRSAQAAV +TAGAKVERALEILGDEVPDHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL +AMADKRAAERGIPGTDAASEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000932.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000932.fa new file mode 100644 index 0000000000000000000000000000000000000000..a4ad3ab5e6fe25b863a0978e89c5431909b7e8cd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000932.fa @@ -0,0 +1,25 @@ +>PROKKA_01123 +MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN +QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI +QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA +IWNIVNWADVQARFEAARAGASGLILPA +>PROKKA_00842 +MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN +QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI +QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA +IWNIVNWADVQARFEAARAGASGLILPA +>PROKKA_01770 +MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAARDADDFAAVN +QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEHFGSFDKFRAHFTAAALGI +QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA +IWNIVNWADVQARFEAARQGASGLILPA +>PROKKA_01663 +MTEFVLPELDYDYAALEPHISAKIMELHHSKHHATYVKGANTALEKLAAAREAEDFASVN +QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEFFGSFDKFQAHFTAAALGI +QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA +IWNIVNWADVQQRFEAARNGASGLILPA +>PROKKA_01073 +MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN +QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI +QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA +IWNIVNWADVQARFEAARAGASGLILPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000933.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000933.fa new file mode 100644 index 0000000000000000000000000000000000000000..30e813ba1582091dc48d7f87c65774e872acc259 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000933.fa @@ -0,0 +1,35 @@ +>PROKKA_01124 +MTKIAINGYGRIGRNIVRVLRDRGHENLELVAVNDLADPEDLFWLTQYDTILGRYPGELE +RTEKGFRIDGRDVAFFQEADPTKLPWGELGVDLVIECTGIFTTGPKAQAHLDAGAKKVLI +SAPAKEVDGTFVMGVNEHTYDAESMHIVSNASCTTNCLAPMAKVLNDEFGIVDGIMTTIH +AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT +GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP +LTKSIGQTVKIIGWYDNEYGYTSQLMDFADLIGSKL +>PROKKA_00843 +MTKIAINGYGRIGRNIVRVLRDRGHEGLELVAVNDLADPEDLFWLTKYDTILGRYPGELE +RTEKGFRIDGRDVAFFQEADPTKLPWGELGVDLVIECTGIFTTGPKAQAHLDAGAKKVLI +SAPAKEVDGTFVMGVNEHTYDAETMHIVSNASCTTNCLAPMAKVLNDEFGIVDGIMTTIH +AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT +GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP +LTKSIGQTVKIIGWYDNEYGYTSQLMDFADLIGSKL +>PROKKA_01769 +MTKIAINGYGRIGRNIVRVLRDRGYENLELVAVNDLADNEDLFWLTQYDTILGRYPGELE +LTETGFRIDGRDVAFFSEPDPAKLPWGELGVDIVIECTGFFTTGPKAKAHLDAGAKKVLL +SAPGKEVDGTFVMGVNEKNYDSATMDIVSNASCTTNCLAPMAKILNDEFGIVDGIMTTIH +AYTGDQNLHDSVHKKDRRRARAAAQNMVPTDTGAAKAIGEVIPELKGKLDGFAMRVPTIT +GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP +LTKSIGQTVKIIGWYDNEYGYTSQLVDFADLIGSKL +>PROKKA_01662 +MTKIAINGYGRIGRNAVRVLLEQGHDDLELVAVNDLAATEDLFWLTKYDTILGRFPGELE +LTDKGFSINGKDVAFFAETDPANLPWGELGVDIVVECTGRFTTGPAAKAHLDAGAKKVLL +SAPGKEVDGTFVMGVNEGDYDSSTMHIVSNASCTTNCLAPMVKVLNDEFGIVDGIMTTIH +AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT +GSATDLTVELTRHVEAEEVNEAFRRAAESGPLVGRLVYSTDPIVSSDIVTAPAACTFDAP +LTKSIGQTVKVIGWYDNEYGYTCQLMDMASHMASKL +>PROKKA_01074 +MTKIAINGYGRIGRNIVRVLRDRGHENLELVAVNDLADPEDLFWLTQYDTILGRYPGELE +RTEKGFRIDGRDVAFFQEADPTKLPWGELGVDLVIECTGIFTTGPKAQAHLDAGAKKVLI +SAPAKEVDGTFVMGVNEHTYDAETMHIVSNASCTTNCLAPMAKVLNDEFGIVDGIMTTIH +AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT +GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP +LTKSIGQTVKIIGWYDNEYGYTSQLMDFADLIGSKL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000934.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000934.fa new file mode 100644 index 0000000000000000000000000000000000000000..7811cc1acd5d234f9c4670af081e8e8c72d3e6ca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000934.fa @@ -0,0 +1,40 @@ +>PROKKA_01125 +MPAPTLTDLLEAGVAGRTVLIRSDLNVPLDGDTVTDDGRIRASLPAIRDLAEAGARVIVM +AHLGRPKGEPDPAYSLRPVAARMAELLGTDVALAADVTGDDARAKAAALQDGQVLLLENV +RFDARETSKDDAERAALAGEMAALAGDDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL +VAAELEVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG +HEVGASLLEEDQLDTVREYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLAVDALTSGA +HGASAMGLDIGPETARAFAEQIRGAQTVFWNGPMGVFEFPAFAEGTRAVARALTEASAAG +GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALAGEGRA +>PROKKA_00844 +MPAPTLTDLLEAGVAGRTVLIRSDLNVPLDGDTVTDDGRIRASLPAIRDLAEAGARVIVM +AHLGRPKGEPDPAYSLRPVAARMAELLGTDVALAADVTGDDARAKAAALQDGQVLLLENV +RFDARETSKDDAERAALADEMAALAGEDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL +VAAELEVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG +HEVGASLLEEDQLDTVREYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLAVDALTSGA +HGASAMGLDIGPETARAFAEQIRGAQTVFWNGPMGVFEFPAFAEGTRAVARALTEASAAG +GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALAGEGRA +>PROKKA_01767 +MPAQTLNDLLEAGVAGRTVLIRSDLNVPLDGETVTDDGRIRASLPAIRQLADAGARVIVM +AHLGRPKGEPDPKYSLRPVAARMGELLGADVALAEDVTGPSARAAAEALADGDVLLLENV +RFDARETSKDDAERAELAAEMAALAGEDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL +VAGELEVLTRLTQSPERPYAVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG +HEVGASLLEEDQLDTVRAYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLPVDALTSGA +HGASAMGLDIGPETARAFAEQIRGAETVFWNGPMGVFEFEAFAEGTRAVAQALTEATAAG +GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALSGEGEA +>PROKKA_01661 +MTAQTLTDLLEAGVAGRTVLIRSDLNVPLDGQTVTDGGRIRASAPAIKDLADAGARVVVM +AHLGRPQGEPDPQYSLAPVARRLGEVLGADVQLASDVTGEDARAKAAALQDGQVLLVENV +RFDARETSKDAAERGELAREMADLAGEDGAYVGDAFGAVHRAHASVADIAGLLPAYQGPL +VAAELQVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLMEKADTLLIGGGMLFTFLKAQG +HEVGASLLEEDQLETVRGYLERSGKDGAAEIVLPTDIVMASAFAKDAEHEVLPVDALTTG +AHGADALGLDIGPGSAAAFGERIRGARTVFWNGPMGVFEFPAFAEGTRAVAQALTEATQA +GGLSVVGGGDSAAAVRSLGFTDEQFGHISTGGGASLEYLEGKELPGVSALSGTDT +>PROKKA_01075 +MPAPTLTDLLEAGVAGRTVLIRSDLNVPLDGDTVTDDGRIRASLPAIRDLAEAGARVIVM +AHLGRPKGEPDPAYSLRPVAARMAELLGADVALAADVTGDDARAKAAALQDGQVLLLENV +RFDARETSKDDAERAALAGEMAALAGDDGAYVGDAFGAVHRKHASVFDVAAQLPAHQGPL +VAAELEVLTRLTESPERPYVVVLGGSKVSDKLAVIDNLLDKADTLLIGGGMLFTFLKAQG +HEVGASLLEEDQLDTVREYLRRSEAGAARIVLPTDIVMASGFAADAEHEVLAVDALTSGA +HGASAMGLDIGPETARAFAEQIRGAQTVFWNGPMGVFEFPAFAEGTRAVARALTEASAAG +GLSVVGGGDSAAAVRTLGFADDAFGHISTGGGASLEYLEGKELPGVTALAGEGRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000937.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000937.fa new file mode 100644 index 0000000000000000000000000000000000000000..cd1faabb4f20e3610e29360f0f7f360eba14bf75 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000937.fa @@ -0,0 +1,35 @@ +>PROKKA_01128 +MKIRMHDTTTSQVAKRITQLREKSGVVALGRVLTLVISTDDAGIESAVQAANAASLEHPC +RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVV +WWPGVPPGVPSATALGRLAHRRITDTASASAAEPALWALRAGHHEGDTDLAWTRLTLWRI +QVAGIFDTLDVATLRSVTVDGAPDSPSTMLLAAWLTLTLKVPVTIAHSKVGHGIRAVRLR +CTDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTIQDCLAEELRRLDPDEVFGAVLHQGL +PRTDLSPVQASER +>PROKKA_00847 +MKIRMHDTTTSQVAKRITQLREKSGVVALGRVLTLVISTDDAGIESAVQAANAASLEHPC +RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVV +WWPGVPPGVPSATALGRLAHRRITDTASASAAEPALWALRAGHHEGDTDLAWTRLTLWRI +QVAGIFDTLDVATLRSVTVDGAPDSPSTMLLAAWLTLTLKVPVTIAHSKVGHGIRAVRLR +CTDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTIQDCLAEELRRLDPDEVFGAVLHQGL +PRTDLSPVQASER +>PROKKA_01764 +MKIRMHDTTTSQVAKRITQLREKGGVVALGRVLTLVISTDDAGIEAAVEAANAASLEHPC +RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVA +WWPGVPPAVPSETALGRLAHRRITDTASAARAEPALWTLRQGHRDGDTDLAWTRLTLWRI +QVAGIFDTLDVAALRSVTVDGAPDSPSTMLLAAWLTLALKVPVTIAHSKAGHGIRAVRLR +CQDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTDQDCLAEELRRLDPDEVFGAVLHRGL +PRTDLSPVQASER +>PROKKA_01658 +MKIRMHDTTTSQVAKRLTALRESAGVSALGRVLTLVIVTDDAGIEAALGAANAASLEHPC +RIVVLALGDPLAPTRLDAEIRVGGDAGASDVVVLWCQGEDAVADEPLVSGLLLPDAPIVV +WWPGEPPAEPATTALGRLAHRRITDSATCRDAKETLQRLAAGLHDGDTDLAWTRLTLWRS +QVAAILDNLDLADVRSVTVDGAPDSPSTLLLAAWLTWGLDRPVTIAHSKAGHGIRAVRLR +GPEGDVVLSRSQSEVARLYQQGRPVQRISLPRRSDQDCLAEELRRLDPDEVYGDVLRVGL +PRTDLAPVDASDR +>PROKKA_01078 +MKIRMHDTTTSQVAKRITQLREKSGVVALGRVLTLVISTDDAGIESAVQAANAASLEHPC +RIVVLALGDPAAPTRLDAEIRVGGDAGASDVVVLWCAGENAHADESLVSGLLLPDAPIVV +WWPGVPPGVPSATALGRLAHRRITDTASASAAEPALWALRAGHHEGDTDLAWTRLTLWRI +QVAGIFDTLDVATLRSVTVDGAPDSPSTMLLAAWLTLTLKVPVTIAHSKVGHGIRAVRLR +CTDGDVVLSRSQSQVARLYQQGRPVQRISLPRRTIQDCLAEELRRLDPDEVFGAVLHQGL +PRTDLSPVQASER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000939.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000939.fa new file mode 100644 index 0000000000000000000000000000000000000000..299215644ed82c88d5b17430cbd4638a15c4e6eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000939.fa @@ -0,0 +1,50 @@ +>PROKKA_01130 +MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED +SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA +LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES +AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ +LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW +DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA +KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY +LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL +EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR +>PROKKA_00849 +MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED +SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA +LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES +AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ +LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW +DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA +KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY +LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL +EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR +>PROKKA_01762 +MSTLGLSATGSALEAIDRHLPTLLEDRVASRLGAQDAGLWGEAAREESARRLGWIDLFED +SRALVRHIDALSRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA +LERDLERTVLVVSSKSGSTVETDSQRRVMEAAFREAGIDPRSRLVAVTDPGSPLHAECES +AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLTADDADNPGLQ +LGAALGGTAPLRDKLVFTDHGSGIDGLPAWAEQLIAESTGKDGTGLLPVVVADGDPETGW +DAPDMLQVQLVGEDAPAAPAHGVQVSGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA +KTAARSLLDAPARERTADRTVDGVELSGPEAVVSAADLAGVLRATADLVPENGYLAVHAY +LSRHDDAELEEVRADLARLAGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQVTGDADLDV +EVPGRPFSLGRLIAAQAAGDARVLVEHGRPVVTLHLPHRAAGIDAIRTAARAR +>PROKKA_01656 +MSTFGLTATGAALDAVDRHVPALVAERFASRLAAEDADLWGPDARDEAAKRLGWISLFEE +SRTVAAEAAALAEELRGQGLTRVVLAGMGGSSLAPEVIAATAGAELEVLDSTDPQQVAAV +LDHDLERTVLVVSSKSGSTVETDSQRRIVEAALAAEDIDPASRIVVVTDPGSPLEEASVE +AGYRAVFTADPTVGGRYSALTAFGLVPAALAGVDVESLLDEAEDVLDLVTADDADNPALQ +LGAAIGGTEPLRDKLVIQDLGSGIDGFGDWVEQLIAESTGKDGTGLLPVVVRPGDPETAW +EAPDLLKVTLVSESEESPAGGDGVRLHGSLGALLLTWEAATAVAGRLLGINPFDQPDVEA +AKAAARELLDSPAEEAEPGTVIHGVEVSGPESVTSADDLRGVLAAVRELVPEDGYLAVHA +YLDRHADVDLAGIRADLASALGRPVTFGWGPRFLHSTGQYHKGGPRNGVYLQVTGDAALD +VEVPGRPFTLGRLIAAQAAGDADVLRRLGRPVVTLRLRDRSAGIAALRTAAREA +>PROKKA_01080 +MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED +SRALVPHIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA +LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES +AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ +LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW +DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA +KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY +LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL +EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000940.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000940.fa new file mode 100644 index 0000000000000000000000000000000000000000..c777693cfd1ec59d5a043e1f03bd2db38b6a4aff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000940.fa @@ -0,0 +1,40 @@ +>PROKKA_01131 +MSTPQNPNTAALAQAGVSIWLDDLSRTRLDEGTLEELIATRSVTGVTTNPSIFAVALADA +GAYQGQLRDLAAAGASVDEAVVALTTEDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR +DAAGTVAQARELAAAVDRPNLMVKIPATVEGLSAIADVLGAGISVNVTLIFSLPRYRRVL +NAWLTGLEKARANGHDVRRLHSVASFFVSRVDTEVDARLRAIGTPEAEALTGRAAVANAR +LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTELVAPHTVTTLPE +KTLEAVADHGVIAADTVTGAYAEADALLDAVGAAGVSYQDVVDVLETEGLEKFEAAWDEL +LGSVRSGLDAHR +>PROKKA_00850 +MSTPQNPNTAALAQAGVSIWLDDLSRTRLDEGTLEELIATRSVTGVTTNPSIFAVALADA +GAYQGQLRDLAAAGASVDEAVVALTTEDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR +DAAGTVAQARELAAAVDRPNLMVKIPATVEGLSAIADVLGAGISVNVTLIFSLPRYRRVL +NAWLTGLEKARANGHDVRRLHSVASFFVSRVDTEVDARLRAIGTPEAEALTGRAAVANAR +LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTELVAPHTVTTLPE +KTLEAVADHGVIAADTVTGAYAEADALLDAVGAAGVSYQDVVDVLETEGLEKFEAAWDEL +LGSVRSGLDAHR +>PROKKA_01761 +MSTQQNPNTAALAEAGVSIWLDDLSRKRLDEGTLEELMATRSVTGVTTNPSIFAVALADA +GSYEGQLRELAAAGADVDEAVTALTTQDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR +DAEGTARQAQELAAAVDRPNLMVKIPATVEGLAAITDVLAEGISVNVTLIFSLPRYRQVL +NAWLAGLEKARENGHDLSRIHSVASFFVSRVDTEVDARLRALGTPEAEALTGQAALANAR +LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTGLVAPRTVTTLPE +QTLEAVADHGEVAGDTVTGGYAEADALLDAVGAAGVSYQDVVDVLETEGLQKFESAWEEL +LGSVRDGLAAHR +>PROKKA_01655 +MTTETTPATAALAAAGVSLWLDDLSRTRLNEGSLERLIATRNVTGVTTNPSIFAAALKDA +GAYEAQLAELAAAGADVDAAVTALTTTDVRRACDLLAPVHQETGGRDGYVSIEVDPRLAR +DTAGTVAQARELVALVDRPNLMVKIPATVEGLPAITEVLGAGISVNVTLIFSLPRYREVL +NAWLSGLELARANGHDVSRIHSVASFFVSRVDTDVDAQLRALAEQGRPEAGELTGRAGLA +NARLAYRAFEQMKDTERWSLLEAAGAPVQRPLWASTGVKDPALADTLYVTALVAPDTVNT +MPEKTLEAYADHGELTAEPVVGGYAQADADLDAIGELGISYTELVDRLETEGLQKFEAAW +DELLASVRAGLAAHR +>PROKKA_01081 +MSTPQNPNTAALAQAGVSIWLDDLSRTRLDEGTLEELIATRSVTGVTTNPSIFAVALADA +GAYQGQLRELAAAGASVDEAVVALTTEDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR +DAAGTVAQARELAAAVDRPNLMVKIPATVEGLSAIADVLGAGISVNVTLIFSLPRYRRVL +NAWLTGLEKARANGHDVRRLHSVASFFVSRVDTEVDARLRAIGTPEAEALTGRAAVANAR +LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTELVAPHTVTTLPE +KTLEAVADHGVIAADTVTGAYAEADALLDAVGAAGVSYQDVVDVLETEGLEKFEAAWDEL +LGSVRSGLDAHR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000942.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000942.fa new file mode 100644 index 0000000000000000000000000000000000000000..94bd6d7b2991dcec98025c5cf0f438048b6b28f7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000942.fa @@ -0,0 +1,35 @@ +>PROKKA_01133 +MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR +GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW +VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW +AAVRGTVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL +YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL +SITYLTLLFIALAVDPFVGAPLMHFGA +>PROKKA_00852 +MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR +GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW +VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW +AAVRGTVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL +YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL +SITYLTLLFIALAVDPFVGAPLMHFGA +>PROKKA_01759 +MSSSLESSSAARVETAPPGVVDRSKPSLSRKVRAYVELTKPRVIELLLVTTLPTMIFAQR +GFPDVLTMAATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW +VQTVVSILVLGFGANWLAAALGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIAW +AAVRGTVEWPAIVLFTVIFLWTPPHYWPLSMKYKRDYQEADVPMLGAIASARHVSNQVVL +YAWATVVCSLLLVPMGWAGIVYTCVALVVGGWFVWESHVLHRQARREDFEDRKAMKVFHL +SITYLTLLFIALAVDPFVGEPLMRFGA +>PROKKA_01653 +MSSSVESTSPATAAPGAAAPSARPPMTVGRKARAYVELTKPRVIELLLVTTLPTMIFAQR +GFPDLLTMIATLVGGALAAGASGAFNCYIDRDIDRVMKRTARRPLVTGEVTPREALVFSW +TLAVVSVLVLGFGANWLAAALGVAAIFFYVVVYSLILKRRTEQNIVWGGIAGCFPVVIGW +AAVRGTVEWPAIVLFTVIFLWTPPHYWPLSMKYKRDYQEAEVPMLGAVASARLVSNQVVL +YAWATVACSLLLVPMGWAGIVYTAVAVGVGGWFVWESHVLQREAQRPDFEDRKAMKVFHL +SITYLTLLFIALAVDPFVGGPLMPAVTGS +>PROKKA_01083 +MSSSLESPSAARVAAAEPGVVDRSPLPLRRKVRAYVELTKPRVIELLLVTTLPTMIFAQR +GFPDVLTMIATLVGGALAAGASGTFNCYIDRDIDRVMKRTENRPLVTGEVTPREALVFAW +VQTVVSILILGFGANWLAAGLGVAAIFFYVVVYSLVLKRRTEQNIVWGGIAGCFPVLIGW +AAVRETVEWPAIVLFLVVFLWTPPHYWPLSMKYKRDYQQADVPMLGAIASARHVSNQVVL +YAWATVACSLLLVPMGWAGIVYTAVALVVGGWFIWESHVLQVQAQREDFEDRKAMKVFHL +SITYLTLLFIALAVDPFVGAPLMHFGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000943.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000943.fa new file mode 100644 index 0000000000000000000000000000000000000000..2bb5331cc7956b68e1f0a2ff35c3f7a3e418bd2d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000943.fa @@ -0,0 +1,35 @@ +>PROKKA_01134 +MSTTTPAAGTAPAGLAARLPQRLTKATMALAVASLASEIGIIVTGGAVRLTGSGLGCPTW +PKCSPESLTNTPEMGIHGYIEFGNRTLTFVLVVIAAAMFLSLWNLRGTHRSPFWLSVGLL +AGIPAQALVGGVVVLTNLNPWWVAGHFIVSSIMVAVATLLVVRIAAERRAGRAGVPLVDG +ATTVRSRAAAWAAFALTWAAVYLGTVVTGTGPHSGDPGSPRHEFDPLLVTRIHVIPVYLL +LAAALVLFFTVRRAAGASRLQRAAVLRLLLALVFQAAVGYTQHFTGLPIGVVLLHMLGSA +LLVASATEAWDRQVARYVTAGPGAAVETATPARTVAAG +>PROKKA_00853 +MSTTTPAAGTAPAGLAARLPQRLTKATMALAVASLASEIGIIVTGGAVRLTGSGLGCPTW +PKCSPESLTNTPEMGIHGYIEFGNRTLTFVLVVIAAAMFLSLWNLRGTHRSPFWLSVGLL +AGIPAQALVGGVVVLTNLNPWWVAGHFIVSSIMVAVATLLVVRIAAERRAGRAGVPLVDG +ATTVRSRAAAWAAFALTWAAVYLGTVVTGTGPHSGDPGSPRHEFDPLLVTRIHVIPVYLL +LAAALVLFFTVRRAAGASRLQRAAVLRLLLALVFQAAVGYTQHFTGLPIGVVLLHMLGSA +LLVASATEAWDRQVARYVTAGPGAAVETATPARTVAAG +>PROKKA_01758 +MASLASEIGIIVTGGAVRLTGSGLGCPTWPKCTPESLTNTPEMGIHGYIEFGNRTLTFVL +VVIAAAMFLSLWRLRRTHRSPFWLSVGLLAGIPAQAVVGGIVVLTELDPWWVAGHFIVSS +VMVAVATLLVIRIGAERRAGRAGVRIVDGVTTGASRAAAWAAFAFTWAAVYLGTVVTGTG +PHGGDPDAPRHAFDPLLVTRVHVIPVYLLIAAALVLLFTVRRAEGASRLQRAAVLRLLLA +IAVQAAIGYTQHFTGLPVVLVILHMLGSALLVAAATEVWDRQRSRYVTAGPAALLDADPT +PVTANAR +>PROKKA_01652 +MTASPTTARPAAGGSSARRPPDRVTGVTVGLALASLISQMVIVVTGGAVRLTGSGLGCPT +WPKCTPESLTTTAEMGIHGIIEFGNRTLTGVLGVIALLMIATLWRLRRSHRQAFTLSLLL +LAGIVLQAVVGGVTVWMHLDPRIVGVHFVISGALIALATMLWVRLRAEHRHGAGAPVADG +TTTPASRTASRVAYAALWLALVVGTLVTGTGPHSGDPAAARHGFDALMITRLHVVPVYIT +VAATLVLLWQVLRTPGSGAGQRVAAWSLLGAVLLQGLLGYWQHFTGLPVGVVAAHLAGAT +VAVVAGTLAWQRQTSRYRAPAVA +>PROKKA_01084 +MSTTTPAARTAPAGLAARLPQRLSKATMALAVASLASEIGIIVTGGAVRLTGSGLGCPTW +PKCSPESLTNTPEMGIHGYIEFGNRTLTFVLVVIAAAMFLSLWNLRGTHRSPFWLSVGLL +AGIPAQALVGGVVVLTNLNPWWVAGHFIVSSIMVAVATLLVVRIAAERRAGRAGVPLVDG +ATTGRSRAAAWAAFALTWAAVYLGTVVTGTGPHSGDPGSPRHEFDPLLVTRAHVVPVYLL +LAAALVLFFTVRRAAGASRLQRAAVLRLLLALVFQAAVGYTQHFTGLPIGVVLLHMLGSA +LLVASATEAWDRQVARYVTAGPGAAVETATPARTVAAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000946.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000946.fa new file mode 100644 index 0000000000000000000000000000000000000000..1c30f28f124828ada33c19007485fc6cf9eb6a6e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000946.fa @@ -0,0 +1,25 @@ +>PROKKA_01137 +MVYSDQSASPPAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDS +LVEVKRVTAARGAGRPSRRYVVTSHAQEHLPKDHLAVALDTLARLEELGGEEEVRRTARH +AFREIEERFTAAVDGRETALQDRTRILARVLDEAGYAGTLRHFGAGLAPTLRADQVCQGH +CPFQGIPARHPEFCEEETALFARLLEVDVRRLSTLAAGAHVCTTHVPLGRD +>PROKKA_00856 +MVYSDQSASPPAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDS +LVEVKRVTAARGAGRPSRRYVVTSHAQEHLPKDHLAVALDTLARLEELGGEEEVRRTARH +AFREIEERFTAAVDGRETALQDRTRILARVLDEAGYAGTLRHFGAGLAPTLRADQVCQGH +CPFQGIPARHPEFCEEETALFARLLEVDVRRLSTLAAGAHVCTTHVPLGRD +>PROKKA_01755 +MVYSDLPSHRAAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDA +LVEVKRVTSARGAGRPSRRYVVTSHAQEHLPKDHLAVALHSLARLEELGGDEEVRRTARR +AFRDVEERFAAAVDGRDTELQERTRILASVLDDAGFAGTLRHFGAGLAPTLRADQVCQGH +CPFQGIPARHPQFCEEETELFARLLQVDVRRLSTLAAGAHVCTTHVPLGRD +>PROKKA_01649 +MYSDSADPAAPAPGTRERVLERVLSHGPVSAAEIGGALGLTAAAVRRHLDALEEEGFVEV +KVVSAARGAGRPSRRYVVAPQAQRRLGGDHLGIALQAVDRLVEVGGEGEVRRLAADALQP +VEEAFQAAVAGREMGLEERTRVLADLLDDAGYAASIRHVGAGLAPTLRAEQLCQGHCPLQ +GLPARHPEFCEEETALFARLLGVDVRRLSTLAAGGHVCTTHIPLGRA +>PROKKA_01087 +MVYSDQSASPPAPAPAEGTRERVLQLVLTRGPVSAAEIGRELELTAAAVRRHLDALEEDS +LVEVKRVTAARGAGRPSRRYVVTSHAQEHLPKDHLAVALDTLARLEELGGEEEVRRTARH +AFREIEERFTAAVDGRETALQDRTRILARVLDEAGYAGTLRHFGAGLAPTLRADQVCQGH +CPFQGIPARHPEFCEEETALFARLLEVDVRRLSTLAAGAHVCTTHVPLGRD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000947.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000947.fa new file mode 100644 index 0000000000000000000000000000000000000000..9714f62e43108c34b5d63f7c48f2102c6de74ad9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000947.fa @@ -0,0 +1,50 @@ +>PROKKA_01138 +MTDQIVQRDSTETADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD +ISGKKDEPEWMRDLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP +EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE +IFEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT +LIIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR +AVVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA +PHTNSSIVSKSVARSGGRAAYRGLVQIAEGANGSANSVVCDALLVDTVSRSDTYPYIDIR +EDDVTLGHEATVSKVSEEQLFYLMSRGMSEDEAMAMIVRGFIEPIARELPMEYALELNKL +IELQMEGSVG +>PROKKA_00857 +MTDQIVQRDSAETADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD +ISGKKDEPEWMRDLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP +EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE +IFEEYFGSVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT +LIIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR +AVVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA +PHTNSSIVSKSVARSGGRAAYRGLVQIAEGANGSANSVVCDALLVDTVSRSDTYPYIDIR +EDDVTLGHEATVSKVSEEQLFYLMSRGMSEDEAMAMIVRGFIEPIARELPMEYALELNKL +IELQMEGSVG +>PROKKA_01754 +MTDQIVQRDPVENADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD +ISGKKDEPEWMRNLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP +EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE +IFEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT +LIIADEDSYVHYIEGCTAPIYNSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR +AVVESGGTMEWVDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA +PNTSSSIVSKSVARNGGRAAYRGLVQVTEGAKNSANSVVCDALLVDTVSRSDTYPYIDIR +EDDVTLGHEATVSKVSEEQLFYLMSRGLSEDEAMAMIVRGFIEPIARELPMEYALELNKL +IELQMEGSVG +>PROKKA_01648 +MTDQIVQQDSRGADPGVISEILEKNPELNAIGAYQYGWADSDAAGSSARRGLNEDVVKDI +SAKKSEPEWMTKLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWDDLPE +DIRNTYERLGIPEAERDRLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPEI +FEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERTL +IIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKRA +VVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEGATGETLSVAFAGKDQHQDTGSKMVHMAP +NTNSSIVSKSVARNGGRAAYRGLVQVNEGARGAANSVVCDALLVDTVSRSDTYPYIDIRE +DDVTLGHEATVSRVSEEQLFYLMSRGLAEDEAMAMIVRGFIEPIARELPMEYALELNKLI +ELQMEGSVG +>PROKKA_01088 +MTDQIVQRDSAETADPGVIQEILDKNPELNAIGAYQYGWADSDAAGEKAVRGLNEDVVRD +ISGKKDEPEWMRDLRLKALKYFERKPMPAWGPDLSGIDFDNIKYFVRSTEGQAKTWEDLP +EDIRNTYERLGIPEAERERLVAGVAAQYESEVVYHQIREDLEEQGVVFLDTDTALKEHPE +IFEEYFGTVIPVGDNKFASLNTAVWSGGSFVYVPKGVHVEIPLQAYFRINTENMGQFERT +LIIADEDSYVHYIEGCTAPIYQSDSLHSAVVEIVVKKNARVRYTTIQNWSTNVYNLVTKR +AVVEAGGTMEWIDGNIGSKVTMKYPAVYLTGEHATGETLSVAFAGKDQHQDTGSKMVHMA +PHTNSSIVSKSVARSGGRAAYRGLVQIAEGANGSANSVVCDALLVDTVSRSDTYPYIDIR +EDDVTLGHEATVSKVSEEQLFYLMSRGMSEDEAMAMIVRGFIEPIARELPMEYALELNKL +IELQMEGSVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000948.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000948.fa new file mode 100644 index 0000000000000000000000000000000000000000..499b209e508dc377cbfecbc2d6a9140c600d36af --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000948.fa @@ -0,0 +1,40 @@ +>PROKKA_01139 +MTDTVENTQRTMIPGMGEEGEKLTAAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT +GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVTVAEQAGVTVETVARDDARVGSVLTP +DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH +RGTAVLAQNVEFDVRRDARLNVVALQAWEGDAVHVSAQQASVATNAHFKHVAVSYGGGVV +RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV +WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ +LFYLMARGISETEARRLIVRGFLNEIIQKIGIGDVEDELTAVMEDELRIAQL +>PROKKA_00858 +MTDTVENTQRTMIPGMGEEGEKLTAAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT +GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVTVAEQAGVTVETVARDDARVGSVLTP +DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH +RGTAVLAQNVEFDVRRDARLNVVALQAWEADAVHVSAQQASVATNAHFKHVAVSYGGGVV +RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV +WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ +LFYLMARGISETEARRLIVRGFLNEIIQKIGIGDVEDELTAVMEDELRIAQL +>PROKKA_01753 +MTDTVENTQGSMIPGMGEEGEKLTVAQTSAPRAGAPERNAAGSRADRVSSYELADFPVLT +GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPSVTVAEQVGVRVETVARDDARVGSVLTP +DDRVSAAAWNSVAQATVVTVSGEVAEPVRIDVVGSSAEPAAMHLTVIVEENAQADVVLAH +RGTAVLAQNVEFDVRRDARLNVVSLQAWEDDAVHVSAQQASVATNARFKHVAVSHGGSVV +RLTPTSRFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPRCVSNVLYKGALQGADARTV +WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ +LFYLMARGISETEARRLIVRGFLNEIIQKIGVRDVEDELTAVMEDELRIAAL +>PROKKA_01647 +MENTERNMIPGMGEEGETLAGGQDAGAPVATRGQGQSRADRVSSKDLADFPVLTGREEDW +RFTPLERLGGLHLPGGDDARLTGAAPAVTVSETAGVSVETVGRDDARVGSVLTPDDRVSA +AAWTSFAEATVVTVSGEPGEPVRIEVTGSGVEPAAQQLTLIAEENAHADVVLTHRGSAVL +AQNVEFEVRRGASLNVVSVQAWDDDAVHVGAHQASVARDAHLKHVTVTHGGSLVRLTPTA +RFSDERGEAEMYGLYYADAGQHLENRLFVDHNRPNCVSNVLYKGALQGQDAHTVWVGDVL +IRTEAEGTDSYEKNENLLLTDGARADSVPNLEIETGVIEGAGHASATGRFDETQLFYLMA +RGIPESEARQLIVRGFLNEILQKIGIADVQDELTAVMEEELRVTAL +>PROKKA_01089 +MTDTVENTQRTMIPGMGEEGEKLTVAQNPAARAGGRERNAAGSRADRLSSFELSDFPVLT +GREEDWRFTPLKRLGGLHLPEGDDARLTGAAPAVAVAEQAGVTVETVARDDARVGSVLTP +DDRVSAAAWNSVSEATVVTISGEVAEPVRIDVVGSSADPAAMHLTVLVEENAQADVVIAH +RGTAVLAQNVEFDVRRDARLNVVALQAWEGDAVHVSAQQASVATNAHFKHVAVSYGGGVV +RLTPTARFAAERGEAEMYGLYFADAGQHLENRLFVDHNQPDCVSNVLYKGALQGTDARTV +WVGDVLIRKEAEGTDTYEKNQNLLLSDGARADSVPNLEIETGVIEGAGHASATGRFDETQ +LFYLMARGIPETEARRLIVRGFLNEIIQKIGVGDVEDELTAVMEDELRIAQL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000949.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000949.fa new file mode 100644 index 0000000000000000000000000000000000000000..f0fa2357f8c7c7861a1c967af66cd637b6c5d90f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000949.fa @@ -0,0 +1,30 @@ +>PROKKA_01140 +MATLQITDLHVQIATENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE +VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGEAPSLR +TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV +DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE +AEGYARFEKAAAGA +>PROKKA_00859 +MATLQITDLHVQIETENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE +VTSGSITLDGEDVLEMSVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGQAPSLR +TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV +DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE +AEGYARFEKAAAGA +>PROKKA_01752 +MATLQITDLHVQIETENGPKEILKGLSLTIETGQTHAIMGPNGSGKSTLASTIAGHPRYE +VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGEAPSLR +TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV +DALRIVSEGVNRAAEQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAAQLE +AEGYARFEKAAAGV +>PROKKA_01646 +MATLQITDLHVQIETENGPKEILKGLSLTINTGETHAIMGPNGSGKSTLASTIAGHPRYE +VTSGSITLDGEDVLEMSVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTAIDGEAPSLR +TWSKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV +DALRIVSEGVNRAAEANEMGTLLITHYTRILNYIKPQHVHVLVDGRVAESGGPELAARLE +SEGYARFEKAAAEA +>PROKKA_01090 +MATLQITDLHVQIATENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE +VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGQAPSLR +TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV +DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE +AEGYARFEKAAAGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000951.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000951.fa new file mode 100644 index 0000000000000000000000000000000000000000..415423cf6c981b76ce352eda8554747d84ac5c4a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000951.fa @@ -0,0 +1,34 @@ +>PROKKA_01142 +MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV +GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVVATTEAADEFWGEYLAQFSDIQW +RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI +VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHATSTVDPESGEPF +LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSAQQEP +DIRQCDTFRAPSLDI +>PROKKA_00861 +MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV +GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVIATTEAADEFWGEYLAQFSDIQW +RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI +VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHAASTVDPESGAPF +LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSSQQEP +DIRQCDTFRASSLDI +>PROKKA_01749 +MGGRGLAIGGGGGLLALLLAIFAPGLAGQLGIDTGGSTGQSQYQQQGAGGTQPVSDEECS +TGADANRNTDCRVIAATEAADQFWGEYMSQFSDVDWRQPQLTLFAGSVSTGCGSASSAMG +PFYCPADESMYFDTSFFETLQSDFGAEGGPLAEQYIVAHEYGHHVQHVTGYLQYSRDGST +GPESGAVRAELQADCLAGMWAGAATTTVDPESGEPYLQPISREQLRQAIDAAAAVGDDRI +QEMSTGRVNPEAFTHGSSEQRMAWFLRGYETSQQEPDFRQCDTFRASSLDI +>PROKKA_01644 +MSFNENVQINAGRARGGGGGGMGGRGLAIGGGGGILALLLAIFAPGLAEDLGIGGAGTGT +GSSYQQQLPQSGSGTSTQPVSQADCSTGADANQNTDCRVIATTESADAFWGDYMGQYSNI +QWRQPDLTLFTTSVSTGGCGSATSATGPFYCPADESMYFDTAFFSTLESDFGATGGPLAE +EYIVAHEYGHHVQNVVGWLQYAQDGRTGAASNAVRSELQADCLAGMWAGHAATTKDPETG +EAFLQPITQEQLAQAIDAAGAVGDDRIQEQYQGRVNPEAFTHGSASQRQAWFMRGYETTS +QQSPDINQCNTFQAATLDI +>PROKKA_01092 +MSFNENVQIDAGRARSGGGGGLGGRGIAIGGGGGLLALLLAIFAPGLAEQLGIDTGGGSV +GQSQYQQQTGSGGQSQPLSDEECASGADANQNTDCRVIATTEAADEFWGEYLAQFSDIQW +RQPQLTLFQGGVSTGCGSASSATGPFYCPADESMYFDTAFFETLQTDFGAEGGPLAEEYI +VAHEYGHHVQQVTGYLQHSKDGTTGPTSGAVRAELQADCFAGMWAGHAASTVDPESGAPF +LKPISQDQLRQAIDAASAVGDDRIQSTHTGRVDPEAFTHGTSEQRMAWFMRGYQSSQQEP +DIRQCDTFRASSLDI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000952.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000952.fa new file mode 100644 index 0000000000000000000000000000000000000000..f5d35f8870befa2dae9678fb38ddf0366819b54d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000952.fa @@ -0,0 +1,50 @@ +>PROKKA_01143 +MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR +TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS +RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIL +LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM +TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG +VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLGIFTGVDLAIDRGSRVVILGYN +GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT +QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE +ILHALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA +>PROKKA_00862 +MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR +TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS +RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM +LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM +TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG +VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN +GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT +QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE +ILHALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA +>PROKKA_01748 +MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKILAGGGQPTAGSVTR +TGRIGYLPQDPKVEDMDQSGRDRILSARDLDHTIRRMREAEAGMAAVDDVERQRAMDRYS +RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM +LLDEPTNHLDHDSIVWLRDYLKTYPGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM +TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG +VEGERAADRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN +GAGKTTLLRMLAGEEAPDTGEVQEGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT +QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE +ILGALRQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNEDYKDLITLA +>PROKKA_01643 +MLTVTDLELRVGARLLMDEVSFRVAKGDKVGLVGRNGAGKTTLTRVLAGITQPTAGSVTV +SGRLGYLPQDPKVEDMDQSGRDRILAARDLDQTIRRMRAAEADMASEDDAARQKAMDRYS +RLQAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADTM +LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDAMRQTIDVYNM +NWKNYQAQRQQDEARRRREFANAEKKASALLAQAEKMRAKATKATAAQNMIKRAERMMRG +VEGERAQDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN +GAGKTTLLRMLAGTESPDTGEVIAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT +QCRTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE +ILNALRQYEGAVVLVTHDEGAVEALAPERVVLLPDGDEDLWSDDYLDLISLA +>PROKKA_01093 +MLTVTDVELRVGARLLMDEVNFRVDKGDKVGLVGRNGAGKTTLTKVLAGGGQPTAGTVTR +TGRIGYLPQDPKVEDMDQSGRDRILSARDLDQTIRRMREAEAGMAAVDDAERERAMNRYS +RLEAEFEARGGYAAESEAARITSNLGLPDRVLDQPLHTLSGGQRRRVELARILFSDADIM +LLDEPTNHLDHDSIVWLRDYLKTYSGGLLMISHDVELMEMTVNKVLYLDANRQTMDVYNM +TWKNYLAQRQQDEARRRREFANAEKKASALMAQAEKMRAKATKATAAQNMIKRAERLMRG +VEGERAVDRVAAIRFPTPQASGKTPLRAENLSKSYGSLEIFTGVDLAIDRGSRVVILGYN +GAGKTTLLRMLAGEETPDTGEVQAGHGLKLGYFAQEHDTLDQDASVLDNMRHAAPQLGDT +QARTLLGSFLFQGDDVDKPARVLSGGEKTRLALATLVASSANVLLLDEPTNNLDPASREE +ILNALQQYEGAVVLVTHDEGAVEALDPERVVLLPDGVEDLWNDDYRDLITLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000955.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000955.fa new file mode 100644 index 0000000000000000000000000000000000000000..f40c6aaf42011a9d4341fd8431daba07c4730fdd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000955.fa @@ -0,0 +1,30 @@ +>PROKKA_01148 +MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA +VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD +AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFTEKGVGF +VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREGLEVGHTE +LVGGAEDFLGQD +>PROKKA_00867 +MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA +VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD +AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFAEKGVGF +VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREDLEVGHTE +LVGGAEDFLQQN +>PROKKA_01744 +MTEKDLTGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQKIEEAGGRA +VAVGGDVTSAEDRAALLDAAVESFGSLDVLVLNASGGMESQFGEDYAMKLNRDAQAALAD +AALERMSAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFEAKGVGF +AVVSGDMIEGTITATLLDRAEPGAIDARREAAGRLYSVEEFAAEVAALVGRDDLEVGHTE +LVGGARDFLARGEG +>PROKKA_01638 +MTTQDLAGKGVVVTGSSRGIGAETAQLLAARGAGVVVNYRQKAPRANKVVQAIEAARGRA +VAVGGDVTVAEDRAALLDAAIDNFGSLDVLVLNASGGMESQFGEDYAMTLNRDAQAALAD +AALERMSAGGQIVFVTSHQAHFIDEVATMDAYEPVARSKRAGEDALRERIPAFEAKGVGF +VVVSGDMIEGTITATLLNRAEPGAIEARREAAGKLYSVEEFAAEVAALVGRTDLEVGHTE +LVGGAQDFLGQD +>PROKKA_01098 +MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA +VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD +AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFAEKGVGF +VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREDLEVGHTE +LVGGAEDFLQQN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000957.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000957.fa new file mode 100644 index 0000000000000000000000000000000000000000..bce18168a39ba1f5f1ba5ab3f42f029fcd715a59 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000957.fa @@ -0,0 +1,30 @@ +>PROKKA_01150 +MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL +LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY +GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL +LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEEVPPGFTHALLLRDGGVVAA +GPIESTLTEEHLSAAFGTDLKVTRTGGRYTAVAR +>PROKKA_00869 +MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL +LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY +GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL +LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEDVPPGFTHALLLRAGGVVAA +GPIESTLTEEHLSSAFGTDLKVTRTGGRYTAVAR +>PROKKA_01742 +MTLPAPSDDWFLPDEDAVLQMRRVRVRRGQTDILGPLDWTVRAGERWIVMGPNGAGKSTL +LQIAATRLHPTGGEVAILEEVLGAVDVFELRPRIGLSSAQLAAQVPHEEKVQDAVVTAAY +GVTGTWRESYEDEDRMRALGLVSSWGLSRLAHRRFGTLSEGERKRVLIARSLMTDPELLL +LDEPAAGLDLAGREALVAQLSELARDEDAPALVLVTHHLEEVPPGFTHALLLRDGHAVAA +GPIEQTLTEGHLSAAFDTPLRVTRTGGRYTAVAQ +>PROKKA_01636 +MNTAPQDPSPRPVVEHDVFTPDEDAVLQLRDVAVRRGAKQILAGIDWTVRAGERWVVMGP +NGAGKSTLLQIAASRMFPTSGDVAILDEVLGAVDVFELRPRIGLSSALLANQVRDDETVQ +DAVITASYGMTGRWREEYEVEDRARALGLVSEWGLSRLAHRRFGTLSEGERKRVLIARAL +MTDPELLLLDEPAAGLDVAGREALVGQLSELAADEDAPATVLVTHHLEEVPPGFTHALLL +ADGAVVQAGPLEETLTAEHLSTAFGTPLRVTRADGRYTAVAA +>PROKKA_01100 +MTTPAPPDDWFLPDEDAVLQMRRVRVRRGTTDILGPLDWTVRAGQRWIVMGPNGAGKSTL +LQLAAARLHPTAGDVGVLDEVLGAVDVFELRPRIGLSSAQLAAQVPANETVQDAVVTAAY +GITGTWRERYETEDRARALGLVATWGLSRLAHRAFGTLSDGERKRVLIARALMTDPELLL +LDEPAAGLDLAGREDLVRQLTALATDEDAPALVLVTHHLEDVPPGFTHALLLRAGGVVAA +GPIESTLTEEHLSSAFGTDLKVTRTGGRYTAVAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000958.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000958.fa new file mode 100644 index 0000000000000000000000000000000000000000..a4db33d75b90df174a9054f36c7cb274c3fcb854 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000958.fa @@ -0,0 +1,30 @@ +>PROKKA_01151 +MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA +MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV +VALTVVVLQPRIQGWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ +GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL +VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG +>PROKKA_00870 +MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA +MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV +VALTVVVLQPRIQRWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ +GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL +VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG +>PROKKA_01741 +MIDVLGADVLGLELWQVVLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQISNA +IGLVAAGFSGVFGYRRELKESGAVLPVLTVASLLGGVLGAFLLILLPAEVFGVAAPVLIV +VALAFVVLQPRLQAWVRRRSAAREDGVVDVPARPSRPVSPVLWVLVFLAGVYGGYFVAAQ +GVLLMGILGVFLVGGTLVHANAIKTWLSLAVNLVAATSYLLFAFDRIDWTAVLLIAASSM +VGGLVGARIGRRISPTVLRIVIVVVGLAGLVSMVLRLVDGG +>PROKKA_01635 +MDLLTAPVLGMDLWQVALVLLAGFWAGTINSIIGSGTLVTFPVLVAVGFPPVTAQVSNAM +GLVASGFSGTYGYRRELRESRALLPRLTLASFLGAVIGATLLTVLPPTVFASVAPCLLVL +ALTIVVLQPRIQAWVRRRSAGEHGHVPGADSPVPVGPASPALWTLVFLTGIYGGYFVAAQ +GVMLMAIFGVMLVGGTLVHANAVKTWLSLTVNLTAAVFYLVFAFDRIDWRAVLLIAVSSL +VGGSVGARIGRRMSPTALRVTIVVIGVAGLVSMLSRLAGA +>PROKKA_01101 +MTGLLTAQLLGMDLWQVLLVLLAGFWAGTINSVIGSGTLVTFPTLVAVGFPPVTAQVSNA +MGLVASGFSGTYGYRRELAQSRALLPKLTVASLLGGVIGAALLTTLPPAVFGYVAPVLLV +VALTVVVLQPRIQRWVRRRAEDQGPTPGADSPVPVGPVTPTLWTLVFLTGIYGGYFVAAQ +GVMLMAIFGVLLVGGTLVHANAVKTWLSLVVNLTAAAFYLVFAFDRIDWRAVLLIALSSL +VGGLVGARIGRRISPTALRVTIVIVGLAGLVVMVMRQVSGG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000959.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000959.fa new file mode 100644 index 0000000000000000000000000000000000000000..635071490484165d634ae1cad88b4a999bc90482 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000959.fa @@ -0,0 +1,15 @@ +>PROKKA_01153 +MKSEIHPDYRYVIFNDLASGEKILTRTTANSDKTAEWTDGNTYPVIDVEISAASHPFYTG +KQRIMDTAGRVERFNARFKGFGGKK +>PROKKA_00872 +MKSEIHPDYRYVIFNDLASGEKILTRTTANSDKTAEWTDGNTYPVIDVEISAASHPFYTG +KQRIMDTAGRVERFNARFKGFGGKK +>PROKKA_01738 +MKSEIHPDYRYVIFNDLASGEKILTRTTANSEKTAEWTDGNTYPVIDVEISAASHPFYTG +KQRIMDTAGRVERFNARFKGFGGSK +>PROKKA_01633 +MKSEIHPDYRYVIFNDLASGEKILTRTTATSEKTAEWTDGNTYPVIDVEISAASHPFYTG +KQRIMDTAGRVERFNARFKGFGGKK +>PROKKA_01103 +MKSEIHPDYRYVIFNDLASGEKILTRTTANSDKTAEWTDGNTYPVIDVEISAASHPFYTG +KQRIMDTAGRVERFNARFKGFGGKK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000960.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000960.fa new file mode 100644 index 0000000000000000000000000000000000000000..dcb6b621d5265446058cc29ac4b1b119af9f4337 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000960.fa @@ -0,0 +1,35 @@ +>PROKKA_01154 +MTTLHGEYKVIGGKLVAADLSLADGRIATASINGDFYLEPDEALEDLNAAVAGLSADAEH +RVIREAVERGLRPEAELFGVDAFAVASAVRRALGKATTWGDHEWEVIGPEPMPIALTVAL +DEVLTRQVAEGRRKPTMRLWQWNEPAVVIGAFQSLANEVDPEGARRHGINVVRRISGGGA +MFMEADNCVTYSMHVPSSLVDGLETAESYPFLDEWTMDALSRLGVHAFYQPLNDIATDQG +KIGGAAQKRVGTAGLLHHVTMSYDIDADKMLEVLRIGREKLRGKGVTSAKKRVDPLRRQT +GVSRAEIWETMMTTFEERYGARRVELDEATREEAEQLARTKFATPEWTARVP +>PROKKA_00873 +MTTLHGEYKVIGGKLVAADLSLADGRIATASINGDFYLEPDEALEDLNAAVAGLSADAEH +RVIREAVERGLRPEAELFGVDAFAVASAVRRALGKATTWGDHEWEVIGPEPMPIALTVAL +DEVLTRQVAEGRRKPTMRLWQWNEPAVVIGAFQSLANEVDPEGARRHGINVVRRISGGGA +MFMEADNCVTYSMHVPSSLVDGLETAESYPFLDEWTMDALSRLGVHAFYQPLNDIATDQG +KIGGAAQKRVGTAGLLHHVTMSYDIDADKMLEVLRIGREKLRGKGVTSAKKRVDPLRRQT +GVSRAEIWETMMTTFEERYGARRVELDEATREEAEQLARTKFATPEWTARVP +>PROKKA_01736 +MTTHHGEYKVIGGKLVAADLTIDDGRIAAASINGDFFLEPDEALEDLNAAVTGLSADAEH +RVIQAAVEAGLREDAELFGVDAHAIATAVRRALGKATTWEDHEWEIIPPEPLPIALTVAL +DEVLTRQVAEGRRRPTMRLWQWNEPAVVIGAFQSLANEVDPEGASRHGINVVRRISGGGA +MFMEADNCVTYSLHVPRSLVDGLETAESYPFLDEWTMDALSRLGVQAFYQPLNDIATDQG +KIGGAAQKRVGQDGLLHHVTMSYDIDADKMLEVLRIGREKLKGKGVASAKKRVDPLRRQT +GVARPEIWETMMATFEERYGARRVELDDATRAEAEELARTKFGTQEWTARVP +>PROKKA_01632 +MSTQTTHHGEFKVLGGKLVAADLEVQDGVIVRASVNGDFFLEPDDALEDINAALTGLPAD +TEHHVLAERVRAGLRPEARLFGFDAEAVATAVRRAVGLATTWESHRWEILPPEPLPIEMN +TALDQILTEDVAAGRRNPVMRLWQWTEPAVVIGAFQSLANEVDPDGVTRHGIHVVRRVSG +GGAMFMEADNCVTFALSAPASLVDGIDTAESYPFLDEWVMEALRELGVQAFYQPLNDIAT +DQGKIGGAAQKRFGATGLLHHVTMSYDIDADKMTEVLRIGREKLRGKGVASAKKRVDPLR +RQTGVPREQIWETMMAVFERRYGARRVELDADTRARAEELARTKFSSPEWTARVP +>PROKKA_01104 +MTTLHGEYKVIGGKLVAADLSLADGRIATASINGDFYLEPDEALEDLNAAVAGLSADAEH +RVIREAVERGLRPEAELFGVDAFAVASAVRRALGKATTWGDHEWEVIGPEPMPIALTVAL +DEVLTRQVAEGRRKPTMRLWQWNEPAVVIGAFQSLANEVDPEGARRHGINVVRRISGGGA +MFMEADNCVTYSMHVPSSLVDGLETAESYPFLDEWTMDALSRLGVHAFYQPLNDIATDQG +KIGGAAQKRVGTAGLLHHVTMSYDIDADKMLEVLRIGREKLRGKGVTSAKKRVDPLRRQT +GVSRAEIWETMMTTFEERYGARRVELDEATREEAEQLARTKFATPEWTARVP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000961.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000961.fa new file mode 100644 index 0000000000000000000000000000000000000000..f6bdb63103d7b016c26842f8102d817a83bda506 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000961.fa @@ -0,0 +1,80 @@ +>PROKKA_01156 +MTDTTPDLDATNVTRAEAADRSRLLTVQDYVVDVDLSDARDAAADTYPVRTVIRFACAEP +GAQTHLDWIHGGVESVALNGTALDVAEVVGEARVLLPDLAAQNVVELVGRSVYSRSGEGL +HRFTDPADGEVYLYTQYEPADARRVFPDFEQPDLKAAFTFSLTGPEDWVLASNRPEVSRT +PTGDGVVRVEFAPTLPQSTYITTLLAGPYAQWEDAWDGHPASGAQAVPLRLFTRRTMADA +FDPEAVFDVTKRGLTFFHDLFGVAYPWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFTSR +ATAVQYEGRANVILHEMAHMWFGDLVTMHWWDDLWLKESFADYMGALGVDEATDFRTAWV +TFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDGITYAKGASVLKQLAAYVGRDAF +LDAAHRYFAAHAWGNASLADFMAVLEAASGRDMRAWADAWLHTSGVPRLRVDVDGDAPVL +RQEGADPVTGGPILRPHVLKVGVFTPGQDGVLRRTAQVTADVPGGAEGAAVPLPDLEVPG +GVRLVLPNDEDLTYAAVALDAGSLRAALTHPIADPLAEATVWAALWSMTRDGELPVARFL +DAVATLSARIATVGVHAQVLAQAAAAVGQYARAEDRDALRSRLGEVLAEQTRTLEAGSDR +QRTAARTWATLARADVGMAAALEAALLGEDAAAFAPGLAVDAELRWLVLQALAATGRADQ +DRLDAELEAGRTAQTVTWHRLAAAARPEAEVKAAAWEAVMSGRTTTGTELSNDLLSATAA +GFAAGGVELLAPYESGFWPRLTSVWASRSNGLASRAIGGLFPGRQDAVAGGADAQESHPT +LAAAQRWLDEHPDAPGALRRLVVEHTDALRRSLRVQAVQPAG +>PROKKA_00875 +MTDTTPDLDATNVTRAEAADRSRLLTVQDYVVDVDLSDARDAAADTYPVRTVIRFACAEP +GAQTHLDWIHGGVESVTLNGTALDVAEVVGEARVLLPDLAAQNVVELVGRSVYSRSGEGL +HRFTDPADGEVYLYTQYEPADARRVFPDFEQPDLKAAFTFSLTGPEDWVLASNRPEVSRT +PTGDGVVRVEFAPTLPQSTYITTLLAGPYAQWEDAWDGHPASGAQAVPLRLFTRRTMADA +FDPEAVFDVTKRGLTFFHDLFGVAYPWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFTSR +ATAVQYEGRANVILHEMAHMWFGDLVTMHWWDDLWLKESFADYMGALGVDEATDFRTAWV +TFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDGITYAKGASVLKQLAAYVGRDAF +LDAAHRYFAAHAWGNASLADFMAVLEAASGRDMRAWADAWLHTSGVPRLRVDVDGDAPVL +RQEGADPVTGGPILRPHVLKVGVFTPGQDGVLRRTAQVTADVPGGAEGAAVPLPDLEVPG +GVRLVLPNDEDLTYAAVALDAGSLRAALTHPIADPLAEATVWAALWSMTRDGELPVARFL +DAVATLSARIATVGVHAQVLAQAAAAVGQYARAEDRDALRSRLGEVLAEQTRTLEAGSDR +QRTAARTWATLARADVGMAAALEAALLGEDAAAFAPGLAVDAELRWLVLQALAATGRADQ +DRLDAELEAGRTAQTVTWHRLAAAARPEAEVKAAAWEAVMSGRTTTGTELSNDLLSATAA +GFAAGGVELLAPYESGFWPRLTSVWASRSNGLASRAIGGLFPGRQDAVAGGADAQESHPT +LAAAQRWLDEHPDAPGALRRLVVEHTDALRRSLRVQAVQPAG +>PROKKA_01733 +MPRPHAAVDLDATNVTRAEAAERSRLLTVSAYEVHVDVSGARDEAAETYPVEATLRFVCA +EPGAAAHVDWIHAGVDAVVLNGRELEPADVVGDARILLPELAAENELVLRGRSRYSRSGE +GLHRFTDPADGQVYLYTQYEPADARRVFPDFEQPDLKAAFTFALTGPADWVLASNRPEAS +RTEVRPGVVRVDFEPTLPQSTYITTLLAGPYASWEDRWDGHAGTDAPAVPLRLFTRQTMA +EAFDPEAVFDVTRRGLDLFHELFGVPYEWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFT +SRATAAQYEGRANVILHEMAHMWFGDLVTMRWWDDLWLKESFADFMGTLGVDEATDFETA +WVTFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDGITYAKGASVLKQLAAYVGRD +AFLDAARRYFRAHAWGNAELTDFMAALEAASGRDMGAWADAWLHTSGVPRLRVEAGDDGA +SMLHQEGADPVTGRPVLRPHALKVGVFTPDEAGVLRRTAQVAADVPGGADGAAVVLEGLT +VPAGVRLVLPNDEDLTYAALALDEASLQAALTHPIADPLAEATVWAALWSMTRDGELSAA +RFLEAVERLSAGIETVGVHTQVLAQAAAAVSQFAAAADRPSLRARLAETLAEQVRTLEAG +SDRQRTAARTWALVARADADLARPLAAALLGGTGAGAADGEAGEDAPGLAVDAEIRWLVL +QALAATGQADEARLDAELAAGRTAQTVTWHRLATAARPEPAVKAAAWEAVMAGRTADGVE +LSNDLLSATAAGFAAGDVELLAEHEAGFWPRLEQVWASRSNGLASRAIGGLFPGHQDAVA +GDAGAQESHPTLASAQRWLDEHPDAPGALRRLVVEHTDHLRRSLRVQAAQPTA +>PROKKA_01631 +MTDSPTLTRDEARARARLITVHDYDVHVDVSGAADASAAAYPVTATIRFDCAEPGAETWL +DWISASVESVELNGEALDPAVVASRSRVRLPDLAAQNTVTLRGTSLYSRSGEGLHRFVDP +ADGRTYLYTQYEPADARRVFPDFEQPDLKASFTFRLTGPADWVLASNGAEVGREDAGEGA +VTVAFAPTRRLSTYITALVAGPYAVVEDRWDGHAATGAEPLPLRVMCRRALAEHLDADEL +FRITKAGLDFFHDLFGIPYEWGAYDQAFVPEYNLGAMENPGLVTFTEHYIHDTAPTRGQL +EGRATTVLHEMAHMWFGDLVTMRWWDDLWLKESFADYMGTLAADEAAGFDESWTTFASRR +KAWAYVQDAYPTTHPIVADIVDLEAARQNFDGITYAKGASVLKQLAAFVGRDAFMEAARV +YFHRHAWGNAELDDFLAVLGAASGRDMSAWADAWLRTAGVPALAVEVDGDGAPVLVQSGV +DPRTGEPIRRPHVLRVGVFTPDADGALTRTAQVDADIAAGAERTTLPGLAVPDGPRLILP +NDEDLTYAAVALDEASLDAVLTRPVADPLAQATVWAALWSMVREGTLPAARFVGAVQELS +ASVAGVAVYTQVVSQAAAAVELYATAAQRGALRAGLGEHLLSALRSLEAGGDRQRAAVRT +LAVLARGDADLARRLETAVLEDAETGAPGLAVDAEIRWLVLQALAATGSADRARLDAALA +EERTAKTVVAHRLAVQAIPDPAVKRAAWDAVLAGEDAEGQALSNDLLSATASGFAAGGHD +LVDPFEPGFWGELEGLWSSRSNGLASRAISGLFPLHQDALPGDAAAQEAHPVLARAQAWL +DEHTAAPGALRRLVVEQTDALRRSLRVQAAQPTP +>PROKKA_01106 +MTDTTPDLDATNVTRAEAADRSRLLTVQDYVVDVDLSDARDAAADTYPVRTVIRFACAEP +GAQTHLDWIHGGVESVTLNGTALDVAEVVGEARVLLPDLAAQNVVELVGRSVYSRSGEGL +HRFTDPADGEVYLYTQYEPADARRVFPDFEQPDLKAAFTFSLTGPEDWVLASNRPEVSRT +PTGDGVVRVEFAPTLPQSTYITTLLAGPYAQWEDAWDGHPASGAQAVPLRLFTRRTMADA +FDPEAVFDVTKRGLTFFHDLFGVAYPWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFTSR +ATAVQYEGRANVILHEMAHMWFGDLVTMHWWDDLWLKESFADYMGALGVDEATDFRTAWV +TFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDGITYAKGASVLKQLAAYVGRDAF +LDAAHRYFAAHAWGNASLADFMAVLEAASGRDMRAWADAWLHTSGVPRLRVDVDGDAPVL +RQEGADPVTGGPILRPHVLKVGVFTPGQDGVLRRTAQVTADVPGGAEGAAVPLPDLEVPG +GVRLVLPNDEDLTYAAVALDAGSLRAALTHPIADPLAEATVWAALWSMTRDGELPVARFL +DAVATLSARIATVGVHAQVLAQAAAAVGQYARAEDRDALRSRLGEVLAEQTRTLEAGSDR +QRTAARTWATLARADVGMAAALEAALLGEDAAAFAPGLAVDAELRWLVLQALAATGRADQ +DRLDAELEAGRTAQTVTWHRLAAAARPEAEVKAAAWEAVMSGRTTTGTELSNDLLSATAA +GFAAGGVELLAPYESGFWPRLTSVWASRSNGLASRAIGGLFPGRQDAVAGGADAQESHPT +LAAAQRWLDEHPDAPGALRRLVVEHTDALRRSLRVQAVQPAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000962.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000962.fa new file mode 100644 index 0000000000000000000000000000000000000000..c6e6e1f66fe50f04b2b5c20a009c7ed24228045a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000962.fa @@ -0,0 +1,40 @@ +>PROKKA_01157 +MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ +YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV +VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE +KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA +GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP +PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG +EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH +>PROKKA_00876 +MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ +YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV +VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE +KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA +GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP +PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG +EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH +>PROKKA_01732 +MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ +YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV +VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE +KPQTTPGLPDDPTLFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA +GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNRDWPLYTRQSVSP +PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVANEAWVEQSVLLDSVVIG +EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTDSGLTVLAKDQSVPKPH +>PROKKA_01630 +MVEKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGEYRLIDFALSNLVNSRFREIVVLTQ +YKSHSLDRHISETWRMSTMLNNYVATVPAQQRRGKDWFTGSANAIYQSMNLISDARPDIV +VVIGADHVYHMDFQQMVDHHVASGAKATVAAVRQPLELADQFGVIETDATDPGRITAFVE +KPATTPGLADDPAQFLASMGNYVFDTDALVEALNADDANPESNNDMGGDIVPYFVGRGEA +GVYDFTTNEVPGGTPGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNRAWPLYTRQSVSP +PAKLVRSASRRPGTAGDSILAQGVVISGGTVAQSVLSTDVRVGNEAWVEQSVLLDSVTVG +EGAHVRNAIIDKNVVIPAGARIGFDRAEDEANGYTVTDSGLTVLSKNQRVPDPR +>PROKKA_01107 +MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ +YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV +VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE +KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA +GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP +PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG +EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000964.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000964.fa new file mode 100644 index 0000000000000000000000000000000000000000..5fe52c8d8d90b7bfd1fa9899793052c98bb92c5a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000964.fa @@ -0,0 +1,65 @@ +>PROKKA_01159 +MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK +DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD +PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT +ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE +GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR +RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR +RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ +EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQFVGKRLLTDYSKEFGRLNVGA +VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA +GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL +RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR +MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG +>PROKKA_00878 +MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK +DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD +PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT +ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE +GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR +RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR +RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ +EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQLVGKRLLTDYSKEFGRLNVGA +VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA +GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL +RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR +MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG +>PROKKA_01730 +MTVHEKLAPQSPTHTTEVPSDVAEIAPEHPEPGSLDSAALQDALLGAWAEDRRTARALVR +DPRLHRDPLLGMDEHRERVLGQLGVLVENGAVHRMFPKEFGGDDNHGGNIAAFADLVLGD +PSLQIKAGVQWGLFAAAILHLGTEEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIGTT +ATYDEAAGEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITKGVNHGVHCFYVPIRDED +GAFLPGVGGEDDGLKGGLNGIDNGRLHFDQVRVPRTNLLNRYGDVAEDGTYSSPIESPGR +RFFTMLGTLVQGRVSLSLAATTASFLGLHGAIAYGEQRRQFNASDPEREEVLLDYQNHQR +RLVDRLARAYADAFASNELLERFDGVFSGRADSDADRQELETLAAAIKPLATWNALDTLQ +ETREACGGAGFMARNRIPQMRADLDVYVTFEGDNNVLLQLVGKRLLTDYSHEFGRLNVGA +VSRYVVAQASDAIHRAGLHKAVQSVSDGGSERRSANWFKDPEVQRDLLTDRVRAKTADIA +GTLAGVRGKTQAEQAAAFNTRQHELIEVARNQGELLQWEAFTRAVQATRDESTRTVLTWL +RDLFALRVLEEDLGWLVAHGRLSSQRARSLRGYVNRLAERLRPFALELVEAFGLEPEHLR +MDIATQAEAERQAEAHAWFEARRAAGEEPEDEKAVRAREKAARGRRG +>PROKKA_01628 +MTDIRTDAASAAEALPATDAVPHDVAEIAPEDPTPGALDAAALQDLLLGSWAEAHRTARG +LVKDERLHRDPALGMDEHRARVLDQLGILVEEKAVHRAFPADLGGQDDHGGSIAAFANLV +LADPSLQIKAGVQWGLFSSAILHLGTREHHEKWLPGAMDLSMPGAFAMTEIGHGSDVASI +ATTATYDEATQEFVIHTPFKAAWKDYLGNAALHGRAATVFAQLITKGVNHGVHCFYVPIR +DESGAFLPGVGGEDDGLKGGLNGIDNGRLHFDHVRVPRTHLLNRYGDVAEDGTYSSDIAS +PGRRFFTMIGTLVQGRVSLSLAASIASFMGLHGALAYAEQRRQFGGPEGSETLLLDYQNH +QRRLIDRLARTYADLFAANELLEKFDHVFSGAGDTDKDREELETLAAAIKPLTTWNALDT +LQEAREATGGMGFMAGRNRLPHLRADLDIFVTFEGDNNILLQLVGKRLLTDYSAEFGKLN +VGAVSRWAASEASDALHRVGLHKAAQSVHDRGDQRRAANWFKDPQVQRDLLTDRVRTRVA +DIASTLGSARGKSKAEQAAAFNSRQHELIEVARHHGELLQWEAFTRQVESLPAGQTRTVL +TWLRDLFALRLIEDDLGWLVAHGRVSSARARVLRGYVNRLAERLRPFALELVEAFGLEPE +HLRMEIATDAESVRQQEAADWFAARRAAGEEPVHEKTLHAGKR +>PROKKA_01109 +MTVHEKLAPQSSTPSTEVPSDVAEIAPERPTPGSLDAAALEEALLGRWAAERRESRELVK +DPALWRDPLLGMDEHRARVLRQLGVLVERNAVHRAFPREFGGEDNHGGNLAAFGDLVLAD +PSLQIKAGVQWGLFSSAILHLGTAEHHRRWLPGAMDLSVPGAFAMTEIGHGSDVASIATT +ATYDEATQEFVIHTPFKGAWKDYLGNAALHGRAATVFAQLITRGVNHGVHCFYVPIRDEE +GAFLPGVGGEDDGLKGGLNGIDNGRLHFTQVRIPRTNLLNRYGDVAEDGTYSSPIASPGR +RFFTMLGTLVQGRVSLSLAATTASFLGLHGALAYAEQRRQFKASDPQREEVLLDYQNHQR +RLIDRLARAYADAFASNELVEKFDDVFSGRSDTDVDRQELETLAAAVKPLTTWHALDTLQ +EAREACGGAGFLAENRVAQMRADLDVYVTFEGDNTVLLQLVGKRLLTDYSKEFGRLNVGA +VSRYVVHQASDALHRAGLHKAVQSVADGGSERRSANWFKDPAVQHELLTERVRAKTADIA +GTLSGARGKGQAAQAEAFNTRQHELIEAARNHGELLQWEAFTRALEGITDETTKTVLTWL +RDLFALRLIEDDLGWFVAHGRVSSQRARALRGYVNRLAERLRPFALELVESFGLEPEHLR +MAVATDAETQRQEEAHAWFTARRAAGEEPEDEKAVRAREKAARGRRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000967.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000967.fa new file mode 100644 index 0000000000000000000000000000000000000000..e0984952b9434ff385cb2434a1a771ee9440afe1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000967.fa @@ -0,0 +1,31 @@ +>PROKKA_01163 +MQTTQLSAPPSLGRLYVRAAGRAATDAVVRRRRPRELPDRQVVVTGHRIPAEAVTAWRGA +VGSANPADLPSVLVHTQVFGAAMELMADPEFPLPLPGLVHLSNTVLHHRPVAAETALRVT +ARAVGLVPHHAGTAVDVVVTVEGPGDDGEEALLWEGVSRYLAKGVHLSGLRPERPARPDF +VPPTPTAQWRFGTGAGRRYAGVSGDWNPIHLTGVSARLFGMKGAIAHGMFLAARMLEGRE +PAGAGFRWHIDFEAPVVLPTTVAVRYEPGPDGGTRVWGWDARRRRPHFSGEITPLEP +>PROKKA_00882 +MQTTQLSAPPSLARLYARAARQAATDAVVRRRRPRELPDRQVVVTGHRIPAEAVSAWRGA +VGSADPADLPSVLVHTQVFGAAMELMADPEFPLPLPGLVHLSNTVLHHRPVAAETPLRVT +ARAVGLVPHHAGTAVDVVVTVEGPGDDGEEALLWEGVSRYLAKGVHLSGLRPERPARPDF +VPPTPTAQWRFGTGAGRRYAGVSGDWNPIHLTGVSARLFGMKGAIAHGMFLAARMLEGRE +PAGAGFRWHIDFEAPVVLPTTVAVRYEPGPDGGTRVWGWDARRRRPHFSGEITPLEP +>PROKKA_01727 +MRTTELAAPPSLAGLYARAAGQAAKDALTRRSRPAVLPEREVVVTGHRIPRAAVAAWRDA +VGPADPAALPSVLVHTQVFGAAMELMADPEFPLPLPGMVHLTNTVLHRRPVPAETALRVT +ARAVGLVPHHAGTAVDVAVTVEGPHPAGGEAVLWEGVSRYLAKGVHLTGLRPERPAREEF +TAPARTAEWRLGAGAGRRYADVSGDWNPIHLTGVSARLFGMKGAIAHGMLLAARMLQGRE +PAAGGFRWEIEFDAPVVLPGTVAVRYEPADGQGTRVIGWDGRRCRRHFTGRIAPLAD +>PROKKA_01624 +MHTRTESSMPALAGLYRRAAGQALADAARRRTRPAELPDERLVVEGHRIPERALRRWQAE +IGPVDPASVPSVLVHTQVFGAAMALMAEPDFPLPLPGMVHLTNAVEHRRPVAAGEALDVT +ARAVGLVPHHAGTAVDLQVAVREAGETDDAPAAWEGVSRYLARGVHLAPLRPERPERPEF +TPPAPTAQWMFDGGAGRRYAEVSGDWNPIHLSALSARAFGQRRAIAHGMLLAARMLNRRE +PRAAAFGEGFGWDVEFHAPVVLPARVAVRYEAAADGSTRVSAWDPRRGRPHLDGRIRHAR +P +>PROKKA_01113 +MQTTQLSAPPSLGRLYVRAAGRAATDAVVRRRRPRELPDRQVVVTGHRIPAEAVTAWRGA +VGSADPADLPSVLVHTQVFGAAMELMADPEFPLPLPGLVHLSNTVLHHRPVPAETALRVT +ARAVGLVPHHAGTAVDVVVTVEGPGDDGGEALLWEGVSRYLAKGVHLSGLRPERPARPDF +VPPTPTAQWRFGTGAGRRYAGVSGDWNPIHLTGVSARLFGMKGAIAHGMFLAARMLEGRE +PAGAGFRWHIDFEAPVVLPTTVAVRYEPGPDGGTRVYGWDARRRRPHFSGEITPLES diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000968.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000968.fa new file mode 100644 index 0000000000000000000000000000000000000000..4eabaa47f3ba079425b33d045e37889083e6d401 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000968.fa @@ -0,0 +1,101 @@ +>PROKKA_01164 +MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAV +EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR +LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA +AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR +RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV +HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR +VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV +PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF +RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV +LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA +QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA +LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA +SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR +VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA +DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE +VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL +RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE +GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY +AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV +TAVPRRSPGLDA +>PROKKA_00883 +MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAV +EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR +LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA +AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR +RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV +HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR +VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV +PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF +RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV +LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA +QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA +LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA +SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR +VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA +DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE +VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL +RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE +GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY +AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV +TAVPRRSPGLDA +>PROKKA_01726 +MSRRFLSALLVHVPDIPEFASLPAAEQDELRAAGAAVQARLERSGTIDRPAVAAALWPAL +RRVHAVPRSPEREAAYAAFRAEAGPGLDDFALWSALRTADDVPGPDLADPAWAPGGEHAE +RVRTERADEVDLHRWVQWVAAEQLAAVQQRARAAGMRMGVMVDLAVGATRETADAWMLGD +VLVPGMSVGAPPEVFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRDAGGIRMDHVL +GLFRLWWIPVGAGATQGAYVEYDHEAMLAVLTLEAERAGAVVVGEDLGTFEPWVQRRLAE +AGVLGTSILWFEQRDGEPLPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTV +DVAQERRRSADEVEAFLGAAVRRGLLDARDARVRPDDAAQREAQTVALHRLLAQAPSALH +SVSLVDAVGERRIQNQPGTTQDQYPNWTLPLGDREGRMLRVEDLASSASAARLFDAVEEE +LRASVPVGIGVSLHTSPLAQPGRGDAGGLNVYVRHAALALARRGVRMILLTRAEEPVGPE +SARVTRLEAGGEAPAVTVVELAVGPAAPLPKAELAALTDEFTAAARAWLASDAVPGGPVL +APQGLDGRGPGAPAAPPVAFVHGHYWLSAPTAAALAAATGAPHLHTMHTTAAVKMLEDPE +LREPGARIEAEGAVVREADLLVVNSPAEVVDLREALGVPRARTRVLPPGADLATFTPEGP +ALWPGDPDDDGALRVLFAGRIQRHKGPHLLVEALAVLRERAGGPGADPGVRLHVNGAPSG +EEGLDLPGLALERGVADLVTFSEPVRAEELAAQLRAADVVAMPSASETYGLVALEAQACG +TPVLAHRVGGLVHAVIDGASGRLVTEGSPEAWADALAAVLADRPAWDALAAGAVRHAAGH +SWEAYADGLLEAAAGLARRQDGA +>PROKKA_01623 +MPENARALLRRLARAHGVQTEYVGQDGSDQSVADETLVRVLSALGVEVDADGVAGLTEAL +DAVDAAPWRDVLPPTVVARQGHRSTVPVHVARGAAVQVRLVQEDGRVVDLPTREAVGATL +VVDGQERVRHDLDLPEDLPLGWHRLEAVSETGSVARATLVSAPAALTTAAPFLARRGWGV +AAQGYSVTSSGSWGVGDAHDAGSLAELAAPHGADFLLLHPLHAVEPAGAPADSPYSPVSR +RFLSAFLIRVTDIPEFAALPAEEQKRLAAAGRAVQEAVLTGGTIDRAAVAEVLWPALEAV +WRAPRTSERDADYAAFRDRQGTGLDDFAAWSVLRRDALRAGVAGPDPTDPAAGPGSDGVR +RVRAERADELDFHRWVQWIADEQLAAAQERAREAGMRMGVMLDLAVGATRGSADAWMLGD +VLVPSMSVGAPPEVFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTLMAHAGGLRMDHVL +GLFRLWWIPEGLGAPQGAYVHYDHEAMLAVLTLEAERAGVVVIGEDLGTFEPWVQRRLAE +AGVLGTSILWFEQEDGVPTPPEQYRRLCMAAVNTHDLPPTAGYLEGVHIDLRERLGLYTA +DVAAERRRSAAEVEAFLGAARKRGLLEATGPDGVETVEDRVVALHRLLAQAPSALHCVGL +VDAVGERRIQNQPGTLQEQYPNWTVPLGDADGRVLTVEDLAGTASVSRLFDAVAAELDAS +VPVGIAVAFHTSPLAQPGQGDAGGLNVYVRHSARALARLGVRMLLLTRAESPVGPSGVRV +TTLPQGEGAPDVTVVELAAGPQEPVAKEELPAHREAFTAAAREWLASADVPGGPLLGAAG +AAAARVRFVHAHYWLSGDTAAAVADDLGAPRVQTMHTTGAVKSAGDPGHPEPAERLAAEA +DLVRRADLLVVNSPAESRDLQELLDVDRDRVRVLPPGVDLESFTPEGPSRWPGGDAVGAD +ALRVLFAGRVQEHKGPHVLVAALAELRARAADGDPRVVLHVNGEQSGPADLDLPALAARL +GVADLVTFSPPVPPVELAAQMRAADVVALPSASETYGLVAVEAQAAGTPVLAHRVGGLVH +AVQDGVSGRLVIPNTASAWADALAAVREDRQAWDAMAPAAVRHARAHAWSGWAEGLLDAV +AGLPRP +>PROKKA_01114 +MALEAPALLHRLARAHGVQPEYVGQDGSAQTVPDEALVKVLAALGVSVRPDGVAALAEAL +EEAETAPWRDVLPPTVAARSGHRLSVPCHVAAGEPVVARVRTEDGRTLEVSVSEPVSEVR +LVDGVERERVHVQIPADLAPGWHRLEVTSGSGSTASAVLVCAPTRLSTARPFLERRGWGA +AAQGYSVTSADSWGIGDAADMASLAEIVARHGADFLLLHPLHAIEPGPHPADSPYSPVSR +RFLSALVVHVPSIPEFADLPAAEQAELRSAGARVQAELERTGRIDRAAVAAVLWPALRRV +HEVPRSPEREAAYARFRAEAGPGLDDFALWSVLRLDGDGTGPDLADPAWAPGGVEAERVR +VERATDVDLHRWVQWIAAEQLAGVQERARAAGMRMGVMVDLAVGATRETADAWMLGDVLV +PTMSVGAPPELFNQLGQDWSQHPWHPRRLAETGYAAFRDMLRTVLRGAGGIRMDHVLGLF +RLWWIPEGAGATQGAYVEYDHEAMLAVLTLEAERAGVVVVGEDLGTFEPWVQRRLAEAGV +LGTSILWFEQEDGEPTPPERYRRLAMAAVNTHDLPPTAGYLEGVQVDLRERLGLYTVDVA +QERRRSAEEVRAFLAAAARRGLLAEADVDVPDAGPEVRERQIVALHRLLAQAPSALHSVA +LVDAVGERRIQNQPGTLQDQYPNWTVPLGDGAGRMVSVEDLADSASAARLFDAVDAELRA +SVPVGIGVSLHTSPLAQPGRGDAGGMNVYVRQAAVALARRGVRMILLTRAEEPVGADGAR +VRMLDAGGQAPPVTVVDLAAGPSAPVPKEELAGLGAEFTRAALDWLASDAVPGGPVLGGA +DAPPVAFVHGHYWLSGSTAAALARAAHAPYLQTMHTTAAAKMLEDPELREPAARIEAERE +VAERADLLVVNSAAEVADLRELLDVPRARTRVLPPGADLETFTPEGAAQWPGAPEDDGAL +RVLFAGRVQRHKGPHLLVAALGVLRERAGGAGADPGVRLHVNGAASGDDELDLAGLAARE +GVADLVTFSGPVPAPALAAQFRAADVVAMPSASETYGLVALEAQACGTPVLAHRVGGLVY +AVLDGVSGRHVTAGTPEAWADALAEILADRDAWAALGTGAVRHAAGHSWEAYADGLLEAV +AAVPRRSPGLDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000970.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000970.fa new file mode 100644 index 0000000000000000000000000000000000000000..73c57ed0bac86067046d95017e5aef08ee4e3c24 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000970.fa @@ -0,0 +1,15 @@ +>PROKKA_01167 +MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYRDGA +RRYWMRRRVMRVASTLQTL +>PROKKA_00886 +MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYRDGA +RRYWMRRRVMRVASTLQTL +>PROKKA_01722 +MREQLMSSTLDSIARGQKWEYLVITVSPDESLGDARRRLVEHAEYGRWELQRSVHFRGGA +RRYWLRRRVVRVASTLASA +>PROKKA_01620 +MDGMREQLMSSTLDSIARGEKWEYLVITVAPHESLADARRRLVDHAEYGQWELQRSVHYR +GGTRRHWMRRRVIRVRSTLQS +>PROKKA_01117 +MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYRDGA +RRYWMRRRVMRVASTLQTV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000971.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000971.fa new file mode 100644 index 0000000000000000000000000000000000000000..a05df1e7992c355d47015ab2f8d98e18f388c0cf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000971.fa @@ -0,0 +1,15 @@ +>PROKKA_01168 +MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT +PLDLFDDEDDDD +>PROKKA_00887 +MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT +PLDLFDDEDDDD +>PROKKA_01721 +MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT +PLEVFDDEEDDEA +>PROKKA_01619 +MSSDARVALEALTSALNEHLVAAQNRRGEDDPAVEAAFFAVADAFDAYEEALYAETEEVT +PLELFDDEDDLDEED +>PROKKA_01118 +MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT +PLDLFDDEDDDD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000972.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000972.fa new file mode 100644 index 0000000000000000000000000000000000000000..1b41a1578d5e777f6f073f2a0df674655eaf5813 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000972.fa @@ -0,0 +1,30 @@ +>PROKKA_01169 +MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSATDPGAAFTAITQLGTELAVLIYF +WRDITRIIGRWCAAVTGRIPHSDPDARMGWLIIVGSIPIAVLGLLLEDWIDTEFRSLWIT +ATMLIVFGVLLALADRLGRQTKPLEKLTVRDGVLYGLAQALALIPGVSRSGGTIAAGLAM +GYTRPAATRYAFLLAVPAVFASGLYKLYTSLTDPGTQGPYGMGETLVATAIAFVVAYAVI +AWLMRFISTNSYLPFVWYRILLGGVLFALLGAGVISA +>PROKKA_00888 +MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSATDPGAAFTAITQLGTELAVLIYF +WRDITRIIGRWCAAVTGRIPHSDPDARMGWLIIVGSIPIAVLGLLLEDWIDTEFRSLWIT +ATMLIVFGVLLALADRLGRQTKPLEKLTVRDGVLYGLAQALALIPGVSRSGGTIAAGLAM +GYTRPAATRYAFLLAVPAVFASGLYKLYTSLTDPGTQGPYGMGETLVATAIAFVVAYAVI +AWLMRFISTNSYLPFVWYRILLGGVLFALLGAGVISA +>PROKKA_01720 +MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSASDPGAAFTAITQIGTELAVLIYF +WRDITRIIGRWFQALAGRLPHSDPDVRMGWLIILGSLPIAVLGLLLQDWIDTEFRSLWIT +ATMLIVFGVLLALADRLGRQAKPLERLTVRDGVLYGFAQALALIPGVSRSGGTITAGLAM +GYTRSAAARYAFLLAVPAVFASGFYKLFQSLAEPGTQGPYGMGETFLATVIAFVVGYAVI +AWLMKFITTNSYMPFVWYRIALGLGLFALLGTGVISA +>PROKKA_01618 +MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSAADPGAAFTAITQLGTETAVLIYF +WKDISRIISRWFQALAGKVPHSDPDVRMGWLIIIGSIPIGVLGLLLQDWIDTEFRSLWIT +ATMLIVFGVLLALADRKGRQTKPLEKLTLKDGIVYGFAQALALIPGVSRSGGTITAGLAM +GYTREAAARYAFLLAVPAVFASGLYKVAKVVTEPGQAGPYGMGETILATAIAFVVGYAVI +AWLMKFITTNSYMPFVWYRIALGLVLFVLLGTGLIAA +>PROKKA_01119 +MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSATDPGAAFTAITQLGTELAVLIYF +WRDITRIIGRWCAAVTGRIPHSDPDARMGWLIIVGSIPIAVLGLLLEDWIDTEFRSLWIT +ATMLIVFGVLLALADRLGRQTKPLEKLTVRDGVLYGLAQALALIPGVSRSGGTIAAGLAM +GYTRPAATRYAFLLAVPAVFASGLYKLYTSLTDPGTQGPYGMGETLVATAIAFVVAYAVI +AWLMRFISTNSYLPFVWYRILLGGVLFALLGAGVISA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000973.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000973.fa new file mode 100644 index 0000000000000000000000000000000000000000..cae8a7fa862a7388d1fb4a3b68500b450b637d37 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000973.fa @@ -0,0 +1,45 @@ +>PROKKA_01170 +MKSWSTPAPPAVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY +VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE +VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG +QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE +CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS +KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH +AAAGVAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLAEAAADPLPVVDVVAALLGLR +LR +>PROKKA_00889 +MKSWSTPAPPTVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY +VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE +VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG +QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE +CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS +KSLGNLELVSRLRARGIEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH +AAAGVAVLDAVHAALSDDLDAPLALEALDAWAAGTLPGLAEAAADPVPVVDVVAALLGLR +LR +>PROKKA_01719 +MKSWSTPVPPAVPTRPDRLRLHDTATGAVRHPGNDAREASLYVCGITPYDATHLGHASTY +VAFDLLNRYWRAAGLEVAYVQNVTDVDDPLLERADATGVDWRELARDQTDLFRTDMAALE +VLAPDHYVGATEAIDLVVDAVEAMLAAGLAYRVPGDADAPDGDVYFDVRAAEAAGDWRLG +QVSAMPLDEMAAVFPERGGDPQRPGKRDPLDPLLWRVHRDGEPAWDGRSLGEGRPGWHIE +CSVISRAHLPSPFTVQGGGSDLRFPHHEFSAAHATAVDGRPLARHYAHTGMVALNGQKMS +KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEDVLARAQERVARWRAALEGPH +AQAGSAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLDAAADAAPVAVADVASALLGL +RLR +>PROKKA_01617 +MKSWSTPAPRALPVQPDRLRVFDTATQALRHPGNDARTASLYVCGITPYDATHLGHATTY +VSFDLLQRYWRAAGLEVAYTQNVTDVDDPLLERAEATGVDWRELAREQTDLFRSDMEALN +VFAPDHYVGATEAIDLVVRAVEAMLEGGTAYRVPGTDGEPDGDVYFDSAAAQARGGWTLG +SVSAMDRAQMEEVFPERGGDPGRPGKRDPLDPLLWRVHREGEPAWDGGALGSGRPGWHIE +CSAIAREHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGRPLAHTFLHSGMVALDGQKMS +KSLGNLELVSRLRARGVEPVAIRAAILDRHYRSDWEWSEDLLTAAEERVARWRSALDGPH +ADAGAAVLAAAHTALSEDLDAPAALRVLDAWADGTLDGLSTTAEPLPVADVVDALLGLRL +R +>PROKKA_01120 +MKSWSTPAPPAVPSRPDRLRLHDTATGRTRHPGNDAQRASLYVCGITPYDATHLGHASTY +VAFDLLHRYWRAAGLEVAYVQNVTDVDDPLLERAEATGVDWRALAEEQTDLFRADMAALE +VLAPDHYVGATEAVGLVVDAVETMLAAGRAYRVPGGDGEPDGDVYFDVRAAQSATDWRLG +QVSAMGLDEMAAVFPERGGDPDRPGKRDPLDPLLWRVHREGEPAWDGRSLGSGRPGWHIE +CSVISRAHLPAPFTVQGGGSDLRFPHHEFSAAHATAVDGLPLAHTYAHTGMVALDGEKMS +KSLGNLELVSRLRARGVEPVAVRAAILAHHYRSDWEWSEQVLADAQARVARWRAALDGPH +AAAGVAVLDAVHAALSDDLDAPRALEALDAWAAGTLPGLAEAAADPLPVVDVVAALLGLR +LR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000975.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000975.fa new file mode 100644 index 0000000000000000000000000000000000000000..bf154bdb26fe436ff2a784871c0387ddc93a4960 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000975.fa @@ -0,0 +1,28 @@ +>PROKKA_01172 +MSRHPAPAPDDRARRLPRAVLWDMDGTLVDTEPLWNAVQRRLVVEHGGTWSEDLAASLVG +RPLDEGARRLQEAGLDLPVQRIIDLTMHEVVQGVVSGVPWRPGARELLVALAEAGVPGAL +VTMSHAPLARALAERAPAGTLDVVVSGDMVSRGKPDPEAYRLGLQLLAERTPGLTAADCV +AVEDSPVGVGAAMAAGLPTVGVPSVLPLPAGLATVEWTTLAGRTPADLAAVRQIAAARGP +GGDGAE +>PROKKA_00891 +MPRHPAPAPDDRARRLPRAVLWDMDGTLVDTEPLWNAVQRRLVAEHGGTWSDDLAASLVG +RPLDEGARRLQEAGLDLPVQRIIDLTMDEVVQGVVRGVPWRPGARELLVALAEAGVPGAL +VTMSHAPLARALAERAPAGTLDVVVSGDMVSRGKPDPEAYRLGLQLLAERTPGLTAADCV +AVEDSPVGVGAAMAAGLPTVGVPSVLPLPAGLATVEWTTLAGRTPADLAAVRRIAAARGP +GADGAG +>PROKKA_01717 +MDGTLADTEPLWNASQRRLLAEHGGVWSEALADSLVGRPLDEGARRLQAAGLDLPVDEII +ERTMGAVTRGVADRVPWRPGARELLAALAEAGVPGALVTMSHAPLARALAERAPAAALDV +VVSGDLVARGKPDPEAYLLALDLLAARHPGLDAAGCVAVEDSPVGVAAAVAAGLPTVGVP +SVLPLPAGAATVEWDTLAGRAPADLAAVRDVAAGRAEDAPAPAGPGGRA +>PROKKA_01615 +MPRTPAAPAPVLPAALLWDMDGTLVDTEPLWNAVQRRLVEEHGGTWSDGLAASLVGRPLD +EGARSLRAAGLRMEVPEIIEATMAEVARGVEAATPWRPGALELLTAQAEAGVPGALVTMS +HAPLARVLAERAPAGALRVVVTGDRVSRGKPDPEAYLLALEELSAHVPGLRAEDCVAVED +SPVGVAAAVAAGLPTVGVPSVLPLPEGAATVQWGTLAGRGLADLAAVRPGAAG +>PROKKA_01122 +MPRHPAPAPDDRARRLPRAVLWDMDGTLVDTEPLWNAVQRRLVVEHGGTWSEDLAASLVG +HPLDEGARRLQEAGLDLPVQRIIDLTMDEVVQGVVGGVPWRPGARELLVALAEAGVPGAL +VTMSHAPLARALAERAPAGTLDVVVSGDMVSRGKPDPEAYQLGLQLLAERTPGLTAADCV +AVEDSPVGVGAAVAAGLPTVGVPSVLPLPAGLATVEWTTLAGRTPADLAAVRRIAAARRP +GADEPG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000976.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000976.fa new file mode 100644 index 0000000000000000000000000000000000000000..5c904f8d2b0c232800ff878c35e950066cace9c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000976.fa @@ -0,0 +1,40 @@ +>PROKKA_01173 +MSGPASVRLGTIAGAPVRLSWSWLLIAAAITLAFGPQIQRALPSLGGGAYGVALGYAVLL +ALSVLVHEAAHALTGRAFGQRTEEIALTLWGGHTQFRSPSARPLDTVLTAMAGPAANLVL +AGLAHLAARAVAGPSVPALLLEVTVWANLLLAAFNALPGTPLDGGRMVESAVWAATGSRA +RGVEAAGWAGRVVAVGVLAAVLGPPILAGRAPDLFVVVLAAWVALTLWRGADDAVRHGRW +SRRLETLRLEQVEAPAVALPEHLSVAEALAQADDGRRAVVAVDGAGRPRGVLDLAAAAGL +TPERRTTTALAAVAVALAPGAVLVRDDVPAAGPDLAARLADPQTPVWVLTDAHGLVRSVV +PRETILAAVDATRRP +>PROKKA_00892 +MSGPASVRLGTIAGAPVRLSWSWLLIAAVITLAFGPQIQRALPLIGGGAYGVALGYAVLL +ALSVLVHEAAHALTGRAFGQRTEEIALTLWGGHTQFRSPSARPLDTVLTAMAGPAANLVL +AGLAHLAARAVAGPSVLALLLEVTVWANLLLAAFNALPGTPLDGGRMVESAVWAATGSRA +RGVEAAGWAGRVVAVGVLAAVFGPPTLAGRAPDLFVVVLAAWVALTLWRGADDAVRHGRW +SRRLETLRLEQVEAPAIALPEHLCVAEALAQADGGRRAVVAVDGAGRPRGVLDHTAAAGL +TPARRTTTALAAVAVALAPEAVLVRDDVPAAGPDLASRLADPQTPVWVLTDAHGLVRSVV +PRETILAAVDATRRP +>PROKKA_01716 +MSGAAARRIGSLRLGSVAGAPVLLSWTWLLIAVAIVLALGPQIRRALPELGAGAYGVALG +YAVLLALSVLVHEVAHALAGRAAGQRAEEIALTLWGGHTQFRGAHAGPLGTVLTAMAGPA +ANLALAGLAHLAARAVDGPSVAALLLDVSVWANLLLAAFNALPGAPLDGGRMVESAVWAA +TGSRDRGVEASGWAGRVIAAGIVAAALLAPLLQGRTPDVLFTALLIWAALTLWRGAGDAV +ARGRWGRRLAGLRLADLELAAVAVPEHLSVAEALAHADGGRRAAVAVDGAGLPRGVLDRT +AVGRLDAAARAGTPVAAAAVALAPQAVLEREALPEAGPELAAVLADPETPVWVLTDVRGL +VRSVVTRERILAAVHATRRP +>PROKKA_01614 +MSGPRALTLGRIAGAPVRLSPAWVAVAGAVVLLFGPQVARALPGLGGAAWLVALGYAALL +ALSVLVHEAAHAVAGRAFGQRPQEIVLTLWGGHTQFAAPQATPVGTVVTALAGPAANVVL +AGLAWALGAAADARGVPGLLVDATVWANLLLAGFNALPGAPLDGGRMVESAVWAATGSRD +RGVAAAGWTGRLIAAALVIGWVAVPLVRGERPGLVVSLLLVWVAVTLWRGASESVERGRW +GRRLAGVRLADLAIPALAVPVDADASAVLAGVPAGLAVVAVDEAGRPVGVLDRAALDGAA +ASARVPVAAACRAVAPHAVLAADSLPPSGGALVASLATAAESAADPRPGVPGLDSTPVWV +LTDGHGAVRSVLPRERILTALATASRPDPEEPRP +>PROKKA_01123 +MSGPASVRLGTIAGAPVRLSWSWLLIAAVITLAFGPQIQRALPSLDGGAYGVALGYAVLL +ALSVLVHEAAHALTGRAFGQRTEEIALTLWGGHTQFRSPSARPLDTVLTAMAGPAANLVL +AGLAHLAARAVPGPSVPALLLEVTVWANLLLAAFNALPGTPLDGGRMVESAVWAATGSRA +RGVEAAGWAGRVVAVGVLAAVFGPPTLAGRAPDLFVVVLAAWVALTLWRGADDAVRHGRW +SRRLETLRLEQVEAPAIALPEHLCVAEALAQADGGRRAVVAVDGAGRPRGVLDHTAAAGL +TPARRTTTALAAVAVALAPEAVLVRDDVPAAGPDLASRLADPQTPVWVLTDAHGLVRSVV +PRETILAAVDATRRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000978.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000978.fa new file mode 100644 index 0000000000000000000000000000000000000000..e638fa9e05be2fa1df2c4035c8547941209bb54f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000978.fa @@ -0,0 +1,55 @@ +>PROKKA_01175 +MDHHAQSGTEHAEQRLAEARELLRQSQAEAERLRHQLQSAQRHAAGLSERRRAAEAQTQT +AARNNRRMVELLEATRAEITTLKENLDAVTHPPFTFATLEAVHAPREPEEGVETGAVVRG +GADVVQNGRRLRVTVSPLLDAARLTPGAQVLLDESSSIVGVAPGTGSGQLLRVKEALPDG +GLVLAGTADEERVVRRAPALEGVDLRHGDAVTVDARVEWALRRVELSEVDEVLLEEVPDV +TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA +LSARSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL +FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR +VDRPDAAGAAEIMAKHLTADVPLHADDVAAAGSADAARATLIARTVAALYDRGADTALAE +LTDVSGTTHALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVAA +VLEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA +>PROKKA_00894 +MDHHAQSGTEHAEQRLAEARELLRQSQAEAERLRHQLQSAQRHAAGLSERRRAAEAQTQT +TARNNRRMVELLEATRAEITTLKENLDAVTHPPFTFATLEAVHAPRDPEEGVETGAVVRG +GADVVQNGRRLRVTVSPLLDAARLTPGAQVLLDESSSIVGVAPGTGSGQLLRVKEALPDG +GLVLAGTADEERVVRRAPALEGVDLRHGDAVTVDARVEWALRRVELSEVDEVLLEEVPDV +TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA +LSARSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL +FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR +VDRPDAAGAAEIMAKHLTADVPLHADDVAAAGSADAARATLIARTVAALYDRGGDTALAE +LTDVSGTTHALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVAA +VMEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA +>PROKKA_01714 +MDQDAQGGPEQLERRLGEARELLRQSQAEAERLRHQLDSAQRHAARLSERRREAEAQTQT +AARNNRRMVELLETTRAEITTLKENLDAVTHPPFTFATLEAVHAPREPEEGVETGAVVRG +GADVVQNGRRLRVTVSPLLDAARLVPGAQVLLDESSAIVGVAPGTGSGQLLRVKEALPDG +GLVLAGTADEERVVRRAPALEGVELRHGDAVTVDSRVEWALRRVELSEVDEVLLEEVPDV +TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA +LSARSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL +FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR +VDRPDAAGAAEIMAKHLTADVPLHADDVATAGSADAARATLIARTVAALYDRGTGTALAE +LTDVSGTTRALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVVA +VLEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA +>PROKKA_01612 +MTEDDTQDRAGVLPAGDDARRLAEARELLRQSQAEAERLRHQLASAQRHGAQLSERRRAA +QAQLDVAARNNRRMVELLEATRTEMTSLKEALDDTTKAPFTFARLEAVHAARAPREGVET +GAVVRAGADVVQNGRRLRVAVSPLLDAAALTAGAEVLLDESSTIVGEVEHSVSGQLLRVK +ESLPDGSLVLAGAADEERVVRRAPALAGEVLRHGDAVTVDPRLEWALARVELSEVDDVLL +EEVPDVTFDDIGGLGPQIERIREAVEVPFLHPDLYREHGLRAPKGIMLYGPPGTGKTMLA +KAVANALSARSAEGGRSFFLNIKGPELLNKYVGETERQIRIIFQRAREHAAAGSPVVVFF +DEMESLFRTRGSGVSSDVETTIVPQLLAEIDGVESLDNVIVIGASNREDMIDPAVLRAGR +LDVKIRVDRPDARGAVDIMARHLDEEVPLHVDEVRDAGSAEQAREELIGAAVTALYERSP +RTALAELTDITGATSTLHLADLVSGAVVADVVDRAKRAAVRDLLAADLDPAARGLRTRHL +LDAVDAVLADQADLLGTVAPGEWARTSGWRGPRLAELRMLPGAGGRP +>PROKKA_01125 +MDHHAQSGTEHAEQRLAEARELLRQSQAEAERLRHQLQSAQRHAAGLSERRRAAEAQTQT +AARNNRRMVELLEATRAEIATLKENLDAVTHPPFTFATLEAVHAPREPEEGVETGAVVRG +GADVVQNGRRLRVTVSPLLDAARLTPGAQVLLDESSSIVGVAPGTGSGQLLRVKEALPDG +GLVLAGTADEERVVRRAPALEGVDLRHGDAVTVDARVEWALRRVELSEVDEVLLEEVPDV +TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA +LSVRSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL +FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR +VDRPDAAGAAEIMAKHLTADVPLHADDVVAAGSADAARATLIARTVAALYDRGADTALAE +LTDVSGTTHALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVAA +VLEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000979.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000979.fa new file mode 100644 index 0000000000000000000000000000000000000000..9191b5dbe34fecd168356861d8be347bc9e57d35 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000979.fa @@ -0,0 +1,55 @@ +>PROKKA_01176 +MSAFGRGAADGFARAAAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEF +GIHAPANPGAHHSVLSVELVNAYADLVTRSGSAVAGTEWDYTGESPLVDARGWRLPRSAA +HPSQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGD +LVAQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFEELTAVLLPFFAA +RQVLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRR +LHVIIGDATLSQHATWLRMGMTALVLAMAEAGTAPRLTLDDPVAALQTISHDPGLRATVP +LLERTADGPVRRHWTGLQILRSYLDAARAHCAAFGVTDPQTREVLEAWAIDLDDATADPL +SLSDRADWAAKLRVLEGLRARTGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTL +ADEAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLV +GAAVDLPGWWEDAAAPRPDDEALVATLAPLFGARA +>PROKKA_00895 +MSAFGRGAADGFARVAAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEF +GIHAPANPGAHHSVLSVELVNAYADLVTRSGSAVAGTEWDYTGESPLVDARGWRLPRSAA +HPSQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGD +LVAQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFEELTAVLLPFFAA +RQVLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRR +LHVIIGDATLSQHATWLRMGMTALVLAMAEAGTAPRLTLDDPVAALQTISHDPGLRATVP +LLERTADGPVRRHWTGLQILRSYLDAARAHCAAFGVTDPQTREVLEAWAIDLDDATADPL +SLSDRADWAAKLRVLEGLRARTGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTL +ADEAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLV +GAAVDLPGWWEDAAAPRPDDEALVATLPPLFGARA +>PROKKA_01713 +MSAFGRGTADGFARAVAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEF +GIHAPANPGAHHSVLSVELVNAYADLVTRSGSAVAGTEWDYTGESPLVDARGWRLPRSAA +HPSQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGD +LVAQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFDELTAVLLPFFAA +RQVLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRR +LHVIIGDATLSQHATWLRMGMTALVLALAEAGTAPRLVLDDPVAALQTISHDPGLRATVP +LLEHTADGPVRRHWTGLQILRSYLDAAHAHCAAFGVTDPQTREVLEAWAIDLDDATADPL +SLSDRADWAAKLRVLEGLRARAGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTL +ADEAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLV +GAAVDLPGWWEDAAAPRPDDEALVATLPPLFGARA +>PROKKA_01611 +MPGGIGGAPEAVAGTPAFAGQRRLFPADLTAPPGGRDAAGWGVHRVMGTESEFGIHAPAN +PGAHHSVLSVELVNSYADLITHSGGAVAGTEWDYAGESPLVDARGWRMPRSAAHPSQLTD +QALVGPDGEPVHLLLSTVLPNGARWYVDHAHPEYSSPEVASPREAVVWDAAGDRVAQAAA +EHIAAAEGAPEVLVYKNNTDGKGQSYGSHENYLVARALPFDELAEVLLPFFAARQVLVGA +GRVGVGLRGERPGFQLSQRADFFEEQVGLETTIRRPIVNTRDEPHARGDAYRRLHVIIGD +ANLSQHATWLRMGMTALVLALAEAGTAPRIVLDDPVAALQTISHDPTLRAAVPGRERGAD +GVWTRREWTGLQILGAYLDAAREHCARCGVDDAETAAVLDAWGTDLADAAADPLALADRA +DWAAKLRVLEGLRARGGLDWSDPRLAMVDLQYADLRPAKSLHRRLVAAGAMRVLVEDAEV +EAAVVAPPRSTRAWTRGNLVRHHARQVSGAAWDSVLVRAAEEAPLHRLRLEEPLVGAAED +LPGWWDDTPGSAAPAPEPNELVTRLGELLRR +>PROKKA_01126 +MSAFGRGAADGFARAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEFGI +HAPANPGAHHSVLSVELVNAYADLATRSGSAVAGTEWDYTGESPLVDARGWRLPRSAAHP +SQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGDLV +AQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFEELTAVLLPFFAARQ +VLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRRLH +VIIGDATLSQHATWLRMGMTALVLAMAEAGTAPRLTLDDPVAALQTISHDPGLRATVPLL +ERTADGPVRRHWTGLQILRSYLDAARAHCAAFGAADPQTREVLDAWAVDLDDATADPLSL +SDRADWAAKLRVLEGLRARTGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTLAD +EAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLVGA +AVDLPGWWEDAAAPRPDDEALVATLAPLFGARA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000980.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000980.fa new file mode 100644 index 0000000000000000000000000000000000000000..6212784818fe0d3a53b43a96840f3d5fafe7ae54 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000980.fa @@ -0,0 +1,25 @@ +>PROKKA_01177 +MIRDESIESYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEGLIAA +CLGLADGDERGFGAVAEAFGLPRDTLEDRARRSAAIQAALAEAVQPPRGIVDVAERALDL +AERVLDAANPNVLSDVGAALGCVRGGLTAAAVTLETNLGPLRDEGLEGIVRTDVDRADRL +VARADALLGRVRAAVTG +>PROKKA_00896 +MIRDESIESYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEGLIAA +CLGLADGDERGFGAVAEAFGLPRDTPEDRARRSAAIQAALAEAVQPPRGIVDVAERALDL +AERVLDAANPNVLSDVGAALGCVRGGLTAAAVTLETNLGPLRDEGLEGVLRTDVDRADRL +VARADALLGRVRAAVAG +>PROKKA_01712 +MIRDESIEAYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEVLIAA +CLGLADGDERGFGAVAEAFGLPRDTPVARSRRSAAIQAALAEAVRPPRGIVDAAARALDL +AERVLDAANPNVLSDVGAALGCIRGGLTAATVTLETNLGPLRDEGVEGILRTDVDRADRL +VARADALLGRVRAAITG +>PROKKA_01610 +MIRHETVEDHLTRLASGEPTPGGGATGALVVAQGAGLVAMAARFSGREEVAVECERVIRD +SLAISDEDEEGFAAVADAYTLPKDGDAARARRSAAVQAALDQAVRPPRAIVDAVDRTVGL +AERVLDDANPHVLSDVGAALGCARAGAGAAVVTLLTNLSPLHDEQLGAELRAEIARADEL +TSRIDALAARVRERIAR +>PROKKA_01127 +MIRDESIESYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEGLIAA +CLGLADGDERGFGAVAEAFGLPRDTPEDRARRSAAIQAALAEAVRPPRGIVDAAARALDL +AERVLDAANPNVLSDVGAALGCVRGGLTAAAVTLETNLGPLRDEGLEGVLRTDVDRADRL +VARADALLGRVRAAVTG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000981.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000981.fa new file mode 100644 index 0000000000000000000000000000000000000000..38d300072bf052167c9fc8dff04530fa7fb6f6b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000981.fa @@ -0,0 +1,20 @@ +>PROKKA_01178 +MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAIGAFL +SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPPAGLAPIPATTGQRDLEWRHLCAKLAA +RSPAWLERWSDTPVPDVHPLFTIVPGPVASWERA +>PROKKA_00897 +MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAIGAFL +SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPPAGLAPIPATTGQRDLEWRHLCAKLAA +RSPAWLERWSDTPVPDVHPLFTIVPGPVASWERA +>PROKKA_01711 +MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAVGAFL +SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPTVGLAPIPATTGQRDLEWRHLCAKLAA +RSPAWLERWADTPVPDVHPLFTIVPGPVASWERA +>PROKKA_01609 +MRLWTLHPRHLDRQGLTGGWREALLAQAVLARRTKGYRDHPQLERFRGHGDPAAAIGAFL +SGIALEASARGYRFDVSKIDRPLLPADGAGELVLPFRIAPIEVTTGQVAHEWGHLRAKLA +ARSPGWLERWADVQTPDVHPLFEVVDGPIASWERP +>PROKKA_01128 +MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAVGAFL +SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPPAGLAPIPATTGQRDLEWRHLCAKLAA +RSPAWLEQWSDTPVPDVHPLFTIVPGPVASWERA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000983.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000983.fa new file mode 100644 index 0000000000000000000000000000000000000000..9853e95273c8eef9e083a88da5cc42e2aa8f0853 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000983.fa @@ -0,0 +1,45 @@ +>PROKKA_01180 +MTDADRARRIFGLETEYGVQHWNPEGRALSPEEVVRYLFRPVVEWGRSSNVFVANGSRLY +LDVGSHPEYATAECSTLDELIASDGAGDLLLHDLVVQAEERMATDGVGGRIHLYRNNADS +SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGEGPAHFAFS +QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEHTHLLRFGATDL +LLRMIEAGFPLGDRVVAHPTRAVRQISHDLTGTARIALREGEASALELQEHYLERARTFV +AAEGAHHDRVGEVLTLWGEVLDAVRTGDRSRIEDRIDWAIKLRLLEDYRARHDLGWDAPR +LAQLDLAFHDIDPDRGLFRLLLRRGAVARLLPEDAARSAVETAPPTTRARVRADFVARAR +ERGLDYAVDWTTLKLTDHPLHAIVTKDPFDTSSAAVDRLFGRIA +>PROKKA_00899 +MTDADRARRIFGLETEYGVQHWNPQGRPLSPEEVVRYLFRPVVEWGRSSNVFVANGSRLY +LDVGSHPEYATAECSTLDELIASDGAGDLLLHDLVVQAEERMAADGVGGRIHLYRNNADS +SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGEGPAHFAFS +QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEHTHLLRFGATDL +LLRMIEAGFPLGDRVVAHPTRAVRQISHDLTGTARIALREGEASALELQEHYLERARAFV +AAEGAHHDRVGEVLTLWGEVLDAVRTGDRSRIEDRIDWAIKLRLLEDYRARHDLGWDAPR +LAQLDLAFHDIDPDRGLFRLLLRRGAVARLLPEDAARSAVEAAPPTTRARVRADFVSRAR +ERGLDYAVDWTTLKLTDHPLHAIVTKDPFDTSSAAVDRLFERIA +>PROKKA_01709 +MTDADRARRIFGLETEYGVQHWNPEGRPLSPEEVVRYLFRPVVEWGHSSNVFVSNGSRLY +LDVGSHPEYATAECSTLDELIASDAAGDLILHDLVTRAQERMAADGISGRIHLYRNNADS +SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGDGAAHFAFS +QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTSLSEHTHLLRFGATDL +MLRMIEAGFPLGDRVLAHPTLAVRQISHDLTGTARVALRDGDASALELQEHYLERARAFV +AAEGAHHERVEEILTLWEDVLEAVRTGDRSRIEDRIDWAIKLRMLEDYRARQNLDWGSAR +LAQLDLAFHDIDPDRGLFRLLLRRGAAARLLPEDAGRLAVDAAPPTTRARVRADFIARAR +QRGLGYAVDWTTLKLTDHPLHAIAAKDPFDASSDAVDRLFERIG +>PROKKA_01607 +MTTDARRIFGLETEYGVQHWNPQARPLSPEEVVRYLFRPVLEWGRSSNVFVRNGSRLYLD +VGSHPEYATAECSTLDELIASDAAGDLMLLDLIARAEEAMAADGIGGRIYLYRNNADSSG +SSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVIPAGVWPEGEGRAHFAFSQR +ADFVQEGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEATTLLRFGATDLML +RMIEAGYPLGDHRVAHPTLAIRQISHDLTGTVRVNLREGTASALDLQDHYLSRARAFVAS +EGAHHDRVEDVLDLWGTVVDAVRSQDFGPIEETIDWAIKLKLLRGYRDRYGLDWDAPRLA +QLDLAFHDIAPGRGLFPLLRERGGVRRVLPEGAARAAVDAAPPSTRATVRAEFIARARAA +GMDYAVDWTTLKLNDHPIHAISTKDPFSTDATPVDRLFERVG +>PROKKA_01130 +MTDADRARRILGLETEYGVQHWNPQGRPLSPEEVVRYLFRPVVEWGRSSNVFVANGSRLY +LDVGSHPEYATAECSTLDELIASDGAGDLLLHDLVVQAEERMAADGVGGRIHLYRNNADS +SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGEGPAHFAFS +QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEHTHLLRFGATDL +LLRMIEAGFPLGDRVVAHPTRAVRQISHDLTGTARIALREGEASALELQEHYLERARAFV +AAEGAHHDRVGEVLTLWGEVLDAVRTGDRSRIEDRIDWAIKLRLLEDYRARHDLGWDAPR +LAQLDLAFHDIDPDRGLFRLLLRRGAVARLLPEDAARSAVETAPPTTRARVRADFVARAR +ERGLDYAVDWTTLKLTDHPLHAIVTKDPFDTSSAAVDRLFERIA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000984.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000984.fa new file mode 100644 index 0000000000000000000000000000000000000000..9f69c2c4f91a2abf8fd108d5ddcd2f11c6d736e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000984.fa @@ -0,0 +1,20 @@ +>PROKKA_01182 +MSFGQRDYDRTKPEIDFPGETPPTELVVEDLIEGSGPAVEAGSRVQVHYVGVAWSTGEEF +DASWNRGTPLPLTVGVGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET +LIFVCDLVSVD +>PROKKA_00901 +MSFGQRDYDRTKPEIDFPGETPPTELVVEDLIEGSGPAVEAGSRVQVHYVGVAWSTGEEF +DASWNRGTPLPLTVGVGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET +LIFVCDLVSVD +>PROKKA_01706 +MSFGQRDYDRTKPEIDFPGENPPAELVVEDLIAGSGPAVEAGSRVQVHYVGVAWSTGEEF +DASWNRGTPLPLTVGVGQVIAGWDQGLLGMQVGGRRRLEIPPHLGYGARGAGSAIGPNET +LIFVCDLVSVD +>PROKKA_01605 +MSFGQRDYDRTKPEIDFPGDTPPTELVVEDLIEGSGPAVEPGSRVQVHYVGVAWSTGEEF +DASWNRGTPLPLTVGIGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET +LIFVCDLVSVD +>PROKKA_01132 +MSFGQRDYDRTKPEIDFPGETPPTELVVEDLIEGSGPAVEAGSRVQVHYVGVAWSTGEEF +DASWNRGTPLPLTVGVGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET +LIFVCDLVSVD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000985.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000985.fa new file mode 100644 index 0000000000000000000000000000000000000000..719ac4342b6791690c165edf435863672962d281 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000985.fa @@ -0,0 +1,65 @@ +>PROKKA_01183 +MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDTAFEKLFQRDRR +VLRAVGVPLETLEPAGLDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL +RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG +RATRRTVRAWYLTLVRGRWYLTGWDLDRGAERSFRLTRMEGEPRRVERATDAPGRPEDHD +HAGLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR +EDGLAAEIGGLLGRAVPSAAHPDLTDRVRAGLAAAAEAHAGPADPALLEVPLAAPVRRRA +RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGITDERLDADLETLRYCGMPERDFPGF +QFEVAEVGGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR +IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA +VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET +FAPRARPARWRVHPDDTAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAA +VAAALVGRHGGAVEVLAPADLRTSVADALGDALAALPAR +>PROKKA_00902 +MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDAAFEKLFQRDRR +VLRAVGVPLETLEPAGFDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL +RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG +RATRRTVRAWFLTLVRGRWYLTGWDLDRAAERSFRLTRMEGEPRRLERATDAPGRPEDHD +HADLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR +EDGLAAEIGGLLGCAVPSAAHPDLTDRVRAGLAAAAESHAGPADPALLEVALAAPVRRRA +RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGITDERLDADLETLRYCGMPERDFPGF +QFEVAEVGGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR +IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA +VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET +FAARARPARWRVHPDDAAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAG +VAAALVGRHGGAVQVLAPADLRASVADALGDALVALPAR +>PROKKA_01705 +MAPPASRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLSDAAFEKLFQRDRR +VLRAVGVPLETLEADSFEEEAQGVRHRVVRDAMLLRDLDLTVDERRALVRARRLWGDSPL +RADVVRAVGLLFAPTPDLAADDELAGYHALTPRADPRLEALTQAVAEEAVLRFPYRDARG +RESRRTVRAWFLTLVRGRWYLTGWDADREAERSFRLTRMEGEPRRVERAASLPGRPADHD +HADLVARLAGQADAERVRVWLAPGRGQGVRAVGARVDPRAEDGAAPGDGWELWEAPAGTH +EDGLAAEVGGLLGRAVPSAAEPDLARRVADALAAAARAHAGPAAPALLEAPLAPPVRRRA +RDSSEDLVGRLLDIVGLANRADGVDRAELRARLGVTEERLDADLETLRYCGMPERDFPGF +QFEVDEEGGRVHVRRAADLAGPVRLTRPEGHSLVAALQTVADLPVLDDADRAAARSAQRR +IAEAVLDAGGAAASAADDEALAEAEAGTAPTPAPGGAVAAHWDVAVDPETVRTLLAAIAE +RRVLRLDYRSVHADALSERDVEPLAVVQDGARLYLRAWCRSAGEDRVFRVDRIGAATATG +EAFAPRARPARWRVHPDEAAGTPAVLRWAHRVRDAASGYRPEAQADLPDGDRLTRVRLTD +ADVAAALVGRHGGAVEVLYPAAMRAHVKDALDRAVDALAAR +>PROKKA_01604 +MSAHGSTAEPAERIISLLWLLLHEPLGYTREQIRRLVVGYEGLTDGAFEKLFQRDRRALR +AVGVPLETVGDPDDEAGPRLRVDRDALLLQDVDFTVDERRALVRARRLWGDSPLRDDVVR +AVGVLFHPGEVGGDDALEGFRTVMPRTDPRVAALSEAAAEQSVVRFSYRDAAGALTERTV +RAWLLTLVRGRWYLTGWDADRAAERSFRLTRMESDPVVLDAGAASPAGEAPTLPAGHDHA +ALRARLAGRAEAETVRVWLAPGRGQGFRVAGRPVPATAADGPAPGPDWELWECPSGPSED +GAVAEAAVAVGQVLFSTVEAAAGRALAADLAAAAAVHAGDPDPAWRDVPLTAPTRRRSRA +SSEDLVGRLLDIVGLANRAEGIGRDELQERLGVTARELDADLEVLRYCGMPEREFPGFQF +DVEDEGGRVRVHQSSELAGPVRLTLPEAHALVAALQTVAEMTVLTPEDREAARSAQRRIR +ASLADAGQSHAGSADAEAPRDGTGKEPGAVVAHWDVVADPDTVRTLLDAVAERAVVHLRY +HGVRSDAVTERDVEPLAVVQDRTRLYLQAWCRRAGGPRVFRVDRIGALHRTGETFRARRV +PAWDPRPAGDGVEAVVRWAHEVRDAADAYAPAAAATLDSGDRLTRVLLADDDAAVGLAAR +HGGRVEILAPAALRGAVRGRLEAAARRAAGAVA +>PROKKA_01133 +MTPPAPRRAGDEAAERIISLLWLLLSAPHGLERDRIRRQVVGYEGLTDAAFEKLFQRDRR +VLRAVGVPLETLEPAGFDEGEAGVRHRVVRDALLLRDLDLTVDERRALVRARRLWGDSPL +RADVVRAVGLLFQPATDLTGDDELAGYHTLMPRADPRLEALTQAVADEAVLRFPYRDARG +RATRRTVRAWFLTLVRGRWYLTGWDLDRGAERSFRLTRMEGEPRRVERATDAPGRPEDHD +HAGLVARLAGQADAERVRVWLAPGRGQGVRAVGEPAEPRVEDGAAPGPDWELWEAPAGPR +EDGLAAEIGGLLGRAVPSAAHPDLTDRVRAGLAAAAETHAGPADPALLEVALAAPVRRRA +RDSSEDLVGRLLDIVGLANRAGGVDRAELRARLGVTDERLDADLETLRYCGMPERDFPGF +QFEVAEVAGRVHVERAADLAGPVRLTRPEAHSLVAALQTVADLPVLDEADREAARSAQRR +IRAAVLDAGAPDADDADDAALREAEAHTAGEPPVAVAAHWDVAVDPATVRTLLAAVAERA +VVHLTYRSVHADALTERDVEPLALVQDGARLYLQAWCRRAEDHRVFRVDRISAPAPTGET +FAPRARPARWRVHPDDAAGVPVLLRWAHPVRDAAAGYRPDAQADLPDGDRLTRVHLTDAA +VAAALVGRHGGAVEVLAPADLRTSVADALGDALAALPAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000987.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000987.fa new file mode 100644 index 0000000000000000000000000000000000000000..2c21f9e512581fbd92827edb3ccba15b56bb5eaa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000987.fa @@ -0,0 +1,30 @@ +>PROKKA_01185 +MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSALAVAVGMVIGFLVYQPVM +AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK +KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL +YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI +PLVVLFGVAIVLCLWGDRRRDRRSGQREVDVEAELAEGPKPLDQI +>PROKKA_00904 +MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSGLAVAVGMVVGFLVYQPVM +AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK +KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL +YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI +PLVVLFGVAIVLCLWGDRRRDRRQGQREMDVEAELAAGPKPLDQI +>PROKKA_01703 +MSEVEEVARRTRRRRRRDNPTGEMPLREHLTELRNRVIKAGVAVLLGMVVGFLIYQPVMA +ELFRPVNELSRDGRISAIAYDTVASPFDLMLKVSLFIGLIVSSPVWLYQIWAFIVPGLKK +AEKKYALGFIAAAVPLFLLGMGLGWLVMPQAVQFFVGFTPEGGATLPTASVYISFVTRLY +LAFGVAMVLPVLLVGLNMLGVLPGRTIVKHWRITVFLIMLIAAIAAPGADAISMVYMAVP +LVLLFGVAIALCLWGDRRRARRAVRREQDVEAELASGPKPLHEI +>PROKKA_01602 +MTSVDEEAAGARGRRKGRKPKNPNGEMPLREHLKELRDRLIKSVLAVVLGAVAGFALYKP +VMEVLTRPMVEARERGVNAALAFDTVSSPFDMMLKVALFIGIVVSSPVWLYQAWAFVVPG +LTKSEKKYAVGFLGTAIPLFLAGLYLAWLVHPQAVQFFIGFTFDGTAALPTASNFLTFSI +TLFLVFGVSMVLPVFLVGLNLLGVLPATTILKHWRIVVFLVALIAAMAAPGSDVISMFYL +AGPLLLLFGISILVCWLNDRRRARRSRDTAEDLEAEIAAGPRSLDEL +>PROKKA_01135 +MTEVDEVARRTRRRRKRRDNPTGEMPLREHLTELRNRLLKSALAVAVGMVIGFLVYQPVM +AELFRPVKEIASQGHTAAVAYDTVASPFDLMLKVSMFIGLILSSPVWLYQIWAFIVPGLK +KAEKKYALGFIAAAVPLFIFGIALGWLVMPQAVQFFVGFTPEGGANLPTASVYISFVTRL +YLAFGVAMVLPVLLVGLNMLGILPGRTIVHHWRITVFVIMLIAAIAAPGADAISMFYMAI +PLVVLFGVAIVLCLWGDRRRDRRSGQREVDVEAELAEGPKPLDQI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000988.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000988.fa new file mode 100644 index 0000000000000000000000000000000000000000..f0a2df906fc1b15136f19669c70625874ef555e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000988.fa @@ -0,0 +1,90 @@ +>PROKKA_01186 +MAHHPASATPHDEPELSPAERYARARAARHHAGSELGRFAARVGFPLDDFQRRACAEVED +GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADFARVHGAENVGL +LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLIDLGFVVMDEVHYLADRFRGPVWEEVII +HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHVMAGGRLYDLFAE +DIAFEDTADRDGEALLNPELKRLGEETERRFQRADWGRPGRQQHRDGRGGGPKGRVRGGR +RTTRDGGRGRNGSSALDRERPVSGRPGGHDGGQRRGPRLSTSRPEMIRALDRDGLLPCIT +FIFSRTGCDAAVEQCLRAGLDLTTAREKALVAERVEEAARLLPVEDLEILGFWAWRDGLS +RGFAAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGINMPARSVVIEKLVKFNGENH +VDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVAGLASRRTYPLRSSFRPTYNM +SANLLAQVGAERARGILESSFAQFQADRSVVGLAREVRSKQASLEKYEEAMQCHLGDFAE +YLTLRKELAAAEKSGSQGRRRAHLAAVKDSLANLAVGDVVELDAGRALGRAVVVFPAGNL +QNPRVGVVTDKAQLRRITVDDVAGPVEPVAGAALPQVVQVKTPAQRKDVAALMREAVRTG +RPPAGGRRTAGFRLREDPAAPRVEELRRALRRHPCHGCQDREEHARWGDRWWAMRREVSV +LRERIAGRTNTIARTFDRVVGLLRAYGYVQEDASSPRAALTERGEALRRIYGERDLFTSL +VLQDPATDGLTPEEWAAVAALLVYQGRGEAEPGLVPMPTPRLARVAEAAERIEERLRTDE +AQARLEPTPRTDPGLVAPMHRWVRGATLRRTLDGADLAAGDFVRWARQVIDVLGQLANVP +GDTRRSRACRRAADLVSRGVVATSLPAASAPRADED +>PROKKA_00905 +MAHHPASATPHDEPELSPAERYARARAARHHAGSELGRFAARVGFPLDDFQRRACAEVED +GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADLARVHGAENVGL +LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLIDLGFVVMDEVHYLADRFRGPVWEEVII +HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHIMAGGRLYDLFAE +DIAFEDAADRDGEALLNPELKRLGEEAERRFQRADWGRPGRQQHRDGRGGGTKGRARGGR +HTGRDGGRGRTGSSALDRERPVSGRPGGHDGGPRRGPRLSTSRPEMIRVLDRDGLLPCIT +FIFSRTGCDAAVEQCLRAGLDLTTAREKALVAERVEEAARLLPVEDLEILGFWAWRDGLS +RGFAAHHAGMLPPFKEAVEDLFTAGALKAVFATETLALGINMPARSVVIEKLVKFNGENH +VDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVARLASRRTYPLRSSFRPTYNM +SANLLAQVGAEQARGILESSFAQFQADRSVVGLARELRSKQASLEKYEEAMQCHLGDFAE +YLTLRKELAAAEKSGSQGRRRAHLAAVKDSLANLAVGDVVELDAGRSLGRAVVVFPAGNP +QNPRVGVVTDKAQLRRITVDDVAGPVEPVAGAALPQVVQVKTPAQRKDVAALMREAVRTG +RPPAGGRSTAGFRLREDPAAPRVEELRRALRRHPCHGCQDREEHARWGDRWWAMRREVSV +LRERIAGRTNTIARTFDRVVGLLRAYGYVHEDAPSPRAALTERGEALRRIYGERDLFTSL +VLQDPAMDGLTPEEWAAVAALLVYQGKGETEPGLVPMPTPRLARVAEAAERIEERLRTDE +AQARLEPTPRTDPGLVAPMHRWVRGATLRRTLDGADLAAGDFVRWARQVIDVLGQLANVP +GDTRRSRACRRAADLVSRGVVATSLPAASAPRADED +>PROKKA_01702 +MSHAPASATPPEEPQLSPAERFARAKAARHHAGSELGRFASRLGFPLDDFQRRACAEVED +GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADLSRVHGAENVGL +LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLTDLGFVVMDEVHYLADRFRGPVWEEVII +HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHVMAGGRLYDLFAE +DIAFEDTADRDGEALLNPELKRLGQEAERRSERPDWGRPGRHRGRGGRDGGQRGRGGRGG +DGRKGGRDADRRGRHGSHAMDREQPATGRVRGQEDGERRGPRLSTSRPEMIRALDREGLL +PCITFIFSRTGCDAAVEQCLRAGLDLTTAHEKALVAERVEQAARLLPVEDLEILGYWAWR +DGLSRGFAAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGINMPARSVVIEKLVKFN +GENHVDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVAGLASRRTYPLKSSFRP +TYNMSANLLAQVGAERARGILESSFAQFQADRSVVGLAREVRSKQASLEKYEKAMQCHLG +DFSEYLALRKELASAEKSGSQGRRRAQLAAVKESLADLAVGDVVELDAGRSLGRAVVVFP +AGNPQNPRVGVVTDKAQLRRITVDDVTGPVEPVAGAALPQVLQVKTPTQRKDVAALMREA +VRTGRPPAGGGRRTSGFRLREDPAAPRVEELRRALQRHPCHACQDREEHARWGDRWWGMR +REVSVLRERIAGRTNTIARTFDRVVGLLRSYGYVHEDASSPRQALTARGEALRRIYGERD +LFTSLVLQDPTVQGLTPEEWAAVAALLVYQGKGEAGHGVVPMPTARLAEVADAAERIEER +LRADEAQARLEPTPPTDPGLVGPMHRWVRGASLRRTLEGADLAAGDFVRWARQVIDVLDQ +LANVPGDARRSRACRKAADLVSRGVVATSLPAATAREADED +>PROKKA_01601 +MAPHTHHDLPPEEPALSPAERFARSRASASRPGTELSRFAARLGFPLDEFQLEACREVEA +GHGVLVAAPTGAGKTVVGEFAVHLGLARGRKAFYTTPIKALSNQKYADLAAVHGADRVGL +LTGDTSVNPDAPVLVMTTEVLRNMLYADSEALTDLGFVVMDEVHYLADRFRGPVWEEVII +HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVVVSEHRPVPLWQHVMAGGRLYDLFAE +DVAFEAAADADGTPLLNPELQRMAQEASRRVERPDWGRTGHRGRGRGGPGGRGAGRGRGK +GGPRGGREGASSGWDRERPHRADASPGDGERRALGLSTSRPEMIRALDREGLLPCITFIF +SRAGCDGAVEQCLRAGLDLTDRREKALIAERVEQAAAALPPEDLEILGFWAWRDGLSRGF +AAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGVNMPARSVVLEKLVKFNGESHVDV +TPGEYTQLTGRAGRRGIDVEGHAVVLWRPGLDPSAVAALASRRTYPLRSSFRPTYNMSVN +LLAQVGAERARGILESSFAQFQADRSVVGLAREVRAKQSSLEKYADAMACDRGDFAEYLS +LRKELAAAEKSGSRGRRREHLRAVKESLADLAVGDVVELHDGRALGRVVVVAAAGNPQNP +RVAVVTDKAQLRKVAVEDLVDPVEPVAGAALPQTVQVKTPSQRKDVAAAMREAVRAHRPP +TGGTRRGTGFRLREEVASPRLEELRRALQAHPCHACPDREDHARWGERWWDMRREVSLLR +ERIAGRTNTIARTFDRVVELLGRLGYVGDDPDAPSRALTERGQTLRRIYGERDLLTSLVL +HDPSTRSLTPEEWACVAALLVYQGKGDTQGLPVAMPTARLQALAEAVDRIEGGLREDETA +ARLEPTPPTDPGLVAPLHRWVRGASLRDSLHGADLAPGDFVRWARQVIDVLGQIAQVPGD +ARRTRACRKAADLVGRGVVAASLPAAAAGADGVEGEEPDRVDR +>PROKKA_01136 +MAHHPASATPHDEPELSPAGRYARARAARHHAGSELGRFAARVGFPLDDFQRRACAEVED +GHGVLVAAPTGAGKTVVGEFAVHLALARGTKAFYTTPIKALSNQKHADFARVHGAENVGL +LTGDTSVNPDAPVVVMTTEVLRNMLYAQSDTLIDLGFVVMDEVHYLADRFRGPVWEEVII +HLPEHVQLISLSATVSNAEEFGAWLDTVRGATTVIVSEHRPVPLWQHVMAGGRLYDLFAE +DIAFEDTADRDGEALLNPELKRLGEETERRFQRADWGRPGRQQHRDGRGGGPKGRVRGGR +RTTRDGGRGRNGSSALDRERPVSGRPGGHDGGQRRGPRLSTSRPEMIRALDRDGLLPCIT +FIFSRTGCDAAVEQCLRAGLDLTTAREKALVAERVEEAARLLPVEDLEILGFWAWRDGLS +RGFAAHHAGMLPPFKEAVEDLFAAGALKAVFATETLALGINMPARSVVIEKLVKFNGENH +VDITPGEYTQLTGRAGRRGIDVEGHAVVMWRPGLDPAAVAGLASRRTYPLRSSFRPTYNM +SANLLAQVGAERARGILESSFAQFQADRSVVGLAREVRSKQASLEKYEEAMQCHLGDFAE +YLTLRKELAAAEKSGSQGRRRAHLAAVKDSLANLAVGDVVELDAGRALGRAVVVFPAGNL +QNPRVGVVTDKAQLRRITVDDVAGPVEPVAGAALPQVVQVKTPAQRKDVAALMREAVRTG +RPPAGGRRTAGFRLREDPAAPRVEELRRALRRHPCHGCQDREEHARWGDRWWAMRREVSV +LRERIAGRTNTIARTFDRVVGLLRAYGYVQEDASSPRAALTERGEALRRIYGERDLFTSL +VLQDPATDGLTPEEWAAVAALLVYQGRGEAEPGLVPMPTPRLARVAEAAERIEERLRTDE +AQARLEPTPRTDPGLVAPMHRWVRGATLRRTLDGADLAAGDFVRWARQVIDVLGQLANVP +GDTRRSRACRRAADLVSRGVVATSLPAASAPRADED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000990.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000990.fa new file mode 100644 index 0000000000000000000000000000000000000000..ee47a8bfaaebb7ac1b99271088acdf602d62809c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000990.fa @@ -0,0 +1,30 @@ +>PROKKA_01188 +MRVLTIIPTYNEIESLPLTLGRLRDAVPESDVLVVDDASPDGTGDWADARAAEDPSVHVL +HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV +PGGKMVNWPTSRKMISWAGSLYPRIMLGLNLTDITAGYRAYRADTLRAIDLDAIESKGYG +FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRAR +LGL +>PROKKA_00907 +MRVLTIIPTYNEIESLPLTLGRLRDAVPESDVLVVDDASPDGTGDWADARAAEDPSVHVL +HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV +PGGKMVNWPTSRKMISWAGSLYPRIMLGLNLTDITAGYRAYRADTLRAIDLDAIESKGYG +FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRAR +LGL +>PROKKA_01700 +MRVLTIIPTYNEIESLPLTLGRLRDAVPTSDVLVVDDASPDGTGQWADARAAQDPSVHVL +HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLDAVRTADLVIGSRRV +PGGKMVNWPASRKMISWAGSLYPRIMLGLRLTDVTAGYRAYRAETLRAIDLDAIESKGYG +FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRSR +LGL +>PROKKA_01599 +MRVLTIIPTYNEIESLPLTLGRLRDAVPDSDVLVVDDASPDGTGAWADARAAEDDHVHVL +HRAEKNGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV +PGGKMVNWPASRKLISAAGSLYPRIMLGLKLTDITAGYRAYRADTLRRIDLGAVQSKGYG +FQVDMTFRVARLGLRIVEVPITFVERELGESKMSGGIVGEAVVNVTKWGLQARWETLTGR +GPQRG +>PROKKA_01138 +MRVLTIIPTYNEIESLPLTLGRLRDAVPESDVLVVDDASPDGTGDWADARAAEDPSVHVL +HRTTKDGLGGAYIAGFRWGLERGYDVLVEMDADGSHQPEQLPRLLEAVRTADLVIGSRRV +PGGKMVNWPTSRKMISWAGSLYPRIMLGLNLTDITAGYRAYRADTLRAIDLDAIESKGYG +FQVDMTFRTARLGKRIVEVPITFVERELGESKMSGGIIGEAVVNVTRWGLAARWEGLRAR +LGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000991.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000991.fa new file mode 100644 index 0000000000000000000000000000000000000000..a77f24ae0fbb4ee74ace2744b0f2c9f734affb2b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000991.fa @@ -0,0 +1,15 @@ +>PROKKA_01189 +MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK +EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA +>PROKKA_00908 +MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK +EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEDVDA +>PROKKA_01699 +MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK +EAFLVSGEKPAEAEGKPVRTHWDMLRERRSLEELQETYALQLNKLRASRGEDVDA +>PROKKA_01598 +MSDRSLRGMRLGAQSLESEAGVEPAPRQRVEYRTEDGEQVFVTFAQEAEVPTTWTSKTGK +EALRVDGEKPEENPGKPVRTHWDMLLERRSMEELEETFQIQLKKLHASRGEAV +>PROKKA_01139 +MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK +EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000992.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000992.fa new file mode 100644 index 0000000000000000000000000000000000000000..7613939ad79823ed66df4fea9ae4967fa67e78f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000992.fa @@ -0,0 +1,40 @@ +>PROKKA_01190 +METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM +VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN +VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA +ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS +GGADSEVLAYQYLQSLPKIADGQANTMFVVPAELTRALQGLGEAFAPGDGDRPTPEHAPR +RRDSGDRAGEPGAEHSGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS +LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH +>PROKKA_00909 +METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM +VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN +VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA +ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS +GGADSEVLAYQYLQSLPKIADGQATTMFVVPAELTRALQGLGEAFAPGDGDRPTPERAPR +RRDSGDRAGEPGAEHVGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS +LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH +>PROKKA_01698 +METIIILVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTMIIPFVDRMLPM +VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN +VVGGMNLEEALTSRDSINSQLRGVLDEATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA +ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS +GGADSEVLAYQYLQALPKIADGESNTMFVVPAELTRALQGLGEAFSPAGDGESRRPSPSG +ARGEAAERAGEHGGASPERPRRPRGSRPTTADALRSSGVMDAMTAGAVTAQEMPQTSLDE +ALATPKELDPDPSAGRAPGRRPAGETDGNGVGH +>PROKKA_01597 +MEFLIVLAVLAVLVGVLLASSVKIIPQARTANVERLGKYQRTAGAGLTLIIPFIDRMLPM +VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN +VVGGMNLEEALTSRDAINSQLRGVLDDATSRWGLRVSRVELKAIDPPMSIQDSMEKQMRA +ERDRRAAILTAEGTKQAAILTAEGERQSAILSAEGEAQARVLRANAEAEAIEVVFDAIHS +GGADSEVLAYQYLQSLPKIAEGTSNTMFVVPAELTRALQGLGEAFSPGSPSAAGTGSSDT +SDDAAPAAGRAATGPGGRRRGRASEGARPTTAEELRSSGLLDAMTAGALTADRMPQTSLD +EALQTPPEAEPAPVRREPGMP +>PROKKA_01140 +METLIVLVVLAVLAAVIVASSVKIIPQARTANIERLGKYNRTAGAGLTLIIPFVDRMLPM +VDMREQVVSFPPQPVITEDNLVVSIDTVVYFQVTDAKAATYEIANYIHAVEQLTTTTLRN +VVGGMNLEEALTSRDSINSQLRGVLDDATTRWGLRVSRVELKAIDPPMSIQDSMEKQMRA +ERDRRAAILTAEGTKQAAILTAEGERQSQILSAEGEAQARVLRANAEAEAIEVVFDAIHS +GGADSEVLAYQYLQSLPKIADGQANTMFVVPAELTRALQGLGEAFAPGDGDRPTPEHAPR +RRDSGDRAGEPGAEHSGVTPERARRPRGSRPTTADALRASGVMDAMTAGAVTAEDMPQTS +LDEALATPQEIEPDPSAGRTPGTRPAGEADGNAVGH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000994.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000994.fa new file mode 100644 index 0000000000000000000000000000000000000000..35a7433273f81380cd94b8104df961f2968cd5f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000994.fa @@ -0,0 +1,65 @@ +>PROKKA_01192 +MTSSPVAVSPLLQPITLGPLTLPNRVVMASMHMGLEDRHDDLPQLAAFYAERARGGVGLI +VTGGLGVVPEGTVTLGGGMLASEEDARAHRVVTDAVHAAGGRILAQLLHAGRYAPSPDLV +SASAVRAPISRHTPREMTAADIERTVNAFARAATLALEAGYDGVEIMASEGYLLNQFLAP +ATNRRADEYGGDAERRRRFPVAVVAAVREALGERGVLSVRTSAADLVPDGQTRAEIADTA +RAFEAAGADVLMTGIGWHESRVPTIVTSVPRAAFLAASADLTAAVDIPVIASNRLTTPAE +AEEALTSGAAALVGLARPLLADPDWMAAIGDPRARTLTPCIACNQACLDHVFTGAKVSCL +MNPRAGRETEPEYAAPVPVALGRRRRIAVVGAGPAGLTAAERAARFGHEVTLFDRHAEPG +GQFRLARRIPGKEEFGPALEHLAARAAASGVTLVTGEEVSAQTLLTDDGRPGYDEVLLTT +GVRPRPVALPGTGEPGAPAVHAYDDVVLGHVDVGPRVAVIGAGGVGVDVAEALAAGTERP +DGTPETQEHWRARWGVALTSQTPGQLAKPAAADPGREVHLLQRSPGPIGVRLRPTTGWVH +RAELRRHGVHLHSGVTYEGLGPDGLRVTAPSPEDPEARVALTLDVTDVVVCAGQESETDL +VEDLVAAGYAPEAVRLIGGAAEARELDAYRAMDHAVRAVQG +>PROKKA_00911 +MTSSPVAVSPLLQPITLGPLTLPNRVVMASMHMGLEDRHDDLPQLAAFYAERARGGVGLI +VTGGLGVVPEGTVTLGGGMLASEEDARAHRVVTDAVHAAGGRILAQLLHAGRYAPSPDLV +SASAVRAPISRHTPREMTAADIERTVNAFARAATLALEAGYDGVEIMASEGYLLNQFLAP +ATNRRADEYGGDAERRRRFPAAVVAAVREALGERGVLSVRTSAADLVPDGQTRAEIADTA +RAFEAAGADVLMTGIGWHESRVPTIVTSVPRAAFLAASADLTAAVDIPVIASNRLTTPAE +AEEALTSGAAALVGLARPLLADPEWMAAISDPRARTLTPCIACNQACLDHVFTGAKVSCL +MNPRAGRETEPEYAAPVPVALARRRRIAVVGAGPAGLTAAERAARFGHEVTLFDRHAEPG +GQFRLARRIPGKEEFGPALEHLAARAAASGVTLVTGEEVSAQTLLTDDGRPGYDEVLLTT +GVRPRPVALPGAGEPGAPAVHAYDDVVLGHVDVGPRVAVIGAGGVGVDVAEALAAGTERP +DGTPETQEHWRARWGVALTAETPGQLAKPAAAHPGREVHLLQRSPGPIGVRLRPTTGWVH +RAELRRHGVHLHSGVTYEGLGPDGLRVTAPSPEDPETRVPLTLDVTDVVVCAGQESETDL +VEDLVAAGYAPEAVRLIGGAAEARELDAYRAMDHAVRAVQG +>PROKKA_01696 +MTVAPAITSPLLEPITLGPLTLPNRVVMASMHLGLEDRHEDLPRLAAFYAERARSGVGLI +VTGGVGVVPEGTVAPGGGLLATAEDARAHRVVTDAVHAEGGRILVQLLHTGRYARGEDLV +CASAVRAPISAHTPREMDEADLERTVAAFARAAALALEAGYDGVEVMASEGYLLNAFLAP +VTNRRQDAYGGSAQARRRFPVRVVEAVRAALGERGVLSVRTSAADLVPGGQTREEVADTA +RAFEAAGADVLMTGIGWHESRVPTIVTSVPRATFLPATAALSAAVDIPVIAANRLTTPAE +AEEAIASGAAALVGLARPLLADPDWMAGIGVDDAAALTPCIACNQACLDHVYTGAPVSCL +MNPRAGRETDPAYARPVPVAIGRRRRVAVVGAGPAGLTAAERAARFGHEVTLFDRHDEPG +GQFRLARRIPGKEEFGPALEHLAARARASGVTVLTGEEVTVQTLLTPEGGPAFDEVLLTT +GVRPRRIALPGAGEPGAPAVHAYDDVVLGHAQLGPRVAVIGAGGVGVDVAEALTAGAHRP +DGTPESAEQWRARWGVALDSPTPGQLGEPTGEPPAREVHLLQRSPEPIGARLRPTTGWVH +RAELRRHGVRLHSGVAYEGLSAAGLHVTVPDPERPEERTPLTLDVTDVVVCAGQESEDGL +AGDLVAAGYPAEAVRLVGGAAEARELDAYRAMDHAVRAIQG +>PROKKA_01595 +MTHMTDAPASHRLLEPLTVRRTVLRNRVVMGSMHLGLEDSHADLPALAAFYAERAAGGVG +LIVTGGVGVTPEGAVSPGGGLLADAADAAAHRTLTDAVHAEGGRILVQLLHAGRYARGAD +LVSASATRAPISRHTAHALTEAEVEELVAAYARSARLALEAGYDGVEVMASEGYLLNQFL +APSTNLREDRYGGSAENRRRFPVAVVAAVREALGETGLLSVRTSLTDLVPGGQTSAEALD +TARAFEAAGADLIMTGIGWHESRVPTVVTSVPRAAWAEASARVRAAVGIPVIAANRLTTP +DDAEALLRGGAADLVAVARPLLADPDWVRTVGRAGAEHLTPCIACNQACLDHVMAGRPVS +CLMNPRAGRETDPRYARPVPVEIGRRRRVAVVGAGPAGLTAAHRAAGFGHDVTLFEATEE +VGGQFRLARRIPGKEEFEPALRHLEARAVAAGVHLRRETRVTPRTLLTEDGRPAFDRVII +ATGVRPRDVDLPGVGEPGAPAVHRYDDVVAGRVRCGAAVAVIGAGGVGVDVAELLASPEG +GAALGEPEPLEHWRARWGVADDDPTAPGGLTRPEPAERARRVFLLQRSPEPVGSRLRPTT +GWVHRLELRALGVEMLSGVSYERVDRDGLHVTAPAVGGDGDPGRRRLVLPVTDVVVCAGQ +ESEDGLAGDLLAAGWDPEAVTVIGGARVAAEVDAYRAMDDAVLAVQD +>PROKKA_01142 +MTSSPVAVSPLLQPITLGPLTLPNRVVMASMHMGLEDRHDDLPQLAAFYAERARGGVGLI +VTGGLGVVPEGTVTLGGGMLASEEDARAHRVVTDAVHAAGGRILAQLLHAGRYAPSADLV +SASAVRAPISRHTPREMTAADIERTVNAFARAATLALEAGYDGVEIMASEGYLLNQFLAP +ATNRRADEYGGDAERRRRFPAAVVAAVREALGERGVLSVRTSAADLVPDGQTRAEIADTA +RAFEAAGADVLMTGIGWHESRVPTIVTSVPRAAFLAASADLTAAVDIPVIASNRLTTPAE +AEEALTSGAAALVGLARPLLADPEWMAAISDPRARTLTPCIACNQACLDHVFTGAKVSCL +MNPRAGRETEPEYAAPVPVALGRRRRIAVVGAGPAGLTAAERAARFGHEVTLFDRHAEPG +GQFRLARRIPGKEEFGPALEHLAARAAASGVTLVTGEEVSAQTLLTDDGRPGYDEVLLTT +GVRPRPVDLPGTGEPGAPAVHAYDDVVLGHVDVGPRVAVIGAGGVGVDVAEALAAGTERP +DGTPETQEHWRARWGVALTSQTPGQLAKPAAADPGREVHLLQRSPGPIGVRLRPTTGWVH +RAELRRHGVHLHSGVTYEGLGPDGLRVTAPSPEDPEARVALTLDVTDVVVCAGQESETDL +VEDLVAAGYAPEAVRLIGGAAEARELDAYRAMDHAVRAVQG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000995.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000995.fa new file mode 100644 index 0000000000000000000000000000000000000000..c282c0409648679cc725d8aeede0c464fbe7bd33 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000995.fa @@ -0,0 +1,25 @@ +>PROKKA_01193 +MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRFDDPTGEIGVESMLVRVGDRL +YQTAFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH +DESGTYLETRAPDLTLRVIGADATGELEVPVELSETGEADVDGPRCLIAEGDGVRAVVAR +LT +>PROKKA_00912 +MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRLDDPAGEIGVESMVVRVGDRL +YQTPFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH +DESGTYLETRAPDLTLRVIGADATGELEVPVELSETDEADVDGPRCLVAEGDGVRAVVAR +LS +>PROKKA_01695 +MALIYTAQLDPDKPEWIRRRLVAHGLPEDVDAEKVGSYRFDDPAGEVGVESMIVRVGDRL +YQTAFAYRGEAPTEGDIVAEADHSVLGRRWVMDAATDPDARRILTAGLRGEIPQAVMDFH +DESGAYLETRQPDVTLRLVGEGDGGELELPVELADAAEESGDGPRRLVAEGEGFTAVVAR +LA +>PROKKA_01594 +MSFIYSAQLDPDKNEWIRRALVAHGEDPDVPFTRAGSYRFDDPAGELGLEVMLVRVGGAD +DGRLVQTPLSYRSAARDGATVLLTAEHSVLGTRWIHDALTDPEAREVLRRGVAGELAQEV +LEVHDEHGVRTGTRQPDMTVTAVGTGPAAGELDMPYELDPADTADGGRALVAEGDGFSGL +VVARLV +>PROKKA_01143 +MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRFDDPTGEIGVESMLVRVGDRL +YQTAFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH +DESGTYLETRAPDLTLRVIGADATGELEVPVELSETDEADVDGPRCLVAEGDGVRAVVAR +LS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000996.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000996.fa new file mode 100644 index 0000000000000000000000000000000000000000..f0eb5403d7513163eecd8015be967836045b9871 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000996.fa @@ -0,0 +1,24 @@ +>PROKKA_01194 +MVSVHLVPIRPTAATADDAQRLSAALLDDPRPGAAVISAAWHIDETDAAPGDGELAVTLD +GMAAGVGLALWAVRSGSWAVLLDTEGNYDKQSALSHITAGERRRARRAPGRLVLPHGRRP +GRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGISQQAV +HSRLRHGLWHESRTAVAAVLPLLERLSADPGE +>PROKKA_00914 +MVFVHLVPIRPTAATADDARRLAAVLLDDPHPDASVAAAVWRGDEGNPDADAAPGDGELA +VVVESMAAAVGLALWAVRTGSWAVLLDPEDALDKDSLLSYLTPAERRRARRAPGRLVLPH +GRRPGRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGIS +QQAVHSRLRHGLWHESRTAVAAVLPLLERLSADPGE +>PROKKA_01693 +MIVLHLLPLTAPDAADAAWTRVGDELNRPGAVSSLVMPFDRQGEGSEARLVGGMDSGVEA +VGILLSLVRSGAWAVVVEVAEGRAAGESLLQREAERARRANGHCAVLGPSGPSAAWIEPA +LQLLGALERRRSEPQQDAGRRVEAGASQREVAAELQVSQQAVHARLRGGLWNETRALAGA +TADALDVLARRGDRVSDGGASPSTSERG +>PROKKA_01591 +MVPVAVRCGSAGAAGRWAASIPGARRLGREGGRDLIVHADDAAAAVALMLAVRRAGAGAV +GAGVAIEQVEGALRRARRRPGGIAVSRVPGSTGTEEERGLLEAGLGVLLTLESRRSAPQQ +AAGVLIEAGRSQREAAADLGVSQQAVQQRLRAGLWEETRTLLDALLPMARRVLEA +>PROKKA_01148 +MVSVHLVLIRPTTATAEDARRLATALRDDPRPDAAVTAAMWLGDESDPVDDDAAPHDGEL +AVVLDDAAAAVGLALWAVRTGSWAVMLDPEGGSDKDSALSYLTPAELRRARRAPGRLVLP +AGGRPGRASESGREADLRCAEATLQLVAAVERRRSADQHAAGRLVEAGASQREAAAELGI +SQQAVHSRLRHGLWHVSRTAVAAVLPLLERLSTDPGE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000997.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000997.fa new file mode 100644 index 0000000000000000000000000000000000000000..78c784ffd3faeec8fc94d6425b1c95f5b2818237 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000997.fa @@ -0,0 +1,20 @@ +>PROKKA_01195 +MTSSPTARRAAPAEHRDPRGALPALAVDLLLTLLFVALGQGQHSTERGPLGLLVTAAPFL +AGLLLMTGVTAGHRTWARAWPHGVIVWLGTVAVGMLLRVAFGLGGAPVSFVLVALGVLGV +LLLGRRAVTAWLVRRTRR +>PROKKA_00915 +MTSSPTARRAVPAEHRDPRGAQPALAVDLLLTLLFVALGQGQHATERGPLGLLVTAAPFL +AGLLVMTGLTAGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV +LLLGRRAVTAWLVRRTRR +>PROKKA_01692 +MADTLSENRSETMAQTGGMTDSPTRRHSPASPPSPLWAATALAVDAVLVVVFVALGQDQH +TTDRGLGGLLATALPFLLGLVAATVLTAGHRTWHRVWPHGVAVWLGTVAVGMALRVLWDQ +GGAPLSFVLVALGVLGVFLLGRRAVTAWVIRRRARV +>PROKKA_01590 +MSTTPLPQDSSPAAHPSDRRRGSAPWVAFALDAALVVLFVALGQREHATDRGGLALVTAA +APFLLAWVAGTALAGGPRTWARVWPQGVVVWAVTVAAGMGLRVLWGLGGAPVPFVLVASA +VLAVFLLGRRWASTLLAHRATDRASRAS +>PROKKA_01149 +MTSSPTARRVVPAEHRAPRGALPALAVDLLLTVLFVALGQGQHSTERGPVGLLVTAAPFL +AGLLLMTGLTSGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV +LLLGRRAVTAWLVRRTRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001000.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001000.fa new file mode 100644 index 0000000000000000000000000000000000000000..5e52dec54995e8fc29556e13eed79330a92f6527 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001000.fa @@ -0,0 +1,25 @@ +>PROKKA_01198 +MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT +AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA +ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV +WIALFFIVYFLK +>PROKKA_00918 +MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT +AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA +ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV +WIALFFIVYFLK +>PROKKA_01689 +MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAENTAILNVPLAAANTLILVLSSVT +AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTIA +ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV +WIALFFIVYFLK +>PROKKA_01586 +MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTVILVLSSFT +AQFGVLAAERLQPRRTGGLFSVKSWGMVEWFILTFIMGSIFVAVQAFEYATLVSEGVTIA +ANAYGSAFYITTGFHALHVTGGLIAFLFIIGRAFLARRFGHHEATSAIVVSYYWHFVDVV +WIALFFIVYFLK +>PROKKA_01152 +MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT +AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA +ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV +WIALFFIVYFLK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001002.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001002.fa new file mode 100644 index 0000000000000000000000000000000000000000..a491818106b0b0dde08cab9d99e6998d90296b3a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001002.fa @@ -0,0 +1,35 @@ +>PROKKA_01200 +MGEKGLEGTERRSGSLEHAGEDAPRYAIDDPGLPPHRPRLADEDPKAAKRAERQVSVMFL +ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD +HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL +DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL +GPDKLNQKAKAVVLLMRLDPAKVRITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH +LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG +>PROKKA_00920 +MGEKGFEGTEHRSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL +ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD +HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL +DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL +GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH +LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG +>PROKKA_01687 +MGEKGFEGTEHGSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL +ISIVGTLLFFVGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD +HETVEDRHEIRSEADRVAATGMISEILDESQIKRRPLLRNTLIGAAVLAPLPFIAVFRDL +DDSDNFSDEETHNFGPERLRHTMWSEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL +GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH +LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG +>PROKKA_01584 +MGEKGYEGAERHSDALEHAGEESPRYAIDNPGLPPHRPRLADEDPRAAKRAERQVSVFFL +ISVIGTVLFFIGYFGVGQVGNGESTSVLYLQNLLLGLGVALAMFGIGIGVVHWAKTLMPD +HEVVEERHEIRTEADRAAAQGMIADILDESQIKRRPLLRNTLIGAAVLAPLPFIAAFRDL +DNTDNFSDEAAKNFGPERLRHTMWHEGVRLVRDPTGSPIKASDVTLGSALHVIPDGLNDL +EHGKLNEKAKAVVLVMRLDPSKVKISPGRENWNVDGIFAYSKVCTHVGCPIALYEQHTHH +LLCPCHQSTFDLAQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG +>PROKKA_01154 +MGEKGFEGTEHRSDSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL +ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD +HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL +DDSDNFSDEEIHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL +GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH +LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001004.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001004.fa new file mode 100644 index 0000000000000000000000000000000000000000..e1c772e6bd374bd07f6cb0f25b9995dba6fbe5e0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001004.fa @@ -0,0 +1,20 @@ +>PROKKA_01203 +MKVAANIFWVIGLFFVGAGTLYGFWNEWTEWAGIPAIYALGGMSWMIAWYLNAAERKYGV +GPADDEDGQIVEYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWVFVIGIIAGAYFTF +GWVYEFSRGKFAH +>PROKKA_00922 +MKVAANIFWIIGLFFIAAATLYGFWVEWTEWAGIPAIYAVGGMSWMIAWYLNVTERKYGV +GPADDADGQIADYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWIFIIGVIAGAYFTF +GWVYEFSRGKYAH +>PROKKA_01684 +MKVAANIFWIIGLFFIAAATLYGFWVEWTEWAGIPAIYAVGGMSWMIAWYLQSTEKKFGL +GPADDEDGEITDYAGTYGTFAPWSWWPLGLGVACAILITGLAVGWWVFIIGAVAAAYFTF +GWVYEFSRGKYAH +>PROKKA_01582 +MKIASNIFWIIGAFLVAVATLYGFWVKWTEWAGIPAIYALGAMCWMIAWYVQSTDKRHGL +GPADDEDGEIVEYAGTYGTFAPSSWWPLGVAVACAMLVTGLAVGWWIFALGVIAGVYFTF +GWVYEFSRGKYAH +>PROKKA_01160 +MKVAANIFWVIGLFFVGAGTLYGFWNEWTEWAGIPALYALAGMSWMIAWYLNAAERKYGV +GPADDEDGQIVDYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWVFIIGVIAGAYFTF +GWVYEFSRGKFAH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001005.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001005.fa new file mode 100644 index 0000000000000000000000000000000000000000..702ec60a22bb8f994fb649d4426c0bf9883aacf0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001005.fa @@ -0,0 +1,55 @@ +>PROKKA_01204 +MTTYEYATDEVRSQAQPRVVPRSLGKIVVSWLTTTDHKVLGYMYLITSFIFFCIGGVMAL +MIRAELFEPGMQILQTKEQYNQLFTMHGTLMLLMFATPLFVGFANVLVPLQIGAPDVSFP +RLNALAFWFFLFGSLIATAGFLTPQGAASFGWYAYAPLSNTTFSPGVGGDLWVFGLALQG +FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILILMAFPPLAAALFALGLDRR +FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGIVSEIIPVFSRKPIFGYKSIVFA +TTAIGALSFSVWAHHMYVTGSVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFENPM +LWTLGFMVTFLFGGLTGVILASPPLDFQLNDTYFVVAHFHYVVFGTVVFAMFAGFFFWWP +KFTGKMLNERLGKIQFWMLFVGFHGTFLIQHWLGVTGMPRRYADYMVEDSFHAMNAFSSV +FSFVLGASLIPFFWNVYITARYGKKVTVDDPWGFGGSLEWATSCPPPRHNFHSLPRIRSE +RPALDLHHPELFPHSPQHTTEAFGEKVAQ +>PROKKA_00923 +MTTYEYATDEVRSQAQPRVVPRSLGKIVVSWLTTTDHKVLGYMYLITSFVFFCIGGVMAL +MIRAELFEPGMQILQTKEQYNQLFTMHGTLMLLMFATPLFVGFANVLVPLQIGAPDVSFP +RLNALAFWFFLFGSLIATAGFLTPQGAASFGWFAYAPLSNTTYSPGVGGDLWVFGLVLQG +FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLASALFALGLDRR +FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSIVFA +TTAIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM +LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVVFGTVVFAMFAGFFFWWP +KFTGKMLNERLGKIQFWMLFVGFHGTFLIQHWLGVIGMPRRYADYMVEDSFQAMNAFSSV +FSFVLGASLIPFFWNVYITSRYGKKVTVDDPWGFGASLEWTTSCPPPRHNFHSLPRIRSE +RPALDLHHPELFPHSPQNTSEAFGEKVAQ +>PROKKA_01683 +MTTYEYATDEVRSQAQPRVVPRSLGKIAVSWLTTTDHKVLGYMYLIVSFMFFCIGGVMAL +MIRAELFEPGMQILQTKEQYNQLFTMHGTIMLLMFATPLFVGFANVLVPLQIGAPDVSFP +RLNALAFWFFLFGSLIATAGFLTPQGAASFGWFAYAPLSNTTYSPGVGGDLWVFGLVLQG +FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLAAALFALGMDRR +FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSLVFA +TTSIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM +LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVIFGTVVFAMFAGFFFWWP +KFTGKMLNERLGKIQFWLLFVGFHGTFLVQHWLGVIGMPRRYADYMIEDGFTAMNQFSTV +FSFILGASLIPFFWNVYVTARYGKKVTVDDPWGFGASLEWATSCPPPRHNFHSLPRIRSE +RPALDLHHPELFPHSPQHTPEAFGEKVAQ +>PROKKA_01581 +MTTYEYATDEVRTQAQPRVAPRSLGKIVVSWLTTTDHKVLGYMYLIVSFVFFCVGGVMAL +MIRAELFEPGMQILQTKEQYNQLFTMHGTIMLLMFATPLFVGFANVLVPLQIGAPDVAFP +RLNALAFWFFLFGSFIACAGFLTPQGAASFGWFAYAPLSDTTYSPGVGGDLWVFGLVLQG +FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLAAALFALGMDRR +FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSLVFA +TTSIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM +LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVIFGTVVFAMFAGFFFWWP +KFTGKMLNERLGKIQFWLLFVGFHGTFLVQHWLGVIGMPRRYADYMIEDGFTAMNQFSTV +FSFLLGASLIPFFWNVYVTTRFGKRVTVDDPWGFGSSLEWATSCPPPRHNFHSLPRIRSE +RPALDLHHPELAAYSPQAEPEVFGEKVASK +>PROKKA_01161 +MTTYEYATDEVRSQAQPRVVPRSLGKIVVSWLTTTDHKVLGYMYLITSFIFFCIGGVMAL +MIRAELFEPGMQILQTKEQYNQLFTMHGTLMLLMFATPLFVGFANVLVPLQIGAPDVSFP +RLNALAFWFFLFGSLIATAGFLTPQGAASFGWFAYAPLSNTTYSPGVGGDLWVFGLVLQG +FGTIMGGVNFITTILTMRAPGMTMWRMPIFTWNTLITGILIMMAFPPLASALFALGLDRR +FGGHIFNPENGGAILWQHLFWFFGHPEVYIIALPFFGVVSEIIPVFSRKPIFGYKSIVFA +TTAIAALSVTVWAHHMYVTGAVLLPFFSVMTMLIAVPTGVKFVNWIGTMWRGSITFETPM +LWTLGFMVTFLFGGLTGVILASPPLDFQVSDTYFVVAHFHYVIFGTVVFAMFAGFFFWWP +KFTGKMLNERLGKIQFWLLFVGFHGTFLIQHWLGVIGMPRRYADYMVEDTFTAMNAFSSV +FSFVLGASLIPFFWNVYITSRYGKKVTVDDPWGFGGSLEWATSCPPPRHNFHSLPRIRSE +RPALDLHHPELFPHSPQHTTEAFGEKVAQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001009.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001009.fa new file mode 100644 index 0000000000000000000000000000000000000000..6efd462ba85be169b986c560859b537bf2cefcdf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001009.fa @@ -0,0 +1,24 @@ +>PROKKA_01208 +MFKRDKTPETAPAPSTHGSSAAPAEGAAVAEAGPRDRSQGKKGPTPRRRDQEAARRRTLV +PEDRKAARKAERQAMAQERMRQRAALETGDERGLPARDKGPQKRWVRDYVDARTGIGEWL +MPVVFAYVLLMFIPGREAQLILMISLYVLVALVLIESFLVSRHIKKGLTERFGTPEPGTG +FYGIMRALQFRRLRLPKPQVKRGEYPA +>PROKKA_00927 +MFKRDKTPETAPAPSTHGSSAAPAEGAVSGAAPRDRSQGKKGPTPRRRDQEAARRRTLVP +EDRKAARKAERQAMAQERMRQRAALETGDERGLPARDKGPQKRWVRDYVDARTGIGEWLM +PVVFAYVVLMFIPGREAQLILMISLYALVALVLIESFLVSRHIKKGLTERFGTPEPGTGF +YGIMRALQFRRMRLPKPQVKRGEYPA +>PROKKA_01679 +MVPEDRKAARKAAREAAAQDRMRQRVALETGDERGLPLRDRGPQKRWVRDYVDARTGIGE +WLMPVVFAYVLLMFLPGREVQLFLMISLYALVALVVIESLIVARRIKKGLTERFGEPESG +TGFYGVMRALQFRRLRLPKPQVKRGQFPA +>PROKKA_01577 +MLNRRKKTENDAPASHGSTALGAGNTPAAQPAPRDRSQGKTGPTPRRRDQEAARRRTLVP +EDRKAARKAERDAATAERMRQRQALETGDERNLPARDKGPQKRYVRDYIDARTGLGEWLM +PIVLVYVIAMFIPGTRAQVILMVTLYVIVGLVIAESFYISAQIKKRLTATFGTPEPGSRF +YGVMRALQFRRLRLPKPQVRRGEFPA +>PROKKA_01165 +MFKRDKTPETAPAPSTHGSSAAPAEGAAVAEAGPRDRSQGKKGPTPRRRDQEAARRRTLV +PEDRKAARKAERQAMAQERMRQRAALETGDERGLPARDKGPQKRWVRDYVDARTGIGEWL +MPVVFAYVLLMFIPGREAQLILMISLYVLVALVLIESFLVSRHIKKGLTERFGTPEPGTG +FYGIMRALQFRRLRLPKPQVKRGEYPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001010.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001010.fa new file mode 100644 index 0000000000000000000000000000000000000000..61985c0c509de2ab5cb1f35737c8214af195cec5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001010.fa @@ -0,0 +1,40 @@ +>PROKKA_01209 +MQLPDPKSAVDGLLTSRAPRLYPPFFRAVFGGMDAEQAHHRGFDAIRLVERTGASAALRA +AFRPDPLLARTVMGLRFPTPFGLAAGFDKDGRGTAALADLGFGHIEVGTITAQPQPGNPQ +PRLFRLVDDRALVNRMGFNNDGAAAVAPRLARTRQTLERRFGPTRPVLGVNIGKTKVVPL +EDAADDYRASTRLLAPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRAVPGR +RVPLTVKIAPDLADDDVRAVGALAERLGLDGVIATNTTVSREGLRTPRADVDALGAGGLS +GAPLQERSMRVLQVLRAALPTGTAVVSVGGVTDADDVQARLDAGADLAQGYTAFLYEGPF +WAGRITAGLARSLRG +>PROKKA_00928 +MQLPDPKSAVDGILTSRAPRLYPPFFRAVFGGMDAERAHHRGFDAIRLAERTGASAALRA +AFRPDPMLARTVMGLRFPTPFGLAAGFDKDGRGTAALADLGFGHIEVGTITAQPQPGNPQ +PRLFRLVDDRALVNRMGFNNDGAAAVAPRLARTRQTLERRFGPARPVLGVNIGKTKVVPL +EDAADDYRASTRLLAPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRAVPGR +RVPLTVKIAPDLADADVRAVGALAERLGLDGVIATNTTVSREGLRTPRADVDALGAGGLS +GAPLQERSMRVLQVLRAALPTGTAVVSVGGVTDADDVQARLDAGADLVQGYTAFLYEGPF +WAGRTTAGLARSLRG +>PROKKA_01678 +MQLPDPKAAVDGVLTSRAPRLYPPFFRAVFGGMDAEQAHHRGFDAIRLAERTGASAALRA +AFRPDPLLARTVMGLRFPTPFGLAAGFDKEGRGTAALADLGFGHIEVGTITAQAQPGNPQ +PRLFRLVEDRALVNRMGFNNDGAAAVAPRLARTRAVLERRFGAVRPVLGVNIGKTKVVAL +EDAAEDYRASTRLLTPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRVVTGR +RVPLTVKIAPDLTDEDVRAVAALAERLGLDGVIATNTTISREGLATPRADVDALGAGGLS +GAPLKERSTEVLRVLRAALPVGTAVISVGGVTDADDVQARLDAGADLVQGYTAFLYEGPF +WAGRISAGLACALRG +>PROKKA_01576 +MQLPDPRFRVQSVLRSSAPRIYPPFFRAVFAGMDPERAHHVGFAGIRAAEASGASRALRS +TMAPDLGLARTVMGLRFPSPFGLAAGFDKTGVGTTALAELGFGHIEVGTITAQAQPGNPA +PRLFRLPEDRALINRMGFNNDGAAAVAPRLAATRRTLEERFGAVRPVLGVNIGKTKVVPL +DGAVEDYRASARLLAPHADYLTVNVSSPNTPGLRQLQEISSLEPILAAVREEADRAVPDR +RVPLTVKIAPDLADEDVRAVAELAGRIGLDGVIATNTTIGRGGLSTPASEVEAMGAGGLS +GAPLAARSLEVLRTLRAALPAGVALIAVGGVTDGDDVLQRLDAGADLVQGYTAFLYEGPF +WAGRINAGLDAAQRAR +>PROKKA_01166 +MQLPDPKSAVDGLLTSRAPRLYPPFFRAVFGGMDAEQAHHRGFDAIWLVERTGASAALRA +AFRPDPLLARTVMGLRFPTPFGLAAGFDKDGRGTAALADLGFGHIEVGTITAQPQPGNPQ +PRLFRLVDDRALVNRMGFNNDGAAAVAPRLARTRQTLERRFGPARPVLGVNIGKTKVVPL +EDAADDYRASTRLLAPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRAVPDR +RVPLTVKIAPDLADDDVRAVGALAERLGLDGVIATNTTVSREGLRTPRADVDALGAGGLS +GAPLQERSMRVLEVLRAALPTGTAVVSVGGVTDADDVQARLDAGADLVQGYTAFLYEGPF +WAGRITAGLARSLRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001011.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001011.fa new file mode 100644 index 0000000000000000000000000000000000000000..8791e9a38ce60a84155034d3e169ceb2eb62f4a5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001011.fa @@ -0,0 +1,39 @@ +>PROKKA_01210 +MARDPIQPPPPDPSAPHGAPAGGPTEEDTRPFLDDPPGLGWVPDGLPGFERCTLGLDTDE +QGQNLVTVVRPRTDAPRDPARRPILSVHGWSDYFYNAPLAHAFEAAGYAFHAVDLRHYGR +SLRAGQTPGWTDDLTRYDADLEAAFETIAQDHPLPPILMGHSTGGLIAALWADRNPGRLA +ALVLNSPWLEMQGSAGVRLLAKSIVGPVSAMKPYATLTLPRIDHYWRTLSDQAEGEWDLH +PLWRPPHAFEVPAAWLSAVLSGHRAVAGRLHVSVPILVLVSARGHRGTSYGEAMLTSDIV +LDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSATEAE +SGAPDDGAG +>PROKKA_00929 +MARDPLQPPPPDPSAPHGAPAGGPTEEDTRPFLDDPPGLGWVPDGLPGFERCTLGLDTDE +QGQNLVTVVRPRTDAARDPARRPILSVHGWSDYFYNAPLAHAFEAAGYAFHAVDLRHYGR +SLRTGQTPGWTDDLARYDADLEAAFETIAQDHPLPPILMGHSTGGLIAALWADRNPGRLA +ALVLNSPWLEMQGSAGVRLLAKSIVGPVSAMKPYAMLTLPRIDHYWRTLSDQAEGEWDLH +PLWRPPHAFEVPAAWLSAVLSGHRAVAGRLDVTVPILVLVSARGHRGTSYAEAMLTSDIV +LDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSASEAG +APDDGAG +>PROKKA_01677 +MSIKPAEQPIPADESEPSRPPEGGPTDEDTRPLLDDPPGLGWVEDGMAGFERLTLGLDTD +EQGQNLVTVVRPQATGPRDRTRRAILSVHGWSDYFYNAPLARAFEEAGYAFHAVDLRHYG +RSLREGQTPGWTDDLARYDADLEAALATIAEDHPLPPVLMGHSTGGLIASLWAHRNPGRI +SALVLNSPWLEMQGSAGVRLLAKTIVDPVSALKPYAMLTLPRIDYYWRTLSDQAEGEWDL +HPLWRPTHAFEVPAAWLSAVLKGHRTVARRLQVSAPILVLVSARGHRGTSYDEAMLASDI +VLDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSASEA +ESGAPDDGAG +>PROKKA_01575 +MTLFPHVRGPWPRHGLGLPADDAAAPPTPVDPEAGWTPDVLDGFERRSLALNADRQGRNV +VTVVRRRAASRHRDPCRRPFVAVHGWSDYFYNTPLAEAVESAGYAFHAVDLRHHGRSLRP +GQTPGFVDRLDRHHEDLDAALALIAEDHPATPVVEAHSTGGLTTALWAADRPEAASALVL +NSPWLQTHGGPLARAVAAPAVRRIARRDPYEILPLPRVDHYWRSLSAEADGEWDLEPAWR +DRWAFAVPAGWLAAVLDGHTTVARGLDLPVPVLVLVSDRGGLPLATRRRAASSDVILSPR +AQARAARRLGPGVVVHRCPGALHDVFASAPPVRRAALDATLSWLAETAPPRIAG +>PROKKA_01167 +MARDPIQPPPPDPSAPHGAPAGGPTEEDTRPFLDDPPGLGWVPDGLPGFERCTLGLDTDE +QGQNLVTVVRPRTDAPRDPARRPILSVHGWSDYFYNAPLAHAFEAAGYAFHAVDLRHYGR +SLRTGQTPGWTDDLTRYDADLEAAFETIAQDHPLPPILMGHSTGGLIAALWADRNPGRLA +ALVLNSPWLEMQGSAGVRLLAKSIVGPVSAMKPYAVLTLPRIDHYWRTLSDQAEGEWDLH +PLWRPPHAFEVPAAWLSAVLSGHRAVAGRLDVSVPILVLVSARGHRGTSYAEAMLTSDIV +LDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSATEAE +SGAPDDGAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001012.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001012.fa new file mode 100644 index 0000000000000000000000000000000000000000..bf6bab132bea1a9bcdcefe58948d4a5970f9a507 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001012.fa @@ -0,0 +1,35 @@ +>PROKKA_01211 +MSADRAPQPPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL +LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN +GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG +EISEDVITRYLDRGFRTGQDVDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP +DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPDSASVADGGA +>PROKKA_00930 +MSADRAPQSPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL +LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN +GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG +EISEDVITRYLDRGFRTGQDIDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP +DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPASDADGGA +>PROKKA_01676 +MSGSGPSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIVEALTPEHGLVRAVAKGVRKT +SSRLGSTVEPFMHTTLQLARGRGELLTVTQAQLLHPYATMLAADYDAYAVAGALAEAVER +IPAVDEAGRRAQYRLLHGALAALARRRHDPRLILHSFLLRTLAQAGWAPTFDRCARCGAP +GPHSAVHVALGGAVCPECRPPGAAHPAPQTLALLAALAAGDWATADSSDAAARREAAGIV +AAYLQFHAERRLVSPVRPGPGPRPPRPARREETMRADRAPQSPPPHPSGAVAPRIDPRFV +PRHVAIVMDGNGRWANQRGLPRTEGHRAGEAALLDVVAGAVELGVGHVSAYAFSTENWRR +SAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWNGRAPRLWTPVIRELQEAEELTRHNTGT +TLHMCVNYGSRAEIQDGVQALAEEVRAGRMRPADITEDVITRYLDRGFRAGQDVDVVPDV +DLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWPDVDRRTLWEAVETYARRDRRYGGAVDT +AQPAPSSGAPDSASDADGGA +>PROKKA_01574 +MSDVPKVSPPPHPSGAVPPKLDPRFVPRHVAVVMDGNGRWANQRGLPRTEGHRAGEAALL +DVVAGAVELGVGHVSAYAFSTENWSRSAEEVRFLMGFSKDVLRRQRDTLDSWNVRIRWNG +RAPRLWTPVIRELREAEDLTRDNTGTTLHMCVNYGSRAEIVDGVQALAEEVAAGRMRPRD +LTEDVITRWLDRGFRAGDRDVDVTPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDELWP +DVDRRTLYAAVLEYAHRDRRFGGAVDAPAAD +>PROKKA_01168 +MSADRAPQPPPPHPSGAVAPRIDPRFVPRHVAIVMDGNGRWANQRGLPRTEGHRAGEAAL +LDVVAGAVELGIGHVSAYAFSTENWRRSAEEVRFLMGFSRDVLRRQRDTLHSWNVRIRWN +GRAPRLWTPVIRELQEAEELTRHNTGTTLHMCVNYGSRAEILDGVQAIAEEVRAGRMRPG +EISEDVITRYLDRGFRTGQDVDVVPDVDLFLRTSGEQRLSNYLLWQSAYAELLFLDVLWP +DVDRRTLWAAVETYARRDRRYGGAVDTPQPAPSSGAPDSASVADGGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001013.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001013.fa new file mode 100644 index 0000000000000000000000000000000000000000..45d6ffa19749670903835150768344e4d279a8f0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001013.fa @@ -0,0 +1,55 @@ +>PROKKA_01213 +MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG +PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI +ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLRGTQI +TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH +RNLEHRDSLLLSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL +YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME +VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR +RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG +AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY +VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA +>PROKKA_00932 +MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVITEAPRWCAVDLRDGNQALIDPMG +PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI +ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLKGTQI +TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH +RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL +YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME +VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR +RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG +AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY +VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA +>PROKKA_01675 +MSAHLQKPSGMKFHKYVPYQDQIQVSLPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG +PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI +ERTFESLEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLKGTQI +TYEYSPESYTGTELEFARRISDEVAQVLEASTDRKMILNLPATVEMATPNVYADSIEWMH +RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL +FSQGVDPMIDFSDMDHIKRTVEYCNQLPVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME +ADAKAAGKTVDEIDWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR +RAQIEFSHVIQEMADAQGGEVSGADLWTAFQDEYLPAEAKDEQWGRYRLRSVTSASGEDG +AFRMEAELEVDGVTQTRTAQGNGPIDAFLRMLGEDDMDVRVLDYTEHALSEGGAAMAAAY +VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRAVRA +>PROKKA_01572 +MRNLQKPSGMKHGKYVPYHEQIEVHLPDRTWPDKVITEAPRWCAVDLRDGNQALIDPMGP +ERKLRMFQLLVQMGYKEIEVGFPSASQTDFDFVRQLIEGDHIPDDVSIQVLTQAREHLIE +RTFESLEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLTGTEIT +YEYSPESYTGTELEFARRISDEVATVLEASTDRQMILNLPATVEMATPNVYADSIEWMHR +NLEHRDSIILSLHPHNDRGTGVAAAELGYLAGGDRIEGCLFGNGERTGNVDLVTLGMNLF +SQGIDPMIDFSDMDHIRRTVEYCNQLPVPERSPWGGDLVFTAFSGSHQDAIKKGFEAMEA +DAAAAGKHVDEIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHKLDLPRR +AQIEFSHVIQELADAHGGEVSGADLWTAFQDEYLPAENKEEAWGRYRVRSVSSESGENGA +FRMTAEIFVDHEPQTRTAEGNGPIDAFLKILGEDGQDVRVLDYTEHALSEGGSAMAAAYV +EAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRSLRA +>PROKKA_01170 +MSAHLQKSSGMKFHKYVPFQDQIEVALPDRTWPDKVIEKAPLWCAVDLRDGNQALIDPMG +PERKLRMFQLLVGMGFKEIEVGFPSASQTDYDFVRQLIEGDHIPDDVTIQVLTQSREHLI +ERTFEALEGADRAIVHLYNSTSVLQRRVVFRQDEDGIVDIATSGARLVKKFEEQLRGTQI +TYEYSPESYTGTELEFARRISDEVATVLEASTDRKMILNLPATVEMSTPNVYADSIEWMH +RNLEHRDSLILSLHPHNDRGTGVAAAELGYLAGADRIEGCLFGNGERTGNVDLVTLGMNL +YSQGIDPMIDFSDMDHIKRTVEYCNQLAVPERSPWGGDLVFTAFSGSHQDAIKKGFEAME +VDAKAAGTDVDGIPWAVPYLPIDPKDIGRSYEAVIRVNSQSGKGGVAYLLKSEHNLDLPR +RAQIEFSHVIQDLADAQGGEVSGADLWRVFQDEYLPADAAEAQWGRYRLRSVSSASGEDG +AFRMEAELEVDGVTQTRTAQGNGPIDAFLRILGEEGVDVRVLDYSEHALSEGGAAMAAAY +VEAAVGDRVLWGVGLDHNTTTASLKAVVSAVNRALRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001015.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001015.fa new file mode 100644 index 0000000000000000000000000000000000000000..197b7a621a338729b15b740de2d5327dbea23671 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001015.fa @@ -0,0 +1,45 @@ +>PROKKA_01215 +MLTPAVLFALFLVFLGLTWTLSLAESAFSYLSRRDAEDIVRERPGSKVLEIARERESHLG +ALRVWRFVAEALSAVCLTAAADAVVDDTWLAVAIAAVVLVGVAALLGVWSPRPIGSRNEA +AVARRLGGLVWVLRRALGPLAARLDRDRRRREVEPEDEDDFQERHLREFVARAHDADVLA +DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGEDAD +DIRGMLHLKDVTRALHHDGAATDTPVTEVMRDVRFVPESKSVATLLQELQRESTHVAVVV +DEYGGTAGLVTLEDLIEEIVGEIYDEDDQPDRPEVEFVAPGVYSVDARMGIHDFREEFEL +PEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGIELVADTLEPRRNRVARLRVSETPDR +PVRLRRREEQAHGAAPADPVA +>PROKKA_00934 +MLTPAVLFALFLVFLGLTWTLSLAESAFSYLSRRDAEDIVREQPGSKVLEIARERESHLG +ALRVWRFVAEALSAVCLTAAADAVVDDTWLAVAIAAVVLVGVAALLGVWSPRPIGSRNEA +AVARRLGGLVWVLRRALGPLAARLDRDRRRREVEPEDEDDFQERHLREFVARAHDADVLA +DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGDDAD +DIRGMLHLKDVTRALHHDGAATDTPVTEVMRDVRFVPESKSVATLLQELQRESTHVAVVV +DEYGGTAGLVTLEDLIEEIVGEIYDEDDRPDRPEVEFVAPGVYSVDARMGIHDFREEFEL +PEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGIELVADTLEPRRNRVARLRVSETPDR +PVRLRRREEQAHGAEPADPVA +>PROKKA_01673 +MLTPAVLFALFLVFLALVWTLSLAESAFTYLSRRDAEDIVRRRPGSRVLDVTAERDSHLG +ALRVWRFVAEALSAVCLTAAADAVVDNTWFAVLIAAAVLVGVAALLGVWSPRPFGSRNEA +AVARRLGGLVWGLRRALGPLADRLGRDRRRREDELEEEDDFQERHLREVVARAHDADVLA +DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGEDAD +DIRGMLHLKDVTRALHQDGAAQSGPVTAAMRDVRFVPESKSVAALLQELQRESTHVAVVV +DEYGGTAGLVTLEDLIEEIVGEIYDEDDLPDRAEVEMIEPGVYSVDARMGLHHFREEFEL +PEEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGLELLADTLEPRRNRVARLRVSETPD +RPARLRRRDEEPHGSSAAETAA +>PROKKA_01570 +MATAVSLVLLFLACLACTWVLALAESAFTYLPRKDAEDVARTRPGSRILDVTADLDGHLG +ALRVWRFLSEAFAAMFLTAGLHALTDSVWAALAVTAVLLVGTAAVLGVWSPRPIGSRNEA +AVAARTAGLVHGLKQALGPVGDRLGRDRRRTEAEAADEDDFHERHLREVVARAHDAEVLE +DSEAELIASVFSMGDTLVRSVMVPRTDVVTIDADHTLGQALDLFLRSGCSRVPVIGEDSD +DVRGMLYLKDAVRALHHEGHASQDAVTAVMREVRFVPESKPVSVLLEELQRESTHVAIVV +DEYGGTAGLVTLEDLIEEIVGEIWDEDDRPDRPEIEELAPGVYSVDARMGIGDFREEFEL +PEDEDEDDDVDTVGGLLAKELGRVPIRGSRVVVHGLELTADTLEPRRNRVARLKVVETED +RPARLRRQHDPTDPD +>PROKKA_01172 +MLTPAVLFALFLVFLGLTWTLSLAESAFSYLSRRDAEDIVRERPGSKVLEIARERESHLG +ALRVWRFVAEALSAVCLTAAADAVVDDTWLAVAIAAVVLVGVAALLGVWSPRPIGSRNEA +AVARRLGGLVWVLRRALGPLAARLDRDRRRREVEPEDEDDFQERHLREFVARAHDADVLA +DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGEDAD +DIRGMLHLKDVTRALHHDGAATDTPVTEVMRDVRFVPESKSVATLLQELQRESTHVAVVV +DEYGGTAGLVTLEDLIEEIVGEIYDEDDQPDRPEVEFVAPGVYSVDARMGIHDFREEFEL +PEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGIELVADTLEPRRNRVARLRVSETPDR +PVRLRRREEQAHGAAPADPVA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001016.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001016.fa new file mode 100644 index 0000000000000000000000000000000000000000..beef13db49b7bd6bd40a39162374750289f33df1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001016.fa @@ -0,0 +1,20 @@ +>PROKKA_01216 +MAVEILNESGIEVPEDALLRMARHVYARLHVHERAETAVTVVDAARMAELHEEWMDLPGP +TDVMSLPMDELTPGSPEAPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL +LGYDHVEDAEREEMFTLQDRLVSEVLGRPAPAPTVED +>PROKKA_00935 +MAVEILNESGIEVPEDALLRMARHVYARLHVHERAETAVTVVDAARMAELHEEWMDLPGP +TDVMSLPMDELTPGSPEAPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL +LGYDHVEDAEREEMFTLQDRLVSEVLGRPAPAPTVED +>PROKKA_01672 +MAVEILNESGIEVPEDELLRMARHVYASLHVHERTETAVTVVDAARMAELHEEWMDLPGP +TDVMSLPMDELTPGTAEAPAEGMLGDVVLCPEVAAEQAARGGHGRDDELMLLLTHGMLHL +LGYDHMDDADRLEMFALQDRLVSEVLGRPAPAPTIED +>PROKKA_01569 +MAVEIVNESGVEVPEEALLGMARHVYAALHVHPLAETAVTVVDAQRMAELHVEWMDLEGP +TDVMSLPMDELTPGTEKSPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL +LGYDHMEEDERAEMFALQDRLVSEVLGRPAPAPTVED +>PROKKA_01173 +MAVEILNESGIEVPEDALLRMARHVYARLHVHERAETAVTVVDAARMAELHEEWMDLPGP +TDVMSLPMDELTPGSPEAPAEGVLGDVVLCPEVAAEQAARGGHSRDDELLLLLTHGMLHL +LGYDHVEDAEREEMFTLQDRLVSEVLGRPAPAPTVED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001017.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001017.fa new file mode 100644 index 0000000000000000000000000000000000000000..295d49ed5f7ccfc6a66135f0c8717f12c479f0f6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001017.fa @@ -0,0 +1,35 @@ +>PROKKA_01217 +MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV +DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG +QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK +EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV +APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG +LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR +>PROKKA_00936 +MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV +DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG +QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK +EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV +APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG +LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR +>PROKKA_01671 +MVRTLGPQDALLRILGGVFPAVDLTVRDQRLEMAGPVPDVASVRRVVEDLRSIARRDQAV +TPEVMEQVVTHVRGAAAGRGAGQLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGI +GPAGTGKTYLAMAKAVQALQAKEVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYD +ALHDMIEPESIPRLMEAGTIEVAPLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGF +GARMVVTGDTSQVDLPRGTRSGLSQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYD +AARGAEPAPRGGRGHRGR +>PROKKA_01568 +MIRPIVSDPSSHVVLPPVSVPGAESVSFESAELMVRTLGAHDALLRILAGVYPDVEVTVR +DQSLGMSGPPRHVAQARRIVEDLRSLARRDAPVTPDVVEQVVSLVRDGETGRASGTLHLD +SILSGRGRKIRAKTLHQQDYVEAIDRATIVFGLGPAGTGKTYLAMAKAVQALQAKEVTRI +ILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMESGTIEVAPLAY +MRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGVRSGLAEAV +EVLEGVDGLEMVRFDSSDVVRHSLVSAIVDAYDGARGSGSAADPRPAGRGAQRGRSGRGR +>PROKKA_01174 +MSRPRDPEVIRPIVTVPPTTPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVFPTV +DVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGRGAG +QLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQALQAK +EVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGTIEV +APLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGTQSG +LAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARGPAERSQKRGGARRGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001018.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001018.fa new file mode 100644 index 0000000000000000000000000000000000000000..3adbdf36b818fc5bc8d5f02738c696998c1f303a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001018.fa @@ -0,0 +1,30 @@ +>PROKKA_01218 +MTAPLFHLEPGALAGASAGAEVVFDGAEARHAAAAMRLAPGEAVLLADGSGTLGHGTVLA +AAPDAVSVRLDAVAEEPAPTPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV +RWKGPKAAKARQKWADTARAAAKQARRARVPAVRDHVSGTAVAGLARDDDGGRLVLVLHE +DAEHGVSAVPAERLSAAVEIAVVVGPEGGIGPAELEACVAAGAVPVRLGPHVLRASTAGP +AALAVLQHRLGRW +>PROKKA_00937 +MTAPLFHLEPGALAGASAGAEVVFDGAEARHAAAAMRLAPGEAVLLADGSGTLGHGTVLA +AAPDAVSVRLDAVAEEPAPTPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV +RWKGPKAAKARRKWADTARAAAKQARRARVPAVRDHVSGTAVAGLAWDDDGGRLVLVLHE +DAEHGVSAVPAERLSAAVEIAVVVGPEGGIGPAELEACVAAGAVPVRLGPHVLRASTAGP +AALAVLQHRLGRW +>PROKKA_01670 +MTAPLFHLEPGALTGAVPGAEVSFGGPEARHAAASMRLAPGESVLLADGSGVRGHGTVLA +AAPDAVTVRLDAVDEEPAAVPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV +RWKGPKAEKARQKWADTARAAAKQARRARVPEVRGHVSGTGVAGLASAPDDGARLVLVLH +EDAERGLSEVPVERLREAAEIAVVVGPEGGVGPAELEACTAAGAVPVRLGPHVLRASTAG +PAALAVLAHRLGRW +>PROKKA_01567 +MTAPLFLLDAGALAGVAPGAEVAFTGAEARHAAASMRLGAGESVLVADGSGARASCVVVD +AAPSAVTVRVESLEHDAAPRPALVLVQALAKGDRDLMAVQASTELGVDAVVPWEAERSIV +RWKGAKAAKAHQKWEDTVRAAAKQARRARVPEVRPVVSGTAVAALAGPDRLLLVLHEDAD +LGLGGLPDADLEAAAEVALVVGPEGGVSPAELDACTAAGAVPVRLGPHVLRASTAGPAAL +AVLQHRLGRW +>PROKKA_01176 +MTAPLFHLEPGALAGASAGAEVVFDGAEARHAAAAMRLAPGEAVLLADGSGTLGHGTVLA +AAPDAVSVRLDAVAEEPAPTPALVLVQALAKGDRDLMAVQAAVELGVDAVVPWEAERSIV +RWKGPKAAKARQKWADTARAAAKQARRARVPAVRDHVSGTAVAGLAWDDDGGRLVLVLHE +DAEHGVSAVPAERLSAAVEIAVVVGPEGGIGPAELEACVAAGAVPVRLGPHVLRASTAGP +AALAVLQHRLGRW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001020.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001020.fa new file mode 100644 index 0000000000000000000000000000000000000000..3c8ed9faa90569c7ac00f88534dc8bfa1f96fd5c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001020.fa @@ -0,0 +1,35 @@ +>PROKKA_01220 +MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH +TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ +VAVAQFPYEDGSTIRHLELVSLTPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL +LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVQDLLEAGREDRIVLAGTANLA +RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG +PGAVAKLGVIGPTRMDYPGTMAAVRAIARYLSRILTT +>PROKKA_00939 +MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH +TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ +VAVAQFPHEDGSTIRHLELVSLAPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL +LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVHDLLEAGRQDRIVLAGTANLA +RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG +PGAVAKVGVIGPTRMDYPGTMAAVRAIARYLSRILTT +>PROKKA_01668 +MTEQPRRLQVLQAIVEEYVARREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH +TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPSTDTEHMMETTVRLLAQLTQQ +VAVAQFPHEDGSTVRHLELVPLTPARVLVVLILSTGRVDQRHVVLETPLAEADLAVLRGL +LLEAVLGLGPAQAAAVVDAAVARMRPEDREAAALVAGAVHALLEAGRQDRIVMAGTANLA +RSTGDFGASIGPILEALEEQVVLLRLLTEMEHDAHGVSVRIGSENAGSLADTSVVAAAYG +PGAVAKVGVVGPTRMDYPGTMAAVRAIARYLSRILTT +>PROKKA_01565 +MTEQPRRLQVLQAIVEDYVSLREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH +TSAGRVPTDKGYRVFVDRISEVKPLSAAERRAVRTLLDSEADTESMMEATVRLLAQLTRQ +VAVVQFPHEDGSTVRHLDLVALTPERVLVVLILSTGRIEQRTVALARPVQDEDLAALRAV +LLPVIEGLGPAQAAAVLDTPLEGLPPARRAAAVDVVGAVRGLLEAERQDRIVLAGTANLA +RSTDDFHSSIGPILEALEEQVVLLRLLTEMGQDAHGVSVRIGAENGASLADTSVVAAAYG +PGAVAKVGVIGPTRMDYPGTMAAVRAIARYLSRILTT +>PROKKA_01178 +MSEQPRRLQVLQAIVEDYVALREPVGSKALVERHALGVSSATVRNDMAALEEEGLIVAPH +TSAGRVPTDKGYRVFVDRLSEVKPLSPAERRAVRTLLDPETDTEHMMESTVRLLAQLTQQ +VAVAQFPHEDGSTIRHLELVSLAPTRVLVVLILSTGRVDQRHAVLDRPVDEAELSVLRGL +LLDALLGLGPVQAATVVDDVVTRVRPEHRQSAALVAAAVQDLLEAGREDRIVLAGTANLA +RSPGDFGASIGPILEALEEQVVLLRLLTEMEQDAHGVSVRIGSENAGSLADTSVVAAAYG +PGAVAKLGVIGPTRMDYPGTMAAVRAIARYLSRILTT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001021.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001021.fa new file mode 100644 index 0000000000000000000000000000000000000000..9d99e55f504f346c685775230fa7b3ca9448a05e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001021.fa @@ -0,0 +1,30 @@ +>PROKKA_01221 +MDWSSWGPAGHDDLTRRPARTVPDVPAAPGTVVEDVASGFTGAVIGIERSGGVHVVVLED +RRGVRRGFPLGGGFWIDGEPVTLVPPTAAAPAAPARTASGSRRVEGARARTARASRIWVE +GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIRAFAPGPRRRLGILVDHLVTGSKE +ERLAAEAMRVPGAAGNVLILGHPYVDVWQVIKPSVLGIPAWPVVPKGQDWKTGILRGLGW +PHGSKEATGLGWKRLLSHVTTYADLEPSLLGRVEELIDFLTAAPEH +>PROKKA_00940 +MDWSSWGPAGHDDLTRRPARTVPDVPATPGTVVEDVASGFTGAVSGIERSGGVHVVVLED +RRGVRRGFPLGGGFWIDGEPVTLVPPTAAAPAAPARTASGSRRVEGARARTARASRIWVE +GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIRAFAPGPRRRLGILVDHLVTGSKE +ERLAAEAMRVPGAAGNVLILGHPYVDVWQVIKPSVFGIPAWPVVPKGQDWKTGILRGLGW +PHGSKEATGLGWKRLLSHVTTYADLEPSLLGRVEELIDFLTAAPEH +>PROKKA_01667 +MDWSSWGPAGHEEMTRRPGRPARDVPAAPGTVVEDVASGFTGAVIRVERAGGVHTVVLED +RRGVRRGFPLGGGFWIDGEPVTLVPHVASAPRPPARTASGSRRVEGVRARTARASRIWVE +GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIAAFDPGPRRRLGILVDHLVPGSKE +ERIAAEAMRVPGAAGNVLILGHPYVDVWQVIKPAVLGIPTWPVVPKGQDWKTGVLQGLGW +PHGTKEATGLGWKRLLSHVGSYADLEPSLLGRVEELIDFLTAEPER +>PROKKA_01564 +MDWSSWGPGAHEDLARPAGRTAGEAPATPGTVVEDVASGFVGAVVRVERSGGTHVVVLED +RRGVRRGFPLGPGFWVDGSPVVLVPPRSAAPAAAARTASGSRRVEGARARTARASRIWVE +GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLPGAIRDFAPGPGRRLGILVDHLVAGSKE +ERLAAEAMAVPGAAGNVLILGHPYVDVWQVIKPAVLGIDAWPVVPRGQDWKTGVLRGLGW +PAGTKEATGLGWKRLLSHVRTYADLEPALLGRVEELIDFLTAPGA +>PROKKA_01179 +MDWSSWGPAGHDDLTRRPARTVPDVPATPGTVVEDVASGFTGAVIGIERSGGVHVVVLED +RRGVRRGFPLGGGFWIDGEPVTLVPPTAAAPAAPARTASGSRRVEGARARTARASRIWVE +GVHDAELVEKVWGEDLRLEGIVVEPLHGVDDLAGAIRAFAPGPWRRLGILVDHLVTGSKE +ERLAAEAMRVPGAAGNVLILGHPYVDVWQVIKPSVLGIPAWPVVPKGQDWKTGILRGLGW +PHGSKEATGLGWKRLLSHVTTYADLEPSLLGRVEELIDFLTAAPEH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001023.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001023.fa new file mode 100644 index 0000000000000000000000000000000000000000..10deb81c38cf24efc5ff180e3a1e5e177dd501ec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001023.fa @@ -0,0 +1,60 @@ +>PROKKA_01224 +MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD +IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ +GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCDPEDVLRVSGKTG +VGVEELLDRVVRAVPSPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM +STGTTYELLEIGVSSPEPVPTKGLAVGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG +GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL +HLEIVRERLEREFGLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT +IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA +SLDWKADGDQAADLVKVDILLQGEQVDAFSSITHKDNAYTYGVMMTGKLKELIPRQQYEV +PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE +AFIAALSSDGAGADQAAKK +>PROKKA_00943 +MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD +IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ +GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCEPEDVLRVSGKTG +VGVEDLLDRVVRAIPGPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM +STGTTYELLEIGVSSPEPVPTNGLAAGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG +GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL +HLEIVRERLEREFDLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT +IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA +SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHRDNAYAYGVMMTGKLKELIPRQQYEV +PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE +AFIAALSSDGAGADQAAKK +>PROKKA_01664 +MSPLASNPPVPAATEPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD +IERERGITIKSQAVRMPWELDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ +GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELATLIGCEPEDVLRVSGKTG +VGVEDLLDRVVRSIPAPEGEADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKIRMM +STGATHELLEIGVSSPEPTPTKGLAVGEVGYLITGVKDVRQSKVGDTVTNHAKPAAEELG +GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL +HLEIVRERLEREFNLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKIHEVREPMASAT +IIVPAEFIGAVMELCQAKRGNLRGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA +SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHKDNAYSYGVMMTGKLKELIPRQQFEV +PIQAAIGSRVIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE +AFIAALSSDGAGADSAAKK +>PROKKA_01561 +MSEAPEPIKDVPVSPLASKPPVPAATDPAVIRNFCIIAHIDHGKSTLADRMLQATGVVQP +REMKAQYLDRMDIERERGITIKSQAVRMPWEVDGVNYALNMIDTPGHVDFTYEVSRSLAA +CEGAILLVDAAQGIEAQTLANLYLAMENELEIIPVLNKIDLPAADPDRYAAELATLIGCE +PDDVLRVSGKTGQGVEALLDRVVERLPAPQGVADAPARAMIFDSVYDTYRGVVTYVRVVD +GMLSPREKIRMMSTGATHELLEIGVSSPEPMPTKGLSVGEVGYLITGVKDVRQSKVGDTV +TNSSRPATEQIGGYEDPKPMVFSGLYPIDGSDYPNLRDALDKLKLNDAALVYEPETSVAL +GFGFRVGFLGLLHLEIVRERLEREFDLDLISTAPNVVYEVKREDKTVVTVTNPSEFPEGK +VLEVKEPMASATVIVPAEYIGAVMELCQTKRGHLKGMDYLSEERVEIRYWIPLAEIVFDF +FDQLKSRTKGYASLDWKADGDQVADLVKVDILLQGEQVDAFSAITHRDNAYSYGVMMTGK +LKELIPRQQFEVPIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKR +MKMVGRVEVPQEAFIAALSSDGAEPAKK +>PROKKA_01182 +MSPLASNPPVPAATDPSVIRNFCIIAHIDHGKSTLADRMLQATGVVQPRDMKAQYLDRMD +IERERGITIKSQAVRMPWSVDGVDYALNMIDTPGHVDFTYEVSRSLAACEGAILLVDAAQ +GIEAQTLANLYLAMEHELEIIPVLNKIDLPAADPDRYAAELASLIGCEPEDVLRVSGKTG +VGVEELLDRVVRAIPGPEGDADAPARAMIFDSVYDTYRGVVTYVRVVDGRLSPREKVRMM +STGTTYELLEIGVSSPEPVPTKGLAAGEVGYLITGVKDVRQSKVGDTVTNHAHPAEQSLG +GYEDPKPMVFSGLYPIDGSDYPVLRDALDKLKLNDAALVYEPETSVALGFGFRVGFLGLL +HLEIVRERLEREFDLDLISTAPNVVYEVTREDREVVTVTNPSEFPEGKILEVREPMASAT +IIVPAEFIGAVMELCQAKRGNLKGMDYLSEERVEIRYWIPLAEIVFDFFDQLKSRTKGYA +SLDWKADGDQVADLVKVDILLQGEQVDAFSSITHRDNAYAYGVMMTGKLKELIPRQQYEV +PIQAAIGSRIIARENIRAIRKDVLSKCYGGDISRKRKLLEKQKEGKKRMKMVGRVEVPQE +AFIAALSSDGAGADQAAKK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001024.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001024.fa new file mode 100644 index 0000000000000000000000000000000000000000..5b8efad983ce5d7876458c7d983a2d24983f8500 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001024.fa @@ -0,0 +1,25 @@ +>PROKKA_01225 +MAFDLHRALSLGRRTARLIGALRDDARPRRAASEAGRRAGDRSGPSPFPGPPGPPGPAWD +PTEPTDSWPMPGPGQERRPRRQDAGRHVSLPDFTGTVRVEYAPVPGPTAGPGEVVWTWVP +YEEMDGRGKDRPVLLIGRDGAHLLGLMLTSRDRNNALARDEDYVDVGAGAWDRSGRASEV +KLDRVVRVDPAAVRREGGVLDRAAFDRVTAALARARRRGR +>PROKKA_00944 +MAFDLHRALSLGRRTARLIGALRDDARPRRAASEAGRRAGERSGPSPFPGPPGPPGPAWD +PTEPTDSWPMPGPGQERRPRRQDTDRHVSLPDFTGTVRVEYAPAPGPTAGPGEVVWTWVP +YEEMDGRGKDRPVLLIGRDGALLLGLMLTSRDRNNALTRDEDYVDVGAGAWDRSGRASEV +KLDRVVRVDPAAVRREGGVLDRAAFDRVTAALARARRRVR +>PROKKA_01663 +MAFDLNRALALGRRAIRLIGSLRDDDARRSWTGDAAGRGSGAAPFPGPPGPAGRAWDPKE +PTDSWPFPDRGHDGRPRGGQDRTRPASGATDPQGRALLADFTGMGRVEYAPVPGPAAGPG +EVVWTWVPYEEMDGRGKDRPVLLVGRDGDLLLGLMLTSRDRNNARVRDEDYVDVGSGPWD +RAGRPSEAKLDRVLRVDPAAVRREGGVLDPAAFERVGDALARAQGWRR +>PROKKA_01560 +MAFDFQRALTLGRTALRLVEQVRSMSGAGTTRGAAPSSPASRAGRRRRADAEETRGARSG +GAGSDHALLPDFTGRARVEYAPVPGATPDPGEVVWTWVPFEEMDGRGKDRPVLLVGRDGD +LLLALMLTSKDHTNAARRDADYVDVGTGPWDRGGRASEAKLDRILRVDPAAVRREGGVLE +RSRFDAVAEALARAQGWDR +>PROKKA_01183 +MAFDLHRALSLGRRTARLIGALRDDARPRRAASEAGRRAGDRSGPSPFPGPPGPPGPAWD +PTEPTDSWPMPGPGQERRPRRQDTGRHASLPDFTGTVRVEYAPVPGPTAGPGEVVWTWVP +YEEMDGRGKDRPVLLIGRDGAHLLGLMLTSRDRNNARARDEDYVDVGAGAWDRSGRASEA +KLDRVVRVDPAAVRREGGVLDRAAFDRVTAALARARRRGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001026.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001026.fa new file mode 100644 index 0000000000000000000000000000000000000000..7cd07c3f73d77931dae1bed2aacad6a387fa4d67 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001026.fa @@ -0,0 +1,35 @@ +>PROKKA_01227 +MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH +RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL +RHTGGTRGKRLLDAVAKAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT +GASLTELAAACAQLVDDTEGVVSVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH +AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG +IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR +>PROKKA_00946 +MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH +RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL +RHTGGNRGKKLLDAVAQAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT +GASLTELAAACAQLVDDTEGVVTVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH +AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG +IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR +>PROKKA_01661 +MSAARSPRSGRAGRVDPLAWRKAEPAPLMLLKGPEDHAARWVTDKVTAALRERHGELEVH +SLRAGEYQAGQLATAASPSLFAEPTLIKVDGLESMNDAFLEDALRLVQHGPGADDVTLVL +RHAGGSRGKRLLDAVAKAGTVVDCVPLKKDEERLAFVLAEFRDRRRRIEEDAARSLLRAT +GASLTELAAACAQLVDDTEGTVTAAMVDTYYGGRVEATSFAVADAALEGHAARAVSLVRH +AMATGVHPVMVTAALALKARQVARMIDAHRPAGELAALLGVAPFQVRYIQQAARHWTPAG +IAQAMEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR +>PROKKA_01558 +MSAARSTRSARGARGVDPLAWRRAEPAPLMLLRGPEEYAARWVADRVVATLQARHGSLET +HRLRASDYQAGQLALAASPSLFAEPTLIRVDGLESMNDAFLEDALRLVAQGPGADDVTVL +LRHTGGSRGKRLIDAVAAAGVVVECPALKKDEDRLALVQAEFREARRRIDEDAARALVRA +TGASLTDLASACRQLIEDVEGTVTPQTVETYYGGRVEATSFAVADATLEGHAARAVSLTR +HALATGVHPVMITSALAVKARQVARIIDARAGQGELASILGVAPFQVRFIQQAARHWTPA +GIARAVEWIAQADAEVKGAARDADFAVERAVIRVATAVSR +>PROKKA_01185 +MSAARSPRSGRAGRTDPLAWRRAEPAPLMLLKGPEDHAARWVTDRVTQALRERHGQLEIH +RLRAGEYQPGQLATAASPSLFAEPTLITVEGLEAMNDAFLEDALRLVQQGPGADDVTLVL +RHTGGNRGKKLLDAVAQAGTVVECVPLKKDEERLAFVQAEFRDRRRRIDEEAARALIRAT +GASLTELAAACAQLVDDTEGVVTVETVDTYYSGRVEATSFAVADAALEGQAARAVSLVRH +AMATGVHPVMITAALALKARQVARMIDARRPAAELPSLLGVAPFQVRYIQQAARHWTAAG +IAQAVEWIAQADAEAKGASRNPEFAVERAVIRVATAVSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001027.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001027.fa new file mode 100644 index 0000000000000000000000000000000000000000..c6540a4f7848a1eccfcefca02bb22e01174aa64d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001027.fa @@ -0,0 +1,79 @@ +>PROKKA_01228 +MNPAPGPPNDPVDRRARHREVPGPLEARWVPALLGCLTLGILGVGWDAPARSAAALTGLA +VAAAAILGAARSTGRIRGVATATALAGVAAALMLQHSAGPAAAASGSGWTGAVHAGSPLR +LELTLDGPATRSEATFGPRWSVPVRVETFGHPPRAPEAAVTARLTGGGAPPATIVAPEGG +TWAPDGGPGSRVCVVARPSRSGSTVFLAAASAPQPGPCPGGTQTAGGATGGDPGPPRREA +LRAAFRQSAEGTVGAAPELIPGLVLGDRSAQGAALDDAMKASGLSHLSAVSGANVAMILG +AVAITLRSARVHRAVVLSAGLAVLGVFVVVVGPEPSVLRAAVMGALGALAVFFGRARQAF +GLLTVGGTALLVAVPALAVEPAFHLSLAATAGIVLAGAPLDRALHAGLGRMLPDVVARWL +SASLAVTVAAHLACQPIILAMTGEVSAYAVPANLLAAPAVPPVTVLGTLAAALALPAPGI +AAALVAVIQWPAAWIGWVAHTSASLPGALRPWPAGALGAGLGVLLVAATLLGFAAVLLLE +RRRTAPVRRVGRSAPRTRERLPALVVLAAALAAATTGAVGAVLVPRSSGSAPPDWAVAFC +DVGQGDMAVFRSGPRAGVVVDVGPEPGLARRCLDDLDVDRVDAVLLTHLHADHAGGLAGV +VDRASRGAVHYATRDAPAQGREGRGGEADGVDPLADAARLRTGATGTAGPVRWHVLLADA +RAPEENDASAQVLVTVESGAGPVTTLVTGDMEEDASAAWVAGRRSDAAAPPRVDVLKVAH +HGARNGGTAVPRAAGARLHVVSVGADNPYGHPHRATVDALGRLGPVARTDLHGTLALTAA +DGPDPDGAPEIAVHTVRPPSSVRTGP +>PROKKA_00947 +MVSPAPGPPSDPVDRRARHREVPGPLEARWVPALLVCLTLGILGVAWDAPARSAAALTGL +AVAATTVLGAARSTGRIRGVATATTLAGVAAALMLQHSAGPAAAASASGWTGAVHAGSPL +RLELTLDGPATRSEATFGPRWSVPVRVETFGHPPRAPEAAVTARLTGGGAPPATIAAPLD +GTAAPGGGPGSRVCVVARPSRSGSTVFLAAAAAPQPGPCPGGAEPAGGATDGGPGPPRRE +ALRAAFRQSAEGTVGTAPELIPGLVLGDRSAQGAALDDAMKASGLSHLSAVSGANVAMIL +GAVAITLRSARVHRAVVLSAGLAVLGVFVVVVGPEPSVLRAAVMGALGALAVFFGRARQA +FGLLTVGGTALLVAVPALAVEPAFHLSLAATAGIVLGGAPLDRALHAGLGRVLPDVVARW +LSASLAVTVAAHLACQPIILAMTGEVSAYAVPANLLAAPAVPPVTVLGTLAAALALPAPG +IAAALVAVIQWPAAWIGWVAHTSASLPGALRPWPAGALGAGLGVLLVAATLLGFAAVLLL +ERRRAAPVRRVGRSAPRTRERLPALVVLAAALAAATTGAVGAVLVPRASGAAPPDWAVAF +CDVGQGDMAVFRSGPRAGVVVDVGPEPGLARRCLDDLDVDRVDAVLLTHLHADHTGGLPG +VVDRASRGAVHYATRDAPAQGRGGRGGEADGVDRPADAARLRTGATGTAGPVRWHVLLAD +ARAPEENDASAQVLVTVESEAGPVTTLITGDMEEDASAAWVAGHRSDAAAPPRVDVLKVA +HHGARNGGTAVPRAVGARLHMVSVGADNPYGHPHRATVDALGRLGPVARTDLHGTLALTA +ADGPDPDGAPEITAHTVRPPSSVRTGP +>PROKKA_01660 +MVSAPAGSRPPEAPGARTDPAARRGDVPGPLDARWVPALLACLTLGIVSDGWEAATRTTV +ALACLGAAAAAVLLAARAPTPAWIRGTGTAVALAGVAVALMLQHSAVPAAALERTGWADV +VREQAAVRVELAVTGAAVETAGTFGPRWSAPVRVRAFGHPARAPEAAVAARLSGPGTVPS +ALGAAPDSEPAPGGRVVGPPAATVLCVVVTPDAGDGTVFLTAAAAPTPGPCPAADAAHGA +ASVEDEPPPRREALRAAFRAAAAGTAGTAPELIPGLVLGDRSAQGRPLDAAMKASGLSHL +SAVSGANVALLLGFTAVALRSLRVHRAVVIAAGLGLLAVFVVVVGPEPSVLRAAVMGALG +AVAVFLGRGRQAFALLAVGGTALLVAVPSLSVEPAFHLSLAATAGIVLAGSWGDRTLHGP +LRRVLPDAAARWLSASLAVTLAALLACQPVLLAMTGELSAYAVLANLVAAPAVAPVTVLG +TLAAALVLPAPAVAAALVWLVQWPSAWIGVVAHAAAGLPGALRPWPSGALGVGLGALLTA +ATLAGFAAVLVLERRRHARVRRVGEGAPLPPERTPALVLLAAVLVAAAVGGVGAVLVPRP +AGAAPPDWAVAFCDVGQGDMAVFRSGPRAGVVVDVGREPEAARRCLEDLGVDRVEAVLLT +HLHADHAGGLAGVADRAVPGAVRYATRDAAGVGRSGATAGEAPGVAPPAGGARLVTGERG +AAGQARWEVLLADARAAEENDASAQLLVTVDAPAGPVTTLVTGDMEEEASGVWAAGRRSD +AAGPPSVDVLKVAHHGARNGGTAVPRAVRARLHVVSVGAENTYGHPHPATLDALHRLGPV +ARTDLHGTVALVAEGPDGAAGAGEIGVYTVRPPSAVRTAP +>PROKKA_01557 +MSLGCAALAAVTLTLRLRIRRTGSSRVRTGAATAVVLAGLCGAVLVQHIAVERSGREQVG +WIETVDTGGPVRLEVTAQGPATAGDSRFGPSWTRPVTVQRFGHPLRPLTPPAEATLTGTG +SLDAAANGAEVLCVVAEPRPADGALFLAARAAPESDGCGEGSTAASSGPTGRDVLRARFR +EAAADGVGLAPELVPGLVLGDRTAQSEQTDQAMKDAGLSHLSAVSGANCALLLGTVALVL +RSLRCPRGVVLGAGLAVLGVFVLVVGPEPSVLRAAVMGALGALAVFLGRGRQAFGLLCAG +GTLLLVSVPDLAGEIAFHLSLAATAGIVLVAAPVDRWLHGRLGRVLPDLAARGLSSSLAV +TLAAHLACQPILLVMTGTVSLWAVPANLMAAPAVAPVTVLGTLAAALVVPAPWAAAPLLW +TVQWPAAWIGVTATAASAAPGAVRPWPEGALGVALGALLTAATLAGFHAVLVLERRPTAP +VRRVGRSARDARVRVPAGVVLAAVLAASATGAAAAVLVPRPPGTVPEGWAVAVCDVGQGD +MTVFRSGPGSAVVADAGPDPAAASRCLDDLRIERVDALLLTHLHADHAAGAPGLSGPRAA +AAVRHGAWSGSGGGGGEEPGLDAPAGSAPLTTGDEGRAGDVAWRVLLADPRAAEQNDSSA +QLLVTVTTPAGPVTTLVTGDMEQEASAAWAAGTRSDAAPPPRVDLLKVAHHGARNGGLDV +PRRVRARLQAISVGADNTYGHPAAATVAGLEELGPVLRTDRHGTVALVPGPDARLTPYTV +RPPT +>PROKKA_01186 +MVSPAPGPPSDPVDRRARHREVPGPLEARWVPALLVCLTLGILGVAWDAPARSAAALTGL +AVAATTVLGAARSTGRIRGVATATTLAGVAAALMLQHSAGPAAAASASGWTGAVHAGSPL +RLELTLDGPATRSEATFGPRWSVPVRVETFGHPPRAPEAAVTARLTGGGAPPATIAAPLD +GTAAPGGGPGSRVCVVARPSRSGSTVFLAAAAAPQPGPCPGGAEPAGGATDGGPGPPRRE +ALRAAFRQSAEGTVGTAPELIPGLVLGDRSAQGAALDDAMKASGLSHLSAVSGANVAMIL +GAVAITLRSARVHRAVVLSAGLAVLGVFVVVVGPEPSVLRAAVMGALGALAVFFGRARQA +FGLLTVGGTALLVAVPALAVEPAFHLSLAATAGIVLGGAPLDRALHAGLGRVLPDVVARW +LSASLAVTVAAHLACQPIILAMTGEVSAYAVPANLLAAPAVPPVTVLGTLAAALALPAPG +IAAALVAVIQWPAAWIGWVAHTSASLPGALRPWPAGALGVGLGVLLVAATLLGFAAVLLL +ERRRAAPVRRVGRSAPRTRERLPALVVLAAALAAATTGAVGAVLVPRASGAAPPDWAVAF +CDVGQGDMAVFRSGPRAGVVVDVGPEPGLARRCLDDLDVDRVDAVLLTHLHADHTGGLPG +VVDRASRGAVHYATRDAPAQGRGGRGGEADGVDRPADAARLRTGATGTAGPVRWHVLLAD +ARAPEENDASAQVLVTVESEAGPVTTLITGDMEEDASAAWVAGHRSDAAAPPRVDVLKVA +HHGARNGGTAVPRAVGARLHMVSVGADNPYGHPHRATVDALGRLGPVARTDLHGTLALTA +ADGPDPDGAPEITAHTVRPPSSVRTGP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001028.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001028.fa new file mode 100644 index 0000000000000000000000000000000000000000..6e600aeace44d87e11cc372aa35e039b01aade21 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001028.fa @@ -0,0 +1,31 @@ +>PROKKA_01229 +MSPSHRLCDDPPAFAPDPAAVPDVDTAGPHAASRWERTPPRGPVLRWRPALLAVTVLLVA +AAAWWAVAWLTTPAPPAAVPAAAAGAGIPQTGAPSAASTAAGTDARTPEAGPSGEASGSA +GSTPLRVHVVGEVARPGVVSLAPGSRVADAVRAAGGPTRHARAERINLAAPLDDGQQVLV +PSAHTPQDALDRVAGAAQAQPTPTTGGAGATGEPGGAEPRGTVDLNTADAAGLQTLPGVG +PATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDLVSW +>PROKKA_00948 +MRDAPDSATGPQTARMSPSHRLCDDPPAFAPDPAPAAAPDVDTAGPHAASRWERTPPRGP +VLRWRPALLAVTVLLVAATAWWAVAWLTTPAPPAAIPAAAAGAGIPQTDAPSTAPSAAGT +DARTSEAGPSGEASGPAGSGPLRVHVVGEVARPGVVSLAPGSRVADAVGAAGGPTRHARA +ERINLAAPLDDGQQVLVPSARTPQDALDRVAGAAQAQPTPTTGRAGGGGEPGGAESGDTV +DLNTADATELQTLPGVGPATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDHVSW +>PROKKA_01659 +MSHPHRLAPDAALSDDPRRGRPASDLVPVPPALAARGPSAWERVPPRGRVLRWRPALLAV +TVLLVAAAAWWAVAWLTSPAPPSPAPAASAVEARVEPETEDGPDAADAAPPSDGAGPAAE +PSGGSGPVATLLRVHVVGEVERPGVVSLAPGARVADAVRAAGGATREARTERINLAAPLA +DGRQVLVPSARTPEEDLARVAGGQDGPGGPEGGAAGTAPDAAASAPAGPARAGGSGGAGA +GPVDLNAADAVALQTLPGVGPATAEKIIAHRETVGPFTGLQDLDAVPGVGPAALERLRDR +VTW +>PROKKA_01556 +MDTKTLTPAVDEPDWEDPPPRGPLLRWRTAGAGLTLVAILGLTWWLVAWLTAPAPPDAVP +AGAVGSASAAGSAAHEASAAPLRATAATPEGQDGGGRSAAAANPSGRVRVHVVGQVRRPG +VVELPAGARVADAVAAAGGARELARTDRINLAAPVVDGQQVVVPDAQTAVEPAAVAGEAP +DGGPTPRTGSGASAADGSGGGPATVDLNTADLAALQTLPGVGPATAEKIIAQRESVGPFS +GLQDLDAVPGIGPATLDRLKDHVTW +>PROKKA_01187 +MSPSHRLCDDPPAFAPDPAPAAAPDVDTAGPHAASRWERTPPRGPVLRWRPALLAVTVLL +VAATAWWAVAWLTTPAPPAAIPAAAAGAGIPQTDAPSTAPSAAGTDARTSEAGPSGEASG +PAGSGPLRVHVVGEVARPGVVSLAPGSRVADAVGAAGGPTRHARAERINLAAPLDDGQQV +LVPSARTPQDALDRVAGAAQAQPTPTTGRAGGGGEPGGAESGDTVDLNTADATELQTLPG +VGPATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDHVSW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001030.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001030.fa new file mode 100644 index 0000000000000000000000000000000000000000..812205dd4a8b06eccb1379b92b8df39573712c86 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001030.fa @@ -0,0 +1,75 @@ +>PROKKA_01231 +MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS +GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI +ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV +LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI +GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE +DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ +RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ +ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA +PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPEAL +RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNDGKAMSK +SLGNGVDLGDQLDQFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA +TGTPAGTDPADGAVALRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA +ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVIRAGWPAVDEALLVEDTVTAVVQ +VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAQIVKVIVREPKLVNLVIR +>PROKKA_00950 +MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS +GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI +ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV +LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI +GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE +DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ +RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ +ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA +PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPDAL +RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK +SLGNGVDLGDQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA +TGAPAGTDPAGGAVTLRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA +ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVVRAGWPAVDEALLVEDTVTAVVQ +VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAEIVKVIVREPKLVNLVIR +>PROKKA_01657 +MFPYPSGDLHMGHAEAFAMGDVVARHWMQRGYDVLHPIGWDSFGLPAENAAIKRDAHPAE +WTYANIETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRKGLAYRKDSPVNWC +PQDQTVLANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLA +MQRNWIGRSEGAHVDFQIEDGPQITVFTTRPDTLHGATFMVVAADAPLAAELADESVRAE +LEAYREELKKVSDIDRQATDRPKTGVFLGRHAINPLNGERLPVWASDYVLADYGTGAIMA +VPAHDQRDLDFARAMGLPVRAVLDTGEENPAVSGVATTGDGTLVNSGELDGLDKTAAIAR +AIEIVEGRGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCEACGEVLVPEDQLPVTLPTDL +NGEQLAPKGQSPLAAATSWVEVACPDCGGPARRDTDTMDTFVDSSWYTLRYASPNDDTQV +FDPEAVRRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNG +GRAMSKSLGNGVDLGAQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRL +ARDVREAGTPADADPATGSVALRRVTHRSVHEAGQLLDDGKFNVVIAKTMELVNAARKEI +DGGAGAADPAVREAAEAVAVLLSLVAPYTAEDMWVMLGHEPSVVRAGWPAVDESLLVEDT +VTAVVQVKGKVRDTLEVPADITAEDLEARARASQKVRTFIGDAEIVKVIVREPKLVNLVI +R +>PROKKA_01554 +MSQTPESAAPATPQVPEDAEYAFSEVEARWAGYWEQAGTFTPRGDGSATRTVVDMFPYPS +GDLHMGHAEAFAMGDVLARYWLQRGYDVLHPIGWDSFGLPAENAAIKRNAHPAEWTYANI +ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRKGLAYRKDSPVNWCPQDQTV +LANEQVVDGKCERCGAEVTKRELNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI +GRSEGAHVDFQVEDGPAVTVFTTRPDTLHGATFMVVAADAPLALELVDDEHRAALEAYRE +ELKKASDIERQATDRPKTGVFLGRHAVNPLTGERLPMWASDYVLADYGTGAIMAVPAHDQ +RDLDFARAMDLPVRTVVDTGEEDPAVSGVATTGEGTLVNSGELDGLSKADGIARAIEIVQ +ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPEHGEVLVPEDQLPVLLPTDLKGGQLA +PKGQSPLAAAEEWVNVPCPECGAPARRDSDTMDTFVDSSWYFLRYASPWDEQQVFDPELV +KTWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK +SLGNGVDLGQQLDEFGVDAVRTTMVFASPPEDDVDWADVAPAAAGKFLARAWRLARDVRA +AGTPAGDPAQGSAALRRVTHRTVHEAAALVEDHKFNVVVAKTMELVNATRKEIDGGAGAA +DPAVREAAEAVAILLSLVAPYVAEDMWAMLGHEPSVVRAGWPAVDESLLVEDTVTAVVQV +KGKVRDQLQVPADVSAADLEAAARASAKVRAFIGDAEIVKVIVREPKLVNLVIR +>PROKKA_01189 +MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPS +GDLHMGHAEAFAMGDVVARHWMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANI +ETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYRRGLAYRKDSPVNWCPQDQTV +LANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI +GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYRE +DLKKVSDIDRQATDRPKSGVFLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQ +RDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNSGELDGLDKTAAIARAIEIVQ +ERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA +PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPDAL +RRWLPVDQYVGGVEHAILHLLYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSK +SLGNGVDLGDQLDEFGVDAVRLTMVFASPPEDDVDWADVAPGAAGKFLARAWRLARDVRA +TGAPAGTDPAGGAVTLRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA +ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVVRAGWPAVDEALLVEDTVTAVVQ +VKGKVRDTLEVPADITAEDLEARARASQKVRNFIGDAEIVKVIVREPKLVNLVIR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001032.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001032.fa new file mode 100644 index 0000000000000000000000000000000000000000..aab2cdf420bcda3e2ba8da58a993afdf344252d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001032.fa @@ -0,0 +1,34 @@ +>PROKKA_01233 +MPVPTPPAAPGPPVRLRDLLRPPAAPADPRVLTGHVARTPRRRTLAVPDPVRRTPSSVAV +WEYAPVPEAAPGSRGAPEGDPAAAPLVFVHGFRGDHHGLALLADALPEHPIHSIELPGFG +DSEPFPHAEHTVAHHADAVAAGVAALGLPAAPVLVAHSYGTTVAAELAVRDPSRWARLVL +LNPIAEPALQASASVTSRVLAAVAEGYYEVAARLPERPARLLLGAPPVVWVTTLATTRTR +DRDVLAYTHDQHRRHFSGFASARMLSEAYRASSTGSVADVAARLTLPVLLVAGREDPLGS +VPAQKALAAAIDAGGGTAELHVLDGVGHLLHYERPAACAALIRDWLRRAGR +>PROKKA_00952 +MPVPTPPAPPGPPVRLRDLLRPPAAPADPRVLTGHPARTPRRRTLAVPDPVRRTPSSVAV +WEYAPVPVAAPGSPGALEGDAAAAPLVFVHGFRGDHHGLALLADALPEHPIHSIELPGFG +ASEPFPRAEHTVAHHADAVAAAVVALGLPAAPVLVAHSYGTTVAAELVAREPSRWGRLVL +LNPIAEPALQASASATSRVLAAVAEGYYEVAARLPERSARLLLGAPPVVWATTLAMTRTR +DRDVLAYTHDQHRRHFSGFASARMLSEAYRASSTGSVADVAARLTLPVLLVAGREDPLGS +VPAQEALAAAIDAAGGTAELHVLDGVGHLLHYERPAACAALIRDWFRRAGR +>PROKKA_01655 +MHGFRGDHHGLALLADALPERAITSIELPGFGDSEPFPDAEHTVAHHADAVAAVLAAMPP +SQRPVLVAHSYGTVVGAELVARDPGRWDRLALLNPIAEPALDASASWTSRGLAALARGYY +ELAARLPERAGRLVLGAAPVVWVTTLAMSRTPDRRVLAYTHDQHRRYFSRFASARMLSES +YRASSTGTVADAADRLRLPVLLVAGREDPLGSVPAQEALAAAIEAGGGRAELHVLDGVGH +LLHYERPGECAALLRAWAARGR +>PROKKA_01552 +MPAPHDADPASPAGPRPIRPWHRLRIPAPTTPPRALTGHDVRVPRRRDVAVPDPISGAPL +SVAVWQHDAAPSSGASVAGAARPHLVFVHGFRGDHHGLQLLADCLPEFGVSSVELPGFGA +SDPFPDAEHTVAHHADALAAAVAALGLDAPPVLVAHSYGTVVAAHLVQRDSGAWPALALL +NPIAEPALDASGSRADRLLAGVAEAYYEAAARLPERVSRLLLGAPPVVWVTTQAMSRTRD +RDVLAYTHDQHRRFFSGFASARMLSESYRASSTGTVAQAADRLDLPVLLVAGREDPLGSV +AAQEALAARIAAAGGVPELHVLDGVGHLLHYERPAACARLLREWLAAGA +>PROKKA_01191 +MPAPTPPAAPGPPVRLRDLLRPPAAPADPRVLTDHPARTPRRRTLAVPDPVSGTPSSVAV +WEYAPVPEAAPGSPSGLKGDTAAAPLVFVHGFRGDHHGLALLADALPEHPIHSIELPGFG +ASEPFPHAEHTVAHHADAVAAVVAALGLPAAPVLVAHSYGTTVAAELVARDPSRWGRLAL +LNPIAEPALQASASVTSRVLAAVAEGYYEVAARLPERSARLLLGAPPVVWVTTLAMTRTR +DRDVLAYTHDQHRRHFSGFASARMLSEAYRASSTGSVADVAARLTLPVLLVAGREDPLGS +VPAQEALAAAIDAGGGTAELHVLDGVGHLLHYERPAACAALIRDWLRRAGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001033.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001033.fa new file mode 100644 index 0000000000000000000000000000000000000000..e4c2de68787decb960c28400ac0bdd1460754aea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001033.fa @@ -0,0 +1,65 @@ +>PROKKA_01234 +MPHLDREFDYLVPVALDARAVPGSRVSVRFGGRAMTGWLVSREQEPATGAQLTELTGVLT +VIPPLTEEVLATARAVARRQAGVVTDVLRAAVPPRVAQVEKAALAEDAEAAADHPVTLTG +TDAERPEPPAAEEGLVPTVWESLEGGTAFVSAVLAGDAARAAAVVPSRLFEWDEAGALAA +LARTVAASDGGVLLLVPDHRDLDRLCAALDEHVGEDAYARIGSEDGNTPRYRAHLAALRG +TRRIVAGTRAAVWSPVRDLRLVVLWDDGDDAWAEPRAPYFHAREVVLERARATGAALLFA +GPSRSVPVQRLVESGWLLHLGPSRAAQRELGPRVVSTADAWETARDPFAQRARLPQAAWA +AARAALLGPRPGPVLVQVARAGFIPALVCERCRTPARCRVCAGPLGFRDARAARHGEVAC +RWCGTRERGFRCTECGGTTLRAGARGVDRTAEELGRAFPRVPVHASSAQHMLGSVPPGPS +LVVATVGAEPVTPDGYAAALLLDGDSQLQREGLDVPGRVLARWLAAACLVRPASDGGVVV +VTADASEAVNALVRRDPDGFAARQVAERRELHLPPAGRLAEVSGDAAAVAEYLELVEAAR +RERPDEDIHEDPHSAPLDGGPARLPWIGPVPDPADETRSRALLIFPYAAAEATVGALRAA +RSAASARRETAPVRVRLDPAGVL +>PROKKA_00953 +MPHLDREFDYLVPVALDDRAVPGSRVSVRFGGRAMTGWLVSREQEPATGAQLTELTGVLT +VIPPLTEEVLATARAVARRQAGVVTDVLRAAVPPRVAQVEKAALAEDAETAADHPVTLTG +TDAERPEPPAAEEGLVPTVWESLEGGTAFVSAVLAGDAARAAAVVPSRLFEWDEAGALAA +LARTVAASDGGVLLLVPDHRDLDRLCAALDEHVGEDAYARIGSEDGNTPRYRAHLAALRG +TRRIVAGTRAAVWSPVRDLRLVVLWDDGDDAWAEPRAPYFHAREVVLERARATGAALLFA +GPSRSVPVQRLVESGWLLHLGPSRATQRELGPRVVSTADAWETARDPFAQRARLPQAAWA +AARAALLGPRPGPVLVQVARAGFIPALVCERCRTPARCRVCAGPLGFRDARAARHGEVAC +RWCGTRERGFRCTECGGTTLRAGARGVDRTAEELGRAFPRVPVHASSAQHMLGSVPPGPS +LVVATVGAEPVTPDGYAAALLLDGDSQLQREGLDVPGRVLARWLAAACLVRPASDGGVVV +VTADAGEAVNALVRRDPDGFAARQVAERRELHLPPAGRLAEVTGEAAAVAEYLELVEAAR +RERPDEDVHEDPHSAPLDGGPARLPWIGPVPDPADEIRSRALLIFPYAAAEATVGALRAA +RSAASARRETAPVRVRLDPAGVL +>PROKKA_01654 +MARVLLDSPVPHLDREFDYLIPVTLDERARPGSRVAVRFGGRPMTGWLVSREDEPATGAQ +LTELTAVLTSVPPLTEEVLASARAVARRQAGVVTDVLRAAVPPRVAQVEKAALAEDAGAA +ADHPVALAVEEAPEGEPVGAGDGIAPTVWESLEGGRAFVAAVLAGDGPRAAAVVPSRLLE +WDEAAAMAHLARAVAAGGGGVLLLVPDHRDLDRLCAALDDAVGEEAYARIGSEDGNTPRY +RAHLAALRGTRRIVAGTRAAAWAPVRDLRLTVLWDDGDDAWAEPRAPYFHAREVVLERTR +RTGSALLFAGPSRSVPVQRLVESGWLLHLGPSRAAQREIGPRIVSTADAWETARDPFAQR +ARLPQAAWGAARAALLGERPGPVLVQVARAGFIPALVCDRCRTPARCRRCAGPLGFRDAR +AARLGEVACRWCGTRERGFRCTECGAGALRAGARGVDRTAEELGRAFPRIPVHSSSAQHR +LGTIPPGPSLVVATVGAEPVAEDGYAAALLLDGDAQLQREGLDVPGRVLARWLAAACLVR +PAADGGVVVVTADAGEAVNALVRRDPDGFAAHQVAERRELHLPPAGRLAEVTGEASAVRE +YLDLVEAARRERPEEDVHEDPHSAPLDGGPARLPWIGPVPDAADETRSRALLLFPYAAAD +ATVAALRAARSAASARRETSPVRVRLDPAGVL +>PROKKA_01551 +MARVLLDSPVPHLDREFDYLVPPALDERAVPGSRVSVRFGGRETTGWLVERVAAPATHAR +LTELAGVLTAVPPLTEHVLAVARAVAARQAGVVSDVLRSAVPPRVVSVEKEVLAELASGP +EVDHPVQGVVADPHARLVWEELTGGTAFVASAVAGDPVRAAAVVPSRVGDWDESSALAAL +ATAVSRAGGGVLLLVPDHRDLDRLSAALAREVGEDGFVRVGSEDGNTPRYRAHLRALTGL +ARVVAGTRAAAWAPVQDLRLVVVWDDGDDAHAEPRAPYFHVREVALERARQSGSALLFAG +PSRSVPVQRLVEHGWLLEVSADRASQRAASPRIVASADSWESARDPFARRARLPHAAWAA +AGEALSGPTPGPVLVQVARAGFIPAVVCGRCRTPARCRVCAGPLAFRDRRSAERGELACR +WCGTRERDFHCAECGFTGLRAGVRGVDRTAEELGRAFPQVPVHSSSADHRLGEVGEGPAL +VVATVGAEPHARGGYAAALLLDGDAQLQREGLDVPVRVLTRWLAAASLVRPAAEGGTVVV +TAEHDAAVGALVRRDPQGFAGHLLAERRELHLPPAGRLAEVTGEAGAVAEYLALVEAARR +ERRRVGPDADPSLDLDVEARPGDATPLPWIGPVPDVADESRSRALLLFPWAASAATVDAL +RVARSAASARRERSAVRVRLDPPGVL +>PROKKA_01192 +MPERAEGWPERPIARVLLDSPVPHLDREFDYLVPVALDARAVPGSRVSVRFGGRAMTGWL +VSREQEPATGAQLTELTGVLTAIPPLTEEVLATARAVARRQAGVVTDVLRAAVPPRVAQV +EKAALAEDAEAAADHPVTLTGTDAERPEPPAAEEGLVPTVWESLEGGTAFVSAVLAGDAA +RAAALVPSRLFEWDEAGALAALARTVAASGGGVLLLVPDHRDLDRLCAALDEHVGEDAYA +RIGSEDGNTPRYRVHLAALRGTRRIVAGTRAAVWSPVRDLRLVVLWDDGDDAWAEPRAPY +FHAREVVLERARATGAALLFAGPSRSVPVQRLVESGWLLHLGPSRAAQRELGPRVVSTAD +AWETARDPFARRARLPQAAWAAARAALLGPRPGPVLVQVARAGFIPALVCERCRTPARCR +VCAGPLGFRDARAARHGEVACRWCGTRERGFRCTECGGTTLRAGARGVDRTAEELGRAFP +RVPVHASSAQHMLGSVPPGPSLVVATVGAEPVTPDGYAAALLLDGDSQLQREGLDVPGRV +LARWLAAACLVRPASDGGVVVVTADAGEAVNALVRRDPDGFAARQVAERRELHLPPAGRL +AEVTGEAPAVAEYLELVEAARRERPDEDVHEDPHSAPLDGGPARLPWIGPVPDPADETRS +RALLIFPYAAAEATVGALRAARSAASARRETAPVRVRLDPAGVL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001035.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001035.fa new file mode 100644 index 0000000000000000000000000000000000000000..33414e754735c49759b24654ec445eb88bb66f07 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001035.fa @@ -0,0 +1,45 @@ +>PROKKA_01236 +MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGAATWEALSGRPVRTDTF +EAVDEVNHVRLGRHADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE +MWHHPATAANVALLRERGVTVVDPAVGRLTGADSGAGRLPEPAEIWERAQAAAAAGAPRR +PRASGSGTEPTPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGAALARAALDAGAIV +RFIAGSMSVPAPEGVERVVQVESTQDLLEAVLAEAADADVLVMAAAVADFRPAEVSDAKM +KKGDDGGAPVIVLERTPDVLATAVRTRSEGGPMAPLIVGFAAETGDPTSSVLEYGRAKLA +RKGCEMLVVNEVGTDKVFGRDETAVTILFADGRPAVEAAGSKDQAAAAVVQAIVDDLAGR +DPAGASGR +>PROKKA_00955 +MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGAATWEALSGRPVRTDTF +EAVDEVNHVRLGRRADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE +MWHHPATVANVALLRERGVTVVDPAVGRLTGADSGAGRLPEPAEIWERAQAAAAAGAPRR +PRASGSDAEPTPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGAALARAALDAGATV +RFVAGSMSVPTPEGVERVVPVESTQDLLDAVQAEAADADVLVMAAAVADFRPAEVSDAKM +KKGDDGGAPVIVLERTPDVLATAVRTRSEGGPMAPLIVGFAAETGDATSSVLEYGRAKLA +RKGCEMLVVNEVGTDKVFGRDETAVTILFADGRPAVEAAGSKDEAAAAVVQAIVDDLAGR +DPVGASGR +>PROKKA_01652 +MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGTATWEALSGRPVRTGTF +EAVDEVNHVRLGRQADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE +MWHHPATVANVALLRERGVTVVEPAVGRLTGADSGARRLPEPDEIWELAQAAAADPAARR +PRATTSRPGPAAAGAAPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGVALARAALA +AGARVRFIAGSMSVPVPEGVERAVHVESTAELLTAVLEQAADADVLVMAAAVADFRPAEA +SESKMKKGDDGSSPVIVLERTEDVLATAVRTRAAGGPMAPLIVGFAAETGDAESSVLEYG +RAKLARKGCEMLVVNEVGRDKVFGRDETAVTILFADGSPAVEAAGSKDEAAAAVVGAVVD +RLAASAPGSASAR +>PROKKA_01549 +MEVVLGVGGGIAAYKAALLLRLMKEAGHGVTVVPTDNALRFVGAPTWEALSGRPVRTDTF +TDVPEVSHVRLGREADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE +MWRHPATVANVALLRERGVHVIEPDSGRLTGADSGPGRLPEPARIWAEAQDAAARAGGRA +GREAAVTAAEPGAASPLAGRTVVISAGGTREALDPVRFLGNRSSGKQGTALAEAVLAAGA +RVRFIAGPMSVAPPAGTEVTAVESTQELLEAVLSEAADADVLIMAAAVADFRPAQVATSK +IKKTDDGGAPTIVLERTPDVLATAVQTRDAGGPMAPVIVGFAAETGDEHTTPLEYGRAKL +ARKGCDLLVVNEVGDGKVFGQDATEVTVLSADGAEPVTRTGSKAEAAAAVVEALERVLAS +REAGGAPGR +>PROKKA_01194 +MEIVLGVGGGIAAYKAALLLRLMTEAGHGVTVVPTANALEFVGAATWEALSGRPVRTDTF +EAVDEVNHVRLGRRADLVVVAPATADLLARTAAGMAPDLLGNVLLTATCPVVLAPAMHTE +MWHHPATVANVALLRERGVTVVDPAVGRLTGADSGAGRLPEPAEIWERAQAAAAAGAPRR +PRASGSDAEPTPGPLAGRTVVITAGGTREALDPVRYLGNRSSGKQGAALARAALDAGATV +RFVAGSMSVPTPEGVERVVPVESTQDLLDAVQAEAADADVLVMAAAVADFRPAEVSDAKM +KKGDDGGAPVIVLERTPDVLATAVRTRSEGGPMAPLIVGFAAETGDATSSVLEYGRAKLA +RKGCEMLVVNEVGTDKVFGRDETAVTILFADGRPAVEAAGSKDEAAAAVVRAIVDDLAGR +DPVGASGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001036.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001036.fa new file mode 100644 index 0000000000000000000000000000000000000000..88bf041c0cc389521560330f33dc3605a8896d0c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001036.fa @@ -0,0 +1,21 @@ +>PROKKA_01237 +MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL +NEKPLSIALREIEAGLLESHEAVEATPEAELAAEDFGDFSLPGEDDPFATLESSDAHQPT +GDPAAIEEAAETVRAEEGISEDAPEA +>PROKKA_00956 +MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL +NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM +GDPAAIEEAAETVRAEEGTSEDATEA +>PROKKA_01651 +MTEQYDGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL +NEKPLSIALREIETDLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLEPSDAGQPV +GDPEAIEEAAEAVRAEEGTSEDAPEA +>PROKKA_01548 +MTPPPPPDGPPPAAPCVPTHGQKTTREQTLETYVTDQYEGIVNPPIDSLLERVDSKYALV +LFAAKRARQINAYYSQLHEGLFEYVGPLVDTQLNEKPLSIAMREIESDMLVMAETAAVEP +AIELAEEEFGDFALPGDDDPFVAEPTAEGVSPEEYGAPVTTGDDDAVEDILSGADVADED +A +>PROKKA_01195 +MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL +NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM +GDPAAIEEAAETVRAEEGTSEDATEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001037.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001037.fa new file mode 100644 index 0000000000000000000000000000000000000000..02fe253121dd3543eb787842fb1d47c111dbab87 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001037.fa @@ -0,0 +1,25 @@ +>PROKKA_01238 +MTDTFDPGPAPAVPVARTVVQERPPGPGVTVLAGPTAVGKGTVSAYVREHYPEAWLSVSA +TTRPARPGEEDGVHYYFTTPEEFDSLVEADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH +VLLEIDLQGARQVRRALPEATFVFLAPPSWEELVSRLLGRGTESPEEQRRRLETARLELA +AEPEFDAVVVNDRVERAAEELVRLMGLDPERRPTEA +>PROKKA_00957 +MTDTFDPGPAPAVPVARTAVQERPPGPGVTVLAGPTAVGKGTVSAYVREHYPEAWLSVSA +TTRPARPGEEDGVHYYFTTPEEFDSLVEADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH +VLLEIDLQGARQVRRALPEATFVFLAPPSWEELVSRLLGRGTESPEEQRRRLETARLELA +AEPEFDAVVVNDRVERAAEELVRLMGLDPERRPTEA +>PROKKA_01650 +MTDAFDHGPAPAVPVARTAAQERRPGPGVTVLAGPTAVGKGTVSAYVREHYPQAWLSVSA +TTRPARPGEEDGVHYYFTTPEEFDSLVAADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH +VLLEIDLQGARQVRESLPEATFVFLAPPSWEELVSRLVGRGTEGPEEQRRRLDTARLELA +AEPEFDAVVVNDRVERAAEELVRLMGLDPEHSSPEA +>PROKKA_01547 +MSDLSDLGPAPSVPGERAPSRPPAPGAGVTVLAGPTAVGKGTVSAYIREHYPQAWLSVSA +TTRAPRPGEEDGVHYFFTTPEEFDELVAGDQMLEWAVVHGRNRYGTRRDRVAEAVAAGRH +VLLEIDLQGARQVRRTLPEATFVFLAPPSWDELVSRLVGRGTEGPEEQRRRLETARLELA +AEPEFDAVVVNDAVERAAAELVKLMGIDPHDAPASA +>PROKKA_01196 +MTDTFDPGPAPAVPVARTAVQERPPGPGVTVLAGPTAVGKGTVSAYVREHYPEAWLSVSA +TTRPARPGEEDGVHYYFTTPEEFDSLVEADEMLEWAVVHGVHRYGTRRDRVMEAVAQGRH +VLLEIDLQGARQVRRALPEATFVFLAPPSWEELVSRLLGRGTESPEEQRRRLETARLELA +AEPEFDAVVVNDRVERAAEELVRLMGLDPERRPTEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001038.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001038.fa new file mode 100644 index 0000000000000000000000000000000000000000..38e947e36c30892a741d2e8d1d38c71df86de1db --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001038.fa @@ -0,0 +1,15 @@ +>PROKKA_01239 +MALRQLSVQERAEARRKALQARQARAELKAAFAAGEVGLADIFARADADDAVARLRTVDL +LLALPGVGEVRAREAMAGCGISPRRRLGGLGRRQREALIAYIGR +>PROKKA_00958 +MALRQLSVQERAEARRKALQARQARAELKAAFAAGAVGLADVFARADTEDAVARLRTVDL +LLALPGVGEVRARETMAGCGISPRRRLGGLGRRQREALIAYIGR +>PROKKA_01649 +MALRQLSVEERAEARSKALAARQERAALKADFAAGQVSLAEVFSRADAEDAIGRLRTVDL +LQALPGVGEVRAREAMAGCGISPRRRLRGLGRRQREALIAYIGR +>PROKKA_01546 +MALRQLSVEERAEARAKALRARQERATLKTSFANRDLSLQEVFARADVDPAIGRLRTVDL +LQAMPGVGEVRASAVMEACEISPARRLKGLGRRQREALIAYIGR +>PROKKA_01197 +MALRQLSVQERAEARRKALQARQARAELKAAFAAGEVGLADIFARADADDAVARLRTVDL +LLALPGVGEVRAREAMAGCGISPRRRLGGLGRRQREALIAYIGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001042.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001042.fa new file mode 100644 index 0000000000000000000000000000000000000000..48d909d769f0272923ae9d0a427a51837a848499 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001042.fa @@ -0,0 +1,25 @@ +>PROKKA_01243 +MSITSLAAALAARPVPPRTPTKDYADVWLPVTLGTLAVVLVLLGLLALGWRARRRAQAGI +PAPAPVPTALYDAEPTLSAEGMHVGTVRGEDRLDRVAVHGLGLRSRAVLEVHDAGTHRGL +LVLRPGAANLFIPADDLVEAGLSGGIAGKFVEPGGLVAWGWRLGDVELTSAFRPDRPEDR +DRLLAALQTIIDPAPADPAGRAGEGDPR +>PROKKA_00962 +MSITSLAAALAARPVPPRTPTKDYADVWLPVTLGTLAVVLVLLGLLALGWRARRRAQAGI +PAPAPVPTALYDAEPTLSAEGMHVGTVRGEDRLDRVAVHGLGLRSRAVLEVHDAGTHRGL +LVLRPGAANLFIPADDLVEAGLSGGIAGKFVEPGGLVAWGWRLGDVELTSAFRPDRPEDR +DRLLAALQTIIDPAPADPAGRAGEGDPR +>PROKKA_01645 +MNALALAAATLASRPVAPQTPGKDYSDVWLPITLGTLAVILVLVGLFALGWRARRRSQAD +LPAPAAVPAALYEQEPAASASGMHVGTVRGEHRLDRVAVHQLGLRSHAVLEVHDAGEHRG +LLVLRPDVANLYIPAADLLEAGLSAGIAGKFVEPGGLVAWGWRLGDAELTSAFRPDRAED +RDRLLAALQTLIDPAPARSAGRAGEGDLR +>PROKKA_01542 +MSAVLPAALPLAATPVPPASPMKDYSDVWLPIVLTTVGVIALLLALIAWGWRGRRRRQAG +IPAPATVPPEVLEREPAVSAEGMWVGTVSGTDRLDRVAVHDLGLRSSGVLEVHTAGDRPG +VLVLRPNIAPLFVPAAHLMEAGRSAGIAGKFVEPGGLVAWGWRLGDVDVTSAFRPRRPED +RDRVLEALQTVIDRAGRPDAGQENAR +>PROKKA_01201 +MSITSLAAALAARPVPPRTPTKDYADVWLPVTLGTLAVVLVLLGLLALGWRARRRAQAGI +PAPAPVPTALYDAEPTLSAEGMHVGTVRGEDRLDRVAVHGLGLRSRAVLEVHDAGTHRGL +LVLRPGAANLFIPADDLVEAGLSGGIAGKFVEPGGLVAWGWRLGDVELTSAFRPDRPEDR +DRLLAALQTIIDPAPADPAGRAGEGDPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001043.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001043.fa new file mode 100644 index 0000000000000000000000000000000000000000..bfdecbbb3ecc44e55742c4aa26e155d87431c259 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001043.fa @@ -0,0 +1,35 @@ +>PROKKA_01245 +MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE +AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV +RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLTGMRVVIVGDILHSRVAR +SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG +AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA +LEQVANGVSVRMAVLHLVLNHDQEVRP +>PROKKA_00964 +MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE +AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV +RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLTGMRVVIVGDILHSRVAR +SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG +AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA +LEQVANGVSVRMAVLHLVLNHDQEVRP +>PROKKA_01643 +MRHLLSTAGLSRADALAVLDTAEEMDAVNRREIKKLPALRGRTVVNFFFEDSTRTRISFE +AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV +RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGRDLAGMHVVIVGDILHSRVAR +SNVWLLATLGAKVTLAAPPTLLPVGVSAWPCEVTYSLDEALDARPDAVMMLRVQAERMGG +AFFPSAGEYTRTWGLTDERFARLTAGSGALLSEPVVMHPGPMNRGLEISPAAADSPRNTA +LEQVANGVSVRMAVLHLVLNHDQEVRP +>PROKKA_01540 +MRHLLDTADLTRAEALAVLDTAEEMAAVNAREVKKLPSLRGRTVVNLFLEDSTRTRISFE +AAAKRLSADVISFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAAAQLAASGWV +DSAVVNAGDGTHAHPTQALLDAFTLRHHLAAHDGVAPTGTDLTGMHVVIVGDILHSRVAR +SNVWLLTLLGARVTLAAPPTLLPVGVASWPARVTYSLDEALADAPDAVMMLRVQAERMGG +AYFPSAGEYTRLWGLNPARFERLTRQSGSRLDTPLVMHPGPMNRGLEICDAAADSPQNTV +LEQVANGVSVRMAVLHLVLNQDPALAPQEARP +>PROKKA_01203 +MRHLLSTADLSRADALAVLDTAEEMAAVNQREVKKLPALRGRTVVNLFLEDSTRTRISFE +AAAKRLSADVINFSAKGSSVSKGESLKDTVQTLEAIGADAIVMRHWSSGAARQLADSGWV +RSAVVNAGDGTHEHPTQALLDAFTLRRRLAAATGEDLVGQDLTGMCVVIVGDILHSRVAR +SNVWLLSTLGAQVTLAAPPTLLPVGVAAWPCQVTYSLDEALDAGPDAVMMLRVQAERMGG +AFFPSAGEYTRTWGLTDDRFARLTAGRGALLDEPVVMHPGPMNRGLEISPAAADSPRNTA +LEQVANGVSVRMAVLHLVLNHDQEVRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001044.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001044.fa new file mode 100644 index 0000000000000000000000000000000000000000..0708ff8da0138e4c7cd275d74caa011486ed4f61 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001044.fa @@ -0,0 +1,25 @@ +>PROKKA_01246 +MGTDPAAPRAARTVLSTSEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAL +LARIEPAFDPTAAVGEVDVTLYRDDLRRGTARTPMPTRLPEVPLDGAVVVLVDDVLFSGR +TVRAALDAIADLGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTAERVQVRLMEVDGP +EGTGEVTEDAVSIVDRVATREG +>PROKKA_00965 +MGTDPAAPRAARTVLSTSEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAL +LARIEPAFDPTAAVGEVDVTLYRDDLRRGTARTPMPTRLPEVPLDGAVVVLVDDVLFSGR +TVRAALDAIADLGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTAERVQVRLMEVDGP +EGTGEVTEDAVSIVDRVATREG +>PROKKA_01642 +MGADPAAPRAARTVLSASEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAV +LARIEPAFDPEAAVGEVDVTLYRDDLRRSAARTPMPTRLPAVPLDGAVVVLVDDVLFSGR +TVRAALDAISELGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTSERVQVRLVEVDGP +EGTGEVSEDAVSIADQADRPEQREA +>PROKKA_01539 +MGGIPAAPRAARTVLTAPEIDRALTRIAHEILESNKGPEGLVLMGIPRRGVPLARRLAAV +LHRIDPAFDPVSAVGEVDVTLYRDDLRRGTARTPAPTRLPDHPLDGAVVVLVDDVLFSGR +TIRAALDALADLGRPAAVRLAVLVDRGHRELPIRADFVGKNLPTSTAERVQVRLTEVDGP +DGSGEVPEDAVRIVDAPAETPREA +>PROKKA_01204 +MGTDPAAPRAARTVLSTSEIDRALTRIAHEILESNKGAEGLVLMGIPRRGAPLARRLGAL +LARIEPAFDPTAAVGEVDVTLYRDDLRRGTARTPMPTRLPEVPLDGAVVVLVDDVLFSGR +TVRAALDAIADLGRPAAVRLAVLVDRGHRELPVRADFVGKNLPTSTAERVQVRLMEVDGP +EGTGEVTEDAVSIVDRVATREG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001045.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001045.fa new file mode 100644 index 0000000000000000000000000000000000000000..c0ca4bc219d471d015b3473ef8ebec00c4cac2b6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001045.fa @@ -0,0 +1,20 @@ +>PROKKA_01247 +MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR +LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA +LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA +>PROKKA_00966 +MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR +LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA +LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA +>PROKKA_01641 +MTEPASAASGAKRGTTARSRSRQRAVEILFEAEQRGATVAEGIRTRRESTDLQVNAYTQR +LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAVSEAVA +LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA +>PROKKA_01538 +MTDTPSASDAKRGTTARSRSRQRAVEILFEAEQRGTDVLQGIRTRRESTDLQVNAYTQRL +VEGVVADQERVDEALTSYSRGWSLDRMPAVDRAILRVGAWELLFEDEVPDAVAVSEAVAL +AAALSTDESPEFVNGLLGRLQQVKPTLLA +>PROKKA_01205 +MTERASAGSAAKRGTTARSRSRQRAVEILFEAEQRGSSALEGIRTRRESTDLQVNAYTQR +LVEGVIADQERLDEALSSYSRGWSLDRMPAVDRAILRVGAWELLFQDDVPDAVAISEAVA +LAAQLSTDDSPEFVNGLLGRLQQVKPTLLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001046.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001046.fa new file mode 100644 index 0000000000000000000000000000000000000000..99ced38accdaff9d2ca145bee9971e2349d31aaa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001046.fa @@ -0,0 +1,25 @@ +>PROKKA_01248 +MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK +VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN +TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ +GTRVKVDTRTGDYLGRVND +>PROKKA_00967 +MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK +VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN +TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ +GTRVKVDTRTGDYLGRVND +>PROKKA_01640 +MATSNDIKNGAVLKLEGQLWNVIEFQHVKPGKGGAFVRTKMKNITTGKVVDKTFNAGAKV +EFATVDRSDYQYLYQDGSDYVFMDVKDYDQITVSESVVGDAAKYMLENTQVVIALNEGTP +LYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQGTRVKVDTRTGD +YLGRVND +>PROKKA_01537 +MATTNDIKNGSVLNLEGQLWNVIEFQHVKPGKGGAFVRTKMRNITSGKVVDKTFNAGTKV +EFATVDRSDYQYLYQDGEDYVFMDVKDYDQITVPAAVVGDAAKYMLENTQVVIAMNEGTP +LYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQGTRVKVNTTNGE +YLGRVND +>PROKKA_01206 +MTVRETDREHTHVATSNDIKNGAVLKLEGQLWNVTEFQHVKPGKGGAFVRTKMKNITTGK +VVDKTFNAGAKVEFATVDRSDYQYLYQDGADYVFMDVKDYDQITVPGAVVGDAAKYMLEN +TQVVIALHEGTPLYLEMPASVVLEITYTEPGLQGDRSSAGTKPATVETGAEIQVPLFVEQ +GTRVKVDTRTGDYLGRVND diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001049.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001049.fa new file mode 100644 index 0000000000000000000000000000000000000000..6bfbd4b33550d6d28fb34e0642fbc77872864219 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001049.fa @@ -0,0 +1,40 @@ +>PROKKA_01251 +MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL +GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG +MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF +PVPEDEARLDADPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW +DRRLDARLAGALMGIQAIKGVQVGDGLATAARRGSAAHDGIARGADGRPRRTSDRAGGIE +AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA +LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPAADVVADGPMGDPLP +>PROKKA_00970 +MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL +GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG +MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF +PVPEDEARLDADPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW +DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGTAAHDGIARGADGRPRRTTDRAGGIE +AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA +LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPGADVVADGPMGDPLP +>PROKKA_01637 +MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL +GGVRHGLTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELEGLARNAALTRPRPGHADLTG +MQKYGFDDARPLLERASARETAARVALGTVARAFLAQLGVRIVSHTTAFGEAALPEGHPF +PLPEDQDRLDADPVRCLDPETSAAMVAEVDDAHKAGETLGGVVEVLAYGVPIGLGSHVHW +DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGSAAHDGIVRGEDGRPRRTSDRAGGIE +AGMSTGEVLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA +LVLADAVLEKFGGDSVGETRRNMAAFQAAVPALPEPSADADASGHMGDPLQ +>PROKKA_01534 +MVRWLTAGESHGPALTGIVEGLPAGIPVTTQEIQDALARRRLGYGRGARMKFEQDAVTVL +GGIRHGLTLGSPVAIQVGNTEWPKWEQVMAADPVPEEELAGLARNARLTRPRPGHADLTG +MQKYGFDEARPLLERASARETAARVALGTVARAFLAELGVRIVSHTVAFGEAALPEPHAF +PVPEDQDRLDADPVRCIDPETSAAMVAEVDAAHKEGETLGGVVEVLAYGVPIGLGSHVHW +DRRLDARLAGALMGIQAIKGVQVGDGFATASRRGSAAHDGIARGADGRPRRTSDRAGGIE +AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA +LVLADAVLEKFGGDSVAETRRNMEAFTAALPALPDAPAEQPAADHMGDPLQ +>PROKKA_01209 +MVRWLTAGESHGPALTGIVEGLPAGIPVTTQDVQDALARRRLGYGRGARMKFEQDAVTIL +GGVRHGRTLGSPVAIQVGNTEWPKWEKVMAADPVPAEELDGLARNAALTRPRPGHADLTG +MQKYGFDEARPLLERASARETAARVALGTVARAFLGELGVRIVSHTVAFGEAALPEGHPF +PVPEDEARLDAEPVRCLDPQTSAAMVAEVDDAHRAGETLGGVVEVLAYGVPIGLGSHVHW +DRRLDARLAGALMGIQAIKGVQVGDGFATAARRGTAAHDGIARGADGRPRRTTDRAGGIE +AGMSTGELLRVSAAMKPIATVPRALPTVDVATGAETTAHHQRSDVAAVPAAGIVAEAMVA +LVLADAMLEKFGGDSVAETRRNLEAFQAAVPALPEPGADVVADGPMGDPLP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001050.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001050.fa new file mode 100644 index 0000000000000000000000000000000000000000..c81900fea80293b66be444802d457343786d7013 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001050.fa @@ -0,0 +1,35 @@ +>PROKKA_01252 +MRPVLRAAVLGRPIAHSLSPVLHAAAYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGAA +DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPAAPGVVHAEN +TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGANAVLFGVRDAARAAE +VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPADAALPPLLDAAY +DPWPSVLAAAWSREGGPVASGLSMLLHQGVEQVRLFTARPRAAAGMPEPDWAAVTRAAAD +ALGPAAG +>PROKKA_00971 +MRPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGTA +DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPSAPGVVHAEN +TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGADAVLFGVRDPARAAE +VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPAGAALPPLLDAAY +DPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAAGMPEPDWAAVTRAAAD +ALGPAAG +>PROKKA_01636 +MGAPSDVRAEASAGAPAAPRLRAAVLGRPIAHSLSPVLHGAAYGVLGLDVDYRRRDLGED +EVGAFVAGRLGAPRTADGGDAAARGEDWLGCSVTMPLKRAVVGCAGRVSERVRLLGTANT +LVRDHPEHPGLVSAENTDVDGILGALASAGLAERGSGGAVGILGNGGTATAAVLAAATLG +ADEVVFGVRDAARAAEVTALADALGLAWRTVGQPELAAAAPGLRAVVATLPPRAADPLAA +HVPVGAALPPLLDAAYDPWPSALASAWTEAGGAVASGLSMLLHQGVEQVRLFTARPRAAA +GMPEPDWAAVTRAAARALGPAAG +>PROKKA_01533 +MAGATFRAAVLGRPIAHSLSPVLHAAAYRALGLDVDYGRADLGEEEVGPWLAARLGAPGS +AARPAGPSGGDWLGVSVTMPLKPAVVPLADELSARVRELGVANTLVRDHPDHPGSLLAHN +TDVDGIVRALAERGLDAGAGGGAVGILGNGGTATAAVAAASLLRAETVVLGVRDAGRARD +VVALADRLGLGVRVEAQDALVRQAADLRAVVATLPPRAADPLADKVPAGVLPPLLDAAYD +PWPSAIARAWSAAGGGVASGLSMLLHQGVEQVRLFTERPRRAAGGVEPDWAEVTAAASRA +LGLPGR +>PROKKA_01210 +MRPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGEDEVLAFAAEHLGAPGTA +DGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANTLVRDHPSAPGVVHAEN +TDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLGADAVLFGVRDPARAAE +VTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAAHVPAGAALPPLLDAAY +DPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAAGMPEPDWAAVTRAAAD +ALGPAAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001051.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001051.fa new file mode 100644 index 0000000000000000000000000000000000000000..9ba92f5b86798febf5f7e5c4870d021522bbd237 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001051.fa @@ -0,0 +1,20 @@ +>PROKKA_01254 +MSAGQDGANAATDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDE +LVAHARELDVVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALAEAGHPVPVRLVDERLS +TVSAQAGLRAAGRSVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREPIR +>PROKKA_00973 +MASDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDELVAHARELD +VVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALVEAGHPVPVRLVDERLSTVSAQAGLR +AAGRSVKYSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREQIR +>PROKKA_01634 +MSAGQDGAATATDAVRRGRTLGVDVGRARVGLATADPDGLIATPVATLARDARRGRDVGE +LVAHALELDVVAVYVGLPVNLRGEHTPSTQDALDYARSVARAPAAAGHAVPVRLVDERLS +TVSAQAGLRAAGRTVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDPEEIA +>PROKKA_01531 +MSAQAAVRGRVLGVDVGRARVGLAASDPDGLIATPVETLRRDARQRRDHAELLDRARELD +AVAVYVGLPRNLRGEHTPSTQDAVEYAAAIEALVAEAGTPIPVRLVDERLSTVSAQAALH +RAGRTVKDSRGVIDQAAAVELLQDALEVQRRRGAWAGITVAEARA +>PROKKA_01212 +MASDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDELVAHARELD +VVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALVEAGHPVPVRLVDERLSTVSAQAGLR +AAGRSVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREQIR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001053.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001053.fa new file mode 100644 index 0000000000000000000000000000000000000000..7883be7b6c95739d2905151b740ed9b77c31f199 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001053.fa @@ -0,0 +1,19 @@ +>PROKKA_01256 +MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR +QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT +TTTQKDTPA +>PROKKA_00975 +MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR +QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT +TTTQKDTPA +>PROKKA_01632 +MLRSLLLVTAGAASGWLAHRALGDRAAADAAPGRSDAGPQARPGRARLDPEHLARQAGQA +VGDAAAAALNEGARRLADRVRAEAPWAAQFLPHTGPIIEGETVEPPSPSGPGGPRPQTTI +PTTTTQKDTHA +>PROKKA_01529 +MSRITSLLLVGAGTAAGWIAHRAVESGRRAVDQEAGRRLQETLDPTRLGRSAGQAVGDAA +AEALAQSAQAFTERLRADAPPWVSQLIGPPRDTIEGEALDTPDTTATPSSARKDPHA +>PROKKA_01214 +MLRSLLLVGAGAASGWFAHRALGDRAHPATDATDAPTSDPGSAGGRAGFSARLDPERLAR +QAGEAAADAAAAALQDGARRLAERVRAEAPWAAPYLPHTGPIISGETVEPPSHGAARPQT +TTTQKDTPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001055.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001055.fa new file mode 100644 index 0000000000000000000000000000000000000000..e8dedd4500283266632317c8106b20dee7aa45d2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001055.fa @@ -0,0 +1,23 @@ +>PROKKA_01258 +MTQSTPQQSTPQHTAAQQPAPYGRPGAGGPALPQADYRILRSVPAYAEAQALVDQLSDAG +FPVERVRIVGTGLRSVEQVLGRMTTGKAAVRGGLQGLWFGLLLGLLFSIFAPGFGFLWIL +LISLGLGALWGAVFGAIGHAATGGRRDFTSLQTMEAESYDVLVEASHLDQAGQLLGADPG +TAATPRA +>PROKKA_00977 +MTQSTPQQSTPQHTAAQQPAPYGRPGAGGPALPQADYRILRSVPAYAEAQALVDQLSDAG +FPVERVRIVGTGLRSVEQVLGRMTTGKAAVRGGLQGLWFGLLLGLLFSIFAPGFGFLWIL +LISLGLGALWGAVFGAIGHAATGGRRDFTSLQTMEAESYDVLVEASHLDQAGQLLGADPG +TAATPRA +>PROKKA_01629 +MSQHQPYAQDPRSTVPATTADAAYAGGPLGAADHRVLESVPDYARAQAIVDQLSDAGFPV +EHVRIVGTGLRTVEQVLGRMTTGKAAGRGAVQGLWFGLLLGLLFSIFSPGFGFLWILLIS +LGLGALWGAVFGAIGHAATRGRRDFSSLQTMDAASYEVQVEAAHLDRARQTLGAGPAAPR +A +>PROKKA_01527 +MSASAAHYAVLSTVPDYAHAQSTVDRLSDSGFPVEHVRVAGTGLRSVEQVTGRLTTGAVG +VC +>PROKKA_01216 +MTQSTPQQSTPQHTAAQQPAPYGRPGAGGPALPQADYRILRSVPAYAEAQALVDQLSDAG +FPVERVRIVGTGLRSVEQVLGRMTTGKAAVRGGLQGLWFGLLLGLLFSIFAPGFGFLWIL +LISLGLGALWGAVFGAIGHAATGGRRDFTSLQTMEAESYDVLVEASHLDQAGQLLGADPG +TAATPRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001056.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001056.fa new file mode 100644 index 0000000000000000000000000000000000000000..9b23c2b6d8d47fb75ebc5ed7298c4746d8f35726 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001056.fa @@ -0,0 +1,45 @@ +>PROKKA_01259 +MDDLFSAAHTGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE +PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE +RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL +TLRPLTDDDIVGLLDRAVTQERGLNGAVVLEDDARDYLVRMAGGDARRALTVLEAAAGVA +LDKAREAGRAGEGAVAVTEEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM +HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVATAQAVQLIGMPEGRIILAQ +AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE +PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD +>PROKKA_00978 +MDDLFSAAHNGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE +PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE +RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL +TLRPLTDDDIVGLLDRAVTQERGLNGAVVLQDDARDYLVRMAGGDARRALTVLEAAAGVA +LDKAREAGRAGEGAVAVTDEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM +HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRIILAQ +AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE +PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD +>PROKKA_01628 +MADLFSAAHESDDDGPSGTVAAPRASAPLAVRMRPRTLEEVLGQRHLMRPGSPLRKLAEP +DPGSPAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRER +DLYDRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLLT +LRPLTDEDIVGLVERAVADERGLNGAVDLADDARDYVVRMAGGDARRALTVLEAAAGVAL +DKARQAGADEDAGGDGGARAGAAAPVTVTEEDAAQAMDHHVQRYDKDGDQHYDVISAFIK +SIRGSDVDAALHWLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLI +GMPEGRIILGQAVTHLATAPKSNASYAAVNEALADVRAGGTGQVPPHLRDAHYPGAAALG +HGKGYVYSHDEPHAVARQQYAPDPLVGKDYYRPKPIGAEKRLVDQVAALRRITRGE +>PROKKA_01526 +MDDLFSAAHADPDDDAPVTASGRARASAPLAVRMRPRSLDEVLGQAHLKQPGSPLRKLAE +PAASAQAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQARR +EREMYDRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLL +LTLRPLDDTDLAALVDRAVADERGLNGTVEPTPNARDYVVRMAGGDARRALTVLEAAAGV +ALDRAEARGETTGPGSAPVEVTEEDAAQAMDAQVQRYDKDGDQHYDVISAFIKSIRGSDV +DAAMHWLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRI +VLGQAVTHLATAPKSNASYTAVNEAIADVRAGGTGVVPAHLRDSHYPGAKALGHGQGYVY +SHDEPHAVARQQYAPDPLVGRDYYRPKPIGHERQLGPQVDALRRIIRGD +>PROKKA_01217 +MDDLFSAAHNGADDDGPAGTVAAPHPGAPLAVRMRPRTLDDVLGQRHLMRPGSPLRKLAE +PDPDSAAGPSSVILYGPPGIGKTTLAHVIARAPGRTFTELSAITAGVKDVRQVMEQAQRE +RDLYGRTTVLFLDEIHRFSKAQQDALLPGVENRWVVLVAATTENPSFSVIAPLLSRSLLL +TLRPLTDDDIVGLLDRAVTQERGLNGAVVLQDDARDYLVRMAGGDARRALTVLEAAAGVA +LDKAREAGRAGEGAVAVTDEDAAQAMDHHVQRYDKDGDQHYDVISAFIKSIRGSDVDASM +HYLARMLEAGEDPRFIARRLIISASEDVGMADPTALQTAVAAAQAVQLIGMPEGRIILAQ +AVTHLATAPKSNASYTAVNEAIADVRAGHTGAVPAHLRDAHYPGAAALGHGQGYVYSHDE +PHAVARQQYAPDPLVGRDYYRPKPIGHEKRLTEQVAALRRIIRGD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001057.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001057.fa new file mode 100644 index 0000000000000000000000000000000000000000..7fdbf40cf200545a7617102f224d7fd15a0e280d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001057.fa @@ -0,0 +1,25 @@ +>PROKKA_01260 +MSPAAPRADHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD +AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD +PAPESAAALAALDHGDGRPAGPDRTALEGRLLWTRCATGVADSPLTPARLDRALGVRGTA +RNLTTVRVLAGLPAGDRPRRTARGASGDVDIRGTPRAGRDVTVRSHPCDGVTPSSASLP +>PROKKA_00979 +MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD +AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD +PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA +RNLTTVRVLAGLPSED +>PROKKA_00445 +MSEHPASPTHVLLLRAVNVGGRNRVPKADLAELAAEAGLADVAVHLNSGNVLGTPDTGDH +VDDVAARLRALLAERLGVDTSVHAAARTELSALVDGLLASDLLAPGETLDSVDPKTVHLV +LLDTVPHPEAGEALAAVDAGDDRAVVVGRGVWVRYAGPSHSSHLGLPRIERAASGDAPPA +QRRVGTARNLATVRVLAGR +>PROKKA_01525 +MSRAAPRTDHTHVLLLRGINVGRSNRVSNARLAAWAEAARARDVTTHLASGNVLFRLPDA +DDDAGPAFLRAFRDAALADDGPDVPLILTTPAELRGALAMHDRLPWSGGEAKLTQLTVLA +ESPRDGAAEALAGLDHGSGRAAGPDRSALEGRFLWIRSPGRISDSPLTPARLEKALGVTG +TARNLATVRVLAGMA +>PROKKA_01218 +MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD +AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD +PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA +RNLTTVRVLAGLPSED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001059.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001059.fa new file mode 100644 index 0000000000000000000000000000000000000000..ff20ff0164c453a8c6dccc468ae68eaa2387c23e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001059.fa @@ -0,0 +1,20 @@ +>PROKKA_01262 +MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER +SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV +FGAKMDVSLTNSGPFTLIVDSDELAGPRRG +>PROKKA_00981 +MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER +SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV +FGAKMDVSLTNSGPFTLIVDSDELAGPRRG +>PROKKA_01626 +MRAVLQRARSASVTVAGEVVGSFEGAGLVILLGVSTQDTGAEADALAAKVATLRMLDGEA +SLVSAGAPALVVSQFTLYGDVRKGRRPSWTGAARPEHAEPLYERFAAGLEAEGVRVERGV +FGAQMDVTLVNDGPFTLVVDTADLTGPRRG +>PROKKA_01522 +MRAVLQRARSASVTVDGEVVGAFDGEGLVILLGVSTEDTEAEAVQLAAKVAGLRILDGER +SLVEASAPALVISQFTLYGDVRKGRRPSWSAAARGDQAEPLYECFAGELGTAGVRVERGV +FRADMDVALTNAGPFTLVVDTADLAGPRRG +>PROKKA_01220 +MRAVLQRARSASVTVDGKVVGSFEGEGLVILLGVTVDDTEAEAVQVARKVAGLRMLDGER +SLTDAGAPALVVSQFTLYGDVRKGRRPSWTRAAKGNQAEPLYERFTAELEAAGVRVERGV +FGAKMDVSLTNSGPFTLIVDSDELAGPRRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001063.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001063.fa new file mode 100644 index 0000000000000000000000000000000000000000..4af1626972fc37d3b711174f66e6fcae8928be61 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001063.fa @@ -0,0 +1,49 @@ +>PROKKA_01266 +MQPDDQQSPATEATPASAEAAETTVPAEARPVPEIVPDAPAHGDSAQPAEAPAVPSPAAM +KKASPAAVRPATPAAASAVPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG +QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSSELGRALGQMTTAVNERHMVGD +MDALRTRLAALETLLADYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA +SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTTFDKTRRAHFSRLDAASAEAKQ +VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA +RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV +RRMEEGFRRLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQAQGDQ +RAVKKAQEALDARLKWKQALEASASELR +>PROKKA_00985 +MQPDDQQSPATESTPASAEAADTTVPAEARPVPEIVPDAPAHGDSSQPAETPAVPSPAAM +KKASPAAVRPATPAAASVAPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG +QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSGELGRALGQMTTAVNERHMVGD +MDALRTRLAALETLLGDYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA +SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTAFDKTRRAHFSRLDAASAEAKQ +VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA +RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV +RRMEEGFRKLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQARGDQ +RAVKKAQEALDARLQWKQALEASASELR +>PROKKA_01621 +MPDASSEDALAYFVRKYDDVRAQMALFEQRIAAGAPSSELGKALGQMTSAVNERHMVGDM +DALRTRLAALETLLGDYRGAEQEARQAAQAQQLATREAIVAEAEEFAATPAERMPWKTAS +TRMTALFEEWKAAQKAGPRLSKSVEDGLWKRFRGARTAFDKTRRAHFSQLDAKSAEAKQV +KERLIARAEELSSSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFDAR +KAVNQEIDREYGANLKVKEQILADGKKLLPFKDVKAGRRALNELRGRWEDAGRVPRGDVR +RMEEGFRSLEDALKQAENEHWRRTDPETKARTSSALTQLEETIAGLEADLAKAQASGDER +AVKKAQEALDARLQWKQALEASASELS +>PROKKA_01516 +MTHQPQSDDQQTPDAEQATPAAAPQQTSPAQDAPEQVVQDQTPAAQADLADALGSIESVE +APAPAQGEEPADAAETDAEKTPEAAPSPAVPAAPSPAALKRSAAPRSAAPRPATAAVPVA +PAPSVEPTPLGEAAAFARVSEDGHVTLLDGADEVAVGQVPDATEQDALAYFVRKYDDVRA +QMALFEQRIAAGAPSSELGKALGQMTAAVTERHMVGDMPALRTRLAALETLLGDYRAAEA +ERRQAAQAEQLATREAIVTEAEKFAATPAERMPWKQASARMTELFDEWKTAQKAGPRLSK +SVEDGLWKRFRGARTQFDKTRRAHFSQLDARSAEAKQVKERLIARAEELSSSTDWGVTAG +KYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAARKAENAAVDREFGENLKVKEQIL +ADGQKLLPFTDLKAGRKALNELRGRWEDAGKVPRGDIRRMEDGFRKLEDALKQAENEHWR +RTDPETKARTNSALTQLEETIAGLEADLAEAQAAGDQKRIATAQEALDARLQWKQALEAS +ASELR +>PROKKA_01224 +MQPDDQQSPATESTPASAEAADTTVPAEARPVPEIVPDAPAHGDSSQPAETPAVPSPAAM +KKASPAAVRPATPAAASVAPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG +QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSGELGRALGQMTTAVNERHMVGD +MDALRTRLAALETLLGDYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA +SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTAFDKTRRAHFSRLDAASAEAKQ +VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA +RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV +RRMEEGFRKLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQARGDQ +RAVKKAQEALDARLQWKQALEASASELR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001065.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001065.fa new file mode 100644 index 0000000000000000000000000000000000000000..5e2fb013cf46e0f7a28a11fe4929a6d0170b1ce5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001065.fa @@ -0,0 +1,70 @@ +>PROKKA_01268 +MSEQDPTPVPVRPRGRIARLTGRHATEYSPLLEPLMRTVRQRATKTELADIVRAFEVARA +AHEGQMRRSGDPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSLERLRADFGSD +VALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNARTWRYVSPES +SARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGERNPEREKHIA +ALRTVIEDHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIRVLVDSVRDCY +AVLGAIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRTQEMHRQAEYG +VAAHWRYKAQAAGQAPVQATPAWLRSVMDWQADTRDPDEFLASLRTQIGADEVYVFTPKG +EIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNGKLVPLSTPLSHGDTVEVFTSRAEDAGP +SRDWLGFVVSPRARSKIRHHFATQRRGEQADRGRESLTRQLRKAGMTVQHVLGGEELVQL +ATDLGYADLDGLFVALGDGHVSAQSVQERVAERLAPPTPTQAEPEGELTVGEVDLQELVP +AQARRAPARATNDAGVLVDGDGGVMAKLARCCNPVPPDAIDGFVTRGSGVSVHRVDCPNL +ATLLAQEPERHTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLSENHVNILSASVNT +TRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT +>PROKKA_00987 +MSEQDPTPAPARPAPARPAPVRPRSRIARLTGRHATEYSPLLEPLMRTVRQRATKTELAE +IVRAFEVARAAHEGQMRRSGDPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSL +ERLRADFGSEVALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNA +RTWRYVSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGE +RNPEREKHIAALRTVIEEHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIR +VLVDSVRDCYAVLGVIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRT +QEMHRQAEYGVAAHWRYKAQVAGQAPVQATPAWLRSVMDWQADTRDPDEFLASLRTQIGA +DEVYVFTPKGEIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNDKLVPLSTPLSHGDTVEV +FTSRAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQADRGRESLTRQLRKAGMAVQQ +VLGGEELVQVATDLGYADLDGLFVALGDGHVSAQSVQERVAERLAPPTSTQAEPEGELTV +GEVDLQELVPAQSRRAPARATNDAGVLVDGDGGVMAKLARCCNPVPPDAIDGFVTRGSGV +SVHRVDCPNLATLLAQEPERRTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLSENH +VNILSASVNTTRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT +>PROKKA_01619 +MSEHDPTHAPARVAAVRPRGRIARLTGRHATEYSPLLEPLMRTVRQRATKAELADLIRAF +EVARAAHEGQMRRSGDPYITHPVAVATILAEIGVSGPTLLAALLHDTVEDTDYSLERLRA +DFGPEVALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNARTWRY +VSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGERNPER +EKHIAALRTVIEDHLREHRIRAEVTGRPKHYYSIYQKMVMRGKDFDEIHDLTGIRVLVDS +VRDCYAVLGVIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMGPGGRPVEIQIRTHEMHR +QAEYGVAAHWRYKAQAAAESSSSSSGTPAWLRSVMDWQKDTRDPDEFLDSLRTQIGADEV +YVFTPSGEIRSLPAGSTPVDFAYAIHTDVGHRTIGAKVNGKLVPLSTPLNHGDTVEAFTS +RAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQAERGRESLTRQLRRAGLAVQSVLG +GEELAQVASDMGYADLDGLLVALGDGHVSAQAVQERVSERLAPPPPARTEPQGELTVGEV +DLAELVPAQARRTPARATNDAGVLVDGDGGVMAKLARCCNPLPPDAIDGFVTRGSGVSVH +RLDCPNLATLLEQEPERRTPVGWAPSRHTVYLVEIQVEALDRKSLLSDVTRVLSENHVNI +LSASVNTTRDRVAMSRFVFEMGDPRFLGHVIAAVRRIDGVFDVHRT +>PROKKA_01514 +MTEQDRRPAAPPRRGRIARLTGRRATEYSPLLEPLMRTVRQSATHAEQEDIVRAFEVAER +AHRGQMRRSGDPYITHPVAVATILAELGVTGPTLLAALLHDTVEDTDYSLEQLTADFGPQ +VALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNARTWRYVSPES +SAKKARETLDIYAPLAHRLGMNTVKWELEDLSFAALQPKVYAEIVRLVGERNPEREKQLA +ALRGVLEEQLREQRVRATVTGRPKHYYSVYQKMVTQKKDFAQIYDLTGIRVLVDSVQDCY +AVLGVVHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMGPEGKPVEIQIRTWEMHRQAEYG +VAAHWRYKAGARGELEAGRSQQTPGWLRSVMDWQEDTRDPDEFLAALRTQIGADEVYVFT +PKGEIRSLPADSTPVDFAYAIHTDVGHRTVGARVNGRLVPLSTVLRHGDTVEVFTSKAED +AGPSRDWLNFVVSPRAKSKIRHHFATRRRDEQIERGREAFTRQLRKAGLSVQRVLGGEDL +GVVAGELGYHDPDTLFAAMADGHVSPQAVTERLEARLAPPPAPTAPDAELRVGEVDLAGL +VPEKARRAPTRSTNEAGVLVNGDGGVLAKLARCCNPVPPDEVVGFVTRGSGVSVHRGDCR +NLATMLENEPERRVDVAWAPSRDAVYLVEIQVQALDRTSLLSDVTRVLSENHVNILSASV +NTTRDRVAMSRFVFEMGDPKFLEHVVNAVRRIDGVFDVRRT +>PROKKA_01226 +MSEQDPTPAPARPAPARPAPVRPRSRIARLTGRHATEYSPLLEPLMRTVRQRATKTELAE +IVRAFEVARAAHEGQMRRSGDPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSL +ERLRADFGSEVALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNA +RTWRYVSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGE +RNPEREKHIAALRTVIEEHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIR +VLVDSVRDCYAVLGVIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRT +QEMHRQAEYGVAAHWRYKAQVAGQAPVQATPAWLRSVMDWQADTRDPDEFLASLRTQIGA +DEVYVFTPKGEIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNDKLVPLSTPLSHGDTVEV +FTSRAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQADRGRESLTRQLRKAGMAVQQ +VLGGEELVQVATDLGYADLDGLFVALGDGHVSAQSVQERVAERLAPPTSTQAEPEGELTV +GEVDLQELVPAQSRRAPARATNDAGVLVDGDGGVMAKLARCCNPVPPDAIDGFVTRGSGV +SVHRVDCPNLATLLAQEPERRTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLSENH +VNILSASVNTTRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001067.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001067.fa new file mode 100644 index 0000000000000000000000000000000000000000..e6827620c47dc14c56fda5880562113fb88e1c44 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001067.fa @@ -0,0 +1,60 @@ +>PROKKA_01270 +MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS +TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD +MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD +PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST +NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ +ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV +YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV +YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG +LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP +RTGLPAEASDEPADADDAAAADAPRPLAATGAPRAGSSARGGRRSRTAPPMTIAERRRAE +RRRQEEDQ +>PROKKA_00989 +MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS +TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD +MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD +PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST +NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ +ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV +YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV +YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG +LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP +RTGLPAEDSDEPADAAAADAPRPLVATGAPRAGSSARGGGRRSRTAPPMTIAERRRAERR +RQEEDQ +>PROKKA_01617 +MAKRTPTGSARRTLAWLAALTVALTAILGWGVASGAASWAPKLALDLEGGTQMVLAPETA +TGESVTSEQLDQAVEIIRQRVDGSGVAEAEVATQGAENVVVSLPGVPDEETRRLIQASAD +MQFRPVLQSGSGEATPEDQRLPEDQLPQPEGEPADAYDPNWVTPALLTQYQALDCAAPRD +PAAPPPPSDQAIVACERPADLGEGVQTPARKYILGPVVIPGTQIEGATNGLAQAQSGVST +NQWVVNIDFDEEGAKTFSEVTQKLTPYPDGDPRKQFAILLDGDVISAPQSNAVITAGSAQ +ISGPTLNEETTAQLAEQLNYGSLPISFSIESEQQISATLGQDQLFWGLIAGLIGLALVAV +YQFFQYRALGLLTFASIVVAGILTYLAIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV +YFERIKDELRAGHSVPMAVHEGWKRAKRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG +LTAIADLIVVFMFTHPIMVLLAQTRFVGGGHRMSGLDPSLLDRQALYQGAGRLREPGGAR +RTGSTAAPAADVAADDGARVPVPVGAAPADEASGEEGTATRGLRRPRPAQPMTIAERRRA +ERRRQEEDQ +>PROKKA_01512 +MAKTSPTRAAGRTLAWLAALIVALTAILGLGVASGQASWAPKLALDLEGGTQMVLAPTTA +SGEQATPEQLQQAVEIIRQRVDGSGVAEAVVATQGDQNVVVSMPGVPDEETRRLIQASAD +MQFRPVLQAVPGGQPTPQDQLVPKDQFPTPSAEPTDAYDPNWITPELADEFQRTDCTLPR +DPNAAPPATDRAVVVCEPQQETPAGTMPATKYIVGPVVIPGTMIEKASNATAQSQTGVTT +NEWVVNIDFDGEGTKRFTEVTQKLTPFAEGDPRKQFAIMLDGQVIAAPQSNVVITGGQAQ +ISGPGFTEESTAQLAEQLNYGSLPISFTIESEQQISATLGRDQLFWGLIAGLIGLALVAV +YQFFQYRALGLLTFASIVVAGALTYLAIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV +YFERIKDELRSGHTLDAALHEGWKRAKRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG +LTAIADLLVVFMFTHPLMVLLSRTDFVGGGHPMSGLDPRVLGVEPALYQGAGRFREPAAA +RAARGGSHAADDDDAGSSAARRGRRSEQPMTIAERRRAERAGAAQTPAAQTPAGSAPAAD +TEEDAL +>PROKKA_01228 +MAKRTPTGSAGRTLAWLAALLVVLAAILGGGVASGAASWAPKLALDLEGGTQMVLAPQTS +TGESVTPEQLDQAVEIIRQRVDGSGVAEAEVATQGSQNVVVSLPGVPDEETRRLIQASAD +MQFRPVLQSGPGEATPEDQRLPEDQLPKPDGEPADAYDPNWVTPALLAEFQATDCTAPRD +PAAPPPPSDRAIVACQPSEELADGAVTPAQKYILGPVVIPGTQIKGASNGMAQAQGGVST +NQWVVNIEFDEEGTKAFTEVTQKLTPYPEGDPRKQFAILLDGDVISAPQSNVVITNGSAQ +ISGPTLNEQTTAQLAEQLNYGSLPISFSIESEQQISATLGRDQLFWGLIAGLIGLGLVAV +YQFFQYRALGLLTFASIIVAGVLTWLTIAILGWTDNYRLSLAGIAGLIVAIGLTADSFIV +YFERIKDELRAGHTVPVAVHEGWKRARRTITASKAVNLLAAVVLYFVAVGNVRGFAFTLG +LTAIADLIVVFMFTHPLMVLLAQTRFVGEGHPMSGLDPSLLGGPSLYQGAGRFREPAHAP +RTGLPAEDSDEPADAAAADAPRPLVATGAPRAGSSARGGGRRSRTAPPMTIAERRRAERR +RQEEDQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001068.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001068.fa new file mode 100644 index 0000000000000000000000000000000000000000..e4184ccd97e7d8e9f91396fe2d38d56f22dfa968 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001068.fa @@ -0,0 +1,20 @@ +>PROKKA_01271 +MPVATAATLPVIAQQAQGGGGSLLMLIAFALLAVMLFLSFRKGKKMQQQQAQMRSTLAPG +VEVMTGAGIFGTVVAVDTEGQRVTLETAPGTRMDVHLQGVTTVVEPETTAAPTTDPSRLD +DAPGTEYRADDADDPRPRRDDLA +>PROKKA_00990 +MPVATAATLPVIAQQAQGGGGSLLMLIAFALLAVMLFLSFRKGKKMQQQQAQMRSTLAPG +VEVMTGAGIFGTVVAVDTEGQRVTLETAPGTRMDVHLQGVTTVVEPETAAAPTTDPSRLD +DAPGTEYRADDADDPRPRRDDLA +>PROKKA_01616 +MPVATAATLPVIAQQAQGGGGSMLMLIAFAMLAVMLFLSFRKGKKVQQQQAEMRSTLAPG +VEVMTGAGIFGTVVSVDAENQRVTIETAPGTRMDVHLQGVTNVVEPTAAAAATPADDEAR +LDRAPGAEYGAQQPVVEPRADDAVDPRDRRGDLA +>PROKKA_01511 +MPLTPLAPVLADDAAGGGNVLVLAMFAALAVMLFLSFRRGKKAQAEAADMRARLTPGQEV +MTGAGIFGRVVAVDAAAQRVTLETAPGTRMDVHLQGIVKIEEPDVAPAADTAPAVGGAHA +AETAPAADDTDRA +>PROKKA_01229 +MPVATAATLPVIAQQAQGGGGSLLMLIAFALLAVMLFLSFRKGKKMQQQQAQMRSTLAPG +VEVMTGAGIFGTVVAVDTEGQRVTLETAPGTRMDVHLQGVTTVVEPETAAAPTTDPSRLD +DAPGTEYRADDADDPRPRRDDLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001070.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001070.fa new file mode 100644 index 0000000000000000000000000000000000000000..69bb36321c8c5e1056e2f479124b8d6d58bb324c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001070.fa @@ -0,0 +1,25 @@ +>PROKKA_01274 +MDPGLTRCGIAVVDVDARRRAALVHVEVTGTPPTAPLDQRLLRIDEAVSAVLAAHRPDRA +AVERMFANTNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAVTGHGDAGKEQVTT +MVTRILRLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTADLASRAGRSQFAAK +APARARQRGQLTAAQRAWLDAERSAGGGRRR +>PROKKA_00993 +MDPGLTRCGIAVVDVDARRRAALVHVEVTGTPPTAPLDQRLLRIDEAVSAVLAAHRPDRA +AVERMFANTNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAVTGHGDAGKEQVTT +MVTRILRLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTADLASRAGRSQFAAK +APARARPRGQLTAAQRAWLDAERSAGGGRRR +>PROKKA_01613 +MVDVDARRRAALVHVEVAGTPPTASLDQRLLRIDEAVSAVLTAHAPDRAAVERMFANTNT +PTVLGTAQAAGVAIAAAARAGIPVGLHTPSEVKAAVTGYGDAGKEQVTTMITRILGLDAP +PRPADAADALALAIAHGWRGTALGAAAGQTGLDTSDLASRAGRSQFAAGTRSRGGRRGEL +TAAQRAWLDAERSAGGGCR +>PROKKA_01508 +MTDRPAGVVRVLGVDPGLTRCGIAVVDVDARRRAELVHVEVAGTAPEESLDARLLCIDRA +VSAVLVRFRPERAAVERMFANNNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAV +TGNGDAGKEQVTTMVTRILRLDAPPRPADAADALALAIAHAWRGTALGRAAGHTGLDTSG +LASRTGASRGAAGARVRRAPKAALTPAQQAWLAAERSAGARPGRRSAG +>PROKKA_01232 +MDPGLTRCGIAVVDVDARRRAALVHVEVTGTPPTAPLDQRLLRIDEAVSAVLAAHRPDRA +AVERMFANTNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAVTGHGDAGKEQVTT +MVTRILRLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTADLASRAGRSQFAAK +APARARPRGQLTAAQRAWLDAERSAGGGRRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001071.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001071.fa new file mode 100644 index 0000000000000000000000000000000000000000..64b345063312f0a498e187b63012a01e7e94e224 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001071.fa @@ -0,0 +1,30 @@ +>PROKKA_01275 +MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGPDVAGNPALDLAVSKAKKAS +VPNDNIDRAVKRGAGLTGEVIDYAEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR +NGGTMADSGSVSFLFERKGLVRLPAEGNTEDGLLEAVLEGGADAEEVVVSGDSFEILSDP +SDLQSVAKALDEAGVEYESDELEFVPTMKVDLDASGARTFLKLADALEDLDDVQNVFSNV +DIAPEVLAELDED +>PROKKA_00994 +MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGPDVAGNPALDLAVSKAKKAS +VPNDNIDRAVKRGAGLTGEVIDYAEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR +NGGTMADSGSVSFLFERKGLVRLPAEGNTEDGLLEAVLEGGADAEEVVVSGDSFEILSDP +SDLQSVAKALDEAGVEYESDELEFVPTMKVDLDASGARTFLKLADALEDLDDVQNVFSNV +DIAPEVLAELDED +>PROKKA_01612 +MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGADLAGNPALDLAVSKAKKAS +VPNDNIDRAVKRGAGLTGEVVDYAEIMYEVRGPQGSAVLVECLTDNKNRAAAEVRTAVTR +NGGTMADSGSVSFLFTRQGVVRLPAEGRTEDELLEAVIEAGAEEVVLSGDEFEILSDPSD +LRAVAEALDAAGIDYESDETEFVPTMKVELEDAKGAGTFLKLADALEELDDVQNVYSNVD +ISPEVLAELDQD +>PROKKA_01507 +MSGHSKWATTKHKKAVIDQRRAKAFAKYIKGIEVAARAGGADLSGNPALDLAVSKAKKNS +VPNDNIDRAIKRGAGLTGEVIDYTEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR +NGGTMADSGSVSFLFHRKGVVRLPAAGNTEDSLLEAVLEGGADAEEVVLSGDDFEIVSEP +GDLRAVAEALDAAGIDYETDEMEHLPTMKVELDAKGARTFLKLADALEDLDDVQNVFSNV +DIAPEVMDELEQD +>PROKKA_01233 +MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGPDVAGNPALDLAVSKAKKAS +VPNDNIDRAVKRGAGLTGEVIDYAEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR +NGGTMADSGSVSFLFERKGLVRLPAEGNTEDGLLEAVLEGGADAEEVVVSGDSFEILSDP +SDLQSVAKALDEAGVEYESDELEFVPTMKVDLDASGARTFLKLADALEDLDDVQNVFSNV +DIAPEVLAELDED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001072.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001072.fa new file mode 100644 index 0000000000000000000000000000000000000000..59690e06851355fe1d8e2dc3284e554fdbc88367 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001072.fa @@ -0,0 +1,65 @@ +>PROKKA_01276 +MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT +APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR +LAARVASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR +LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW +LASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA +APSTAAVEELLAAMAPRAMANARADAATAAAHAGRADAEVAPWDWPALSAGYAREEFAVD +ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL +FVADLFARPTKSGGAWMHTVRDRADALGERPVVFTTMNVPAPAAGRPALLTLDETTTLFH +EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVETGEPLPA +GTLERLEAADLWGEGHRTVEYLGATLVDWAWHSLTEETVDAATADPAAFERRVLTEAGID +PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL +LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA +>PROKKA_00995 +MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT +APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR +LAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR +LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW +LASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA +APSTAAVEELLAAMAPRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVD +ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL +FVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEATTLFH +EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPA +GTLERLEAADLWGEGHRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGID +PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL +LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA +>PROKKA_01611 +MTPTPASSVLPADHPLATPSELPYGLPDFSAVTDAQLAEAVRAGMAAQRAEVEQILGAAT +APTFENTVRAFELSGQLLRRSAAMFFTLVSADGTDARQGLAEELSPELAAHEDALLLDPR +LAERVAAIDGAGLTGEDARLLEVLRRRLDLAGAGLGEAERAELGRINTELAGLTAAYTRR +LVADTAERAVLVTDRERLAGLSEDDLASAAAAAREAGHGGADGEGGDEAGPWLLTLSLFT +SQPWLASLEDEALRREVFEASVGRGAAGDHETLSTAMEVVRLRLRKARLLGSASWAEHAL +KDRAAPSTTAVEELLATMAPRAMANARTDAATAAAHAGRVGGAVAPWDWPALSAAYARER +FAVDAGALRPHFELDRVLHAGVFAAATALYGITFEERPELAGRLYRPGIRVFEVRDEDGA +GVGLFVADLFARSTKSGGAWMHTVRDAADALDERPVVFNTMNVPAPAPGRPALLTLDEAT +TLFHEFGHALHGLLAKGEYVSLSGTHVPRDVVEFPSQVNEVWLREPALLAEYARHVETGE +PLPAGTLERLEAADLWGEGYRTVEYLGATLVDWAWHSLTEDTVEAATADPAAFERRVLTE +AGIDPELVPPRYGTGYFKHIFGNDYAAGYYSYIWAEVLDADAVEWFREHGGMTRENGRRF +AEELLSRGETRDLLESYRAFRGRDAELEPLLRRRGLVDAAA +>PROKKA_01506 +MTQITHRLPAGHPLLSPSPLPHGLPDFAAVSDADLATGMRQGMAEQRAEVEEILSSPEAP +TFENTVRALELSGALLRRVAPMFSTLVGSDGTDARQALAEELSPELAAHEDAILLDPRLS +ARVAAVDDAGLAGEDARLLERTRTRLEIAGAGLDEAGRAELARLNGELATLSAAYTRRLV +ADTAARAVLVTDRERLAGLRADDLAAAAERAAAEAGHRRADAAEGAGPWLLTLSLFTSQP +WLADLEDAGLRREVFEASVGRGSSGEHETLTTAMRIVRLRLEKARLLGAASWAEHALRDR +AAPSVAAVEGLLGSLTGPAMANARRDAEAVAEGDAPVVPWDWPFLSAAHAREAFDVDAGA +LRPWFELDRVLTRGVFAAATALYGLRFAEREDLAGHLYRPAIRVWEVTDEDGRGVGLFVG +DFFARPTKSGGAWMHNVVDASAALGTRPVVFCTMNVPAPAEGRPALLTLDEATTLFHEFG +HVLHGLLAEGEYPSLTGTAVPRDTVEFPSQVNEVWLREPSLLADYARHVETGAELPTGTL +ERLEAADLWGEGYRTVEYLGATLLDWAWHTLTEDTVDAATADPAGFERRVLTEAGIDVDL +VPPRYGTGYFKHVFGNDYAAGYYSYIWAEVLDADAVEWFREHGGLTRENGRRFAEELLSR +GDTRDVLESYRAFRGRDAELEPLLRRRGLLPEGA +>PROKKA_01234 +MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAAT +APTFENTVRALELSGQLLRRSAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPR +LAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAREELRGINTELASLSAAYTRR +LVADTAARAVLVTDRERLAGLSEDDLAAAAGAAAEAGHGDGDAAAGPWLLTLSLFTSQPW +LASLQDEGMRREVFEASTGRGGAGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRA +APSTAAVEELLAAMAPRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVD +ADALRPYFELDRVLTEGVFAAATALYGLTFAERPELARHLYRPGIRVFEVTGEDGAGVGL +FVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEATTLFH +EFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPA +GTLERLEAADLWGEGHRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGID +PDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLDADAVEWFREHGGMTRENGRRFADEL +LSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001074.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001074.fa new file mode 100644 index 0000000000000000000000000000000000000000..bf80863d34896b838fe645ffc4c234c5814fbec4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001074.fa @@ -0,0 +1,20 @@ +>PROKKA_01278 +MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP +FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER +IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR +>PROKKA_00997 +MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP +FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER +IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR +>PROKKA_01609 +MTDTPQTPQDPDRTDAAQASPVVGHGAGAPRGARLTDEEWARRLTPEEFQVLRRAGTERA +YTGEYWDSHVQGVYACRACGAELFRSDEKFDSHCGWPSFFAPLAEDRVEYLKDTTLGVER +VEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADASGAGSDDDAAGRA +>PROKKA_01504 +MSQNHATVPSGADDAARPAALTDEEWARRLTPEEFHVLRRAGTERPYTGEYWDSRVQGVY +ACRACGVELFRSEEKFDSHCGWPSFFAPLAEDRVVYVKDATLGMERIEVRCAACGSHMGH +VFAGEGYDTPTDLRYCINSISLRLTPADVAAIGTEADPAGDRA +>PROKKA_01236 +MTETPHTPHDGPTPDPARDVPAPEQTLAAPGGARLTDEEWARRLTPEEFQVLRRAGTERP +FTGEYWDSHVKGVYACRACGSELFRSDEKFDAHCGWPSFFAPLAEDRVEYLKDTTLGMER +IEVRCAACGSHMGHVFAGEGYDTPTDLRYCINSISLRLAPADDAAAPDGAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001076.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001076.fa new file mode 100644 index 0000000000000000000000000000000000000000..99f344a444769874879769890b6ebee61506f18e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001076.fa @@ -0,0 +1,42 @@ +>PROKKA_01280 +MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAVDAERASGIRY +GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR +LFDTELAARVAGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV +PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL +WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI +RAGVEDAERGDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN +LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA +>PROKKA_00999 +MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAIDAERASGIRY +GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR +LFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV +PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL +WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI +RAGVEDAERDDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN +LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA +>PROKKA_01606 +MTDVPEPAEPDATPRLIAEPADGVPRVTDTPAGLEACAAALAAGTGPVAVDAERASGIRY +GQRAMLVQLKREGAGIWLVDPEALDGLEPLQEALSGVEWILHAASQDLPCLAEQGLRPDR +LFDTELAARVAGLPRVGLAAVLESMLGVTLAKEHSAADWSVRPLPEAMLAYAALDVELLV +PLRAAMLELLEAEGKREWAEQEFEHVRTAPAPGPRADPWRRTSGSQTLRRPVQRAVLKRL +WEAREDLARHRDVAPGRLIPDRSLIAAAESQPRTVPALRQTSGFHGRAASREAPPLDHRD +PRRRRGRRARRRPARPGARRGRPAPAPGVEGPRPARRPPPEDRQGARGPARRAAGPAHGE +PAHPGHPAPALLGAAAAADARGRGRVPPRARGPALAGGPGGRGGHRGPAGPGPRRGLSRG +GRRADAAVGRGPTHR +>PROKKA_01501 +MTSPTSPAVATSPDPSDRPGGEQAAPTLVAEPAGGVPVVTDTPAGLAACAAALAAGTGPV +AVDAERASGIRYGQRAFLVQLKRAGAGIWLVDPEAFEDLAPLDEALRGVEWVLHAASQDL +PCLADCGMRPDLLFDTELAARLAGLPRVGLAAVLESQLGLTLAKEHSMADWSTRPLPVDW +LNYAALDVELLVELRDALAVLLEEQGKLAWAEQEFEHVRTTPPAAPRQDPWRRTSGMAAL +KRPVQLAVLRRLWQAREDLAQHRDLAPGRLLPDSALVAAASTLPRTVPELRATRGFHGRS +AAREAPRWITAIRAGIEDAAAGQAPPRHGPGSDAPPPPRAWRDRDPLADRRLTTAKPRIA +RAAEALGMPPENLLTPDTLRRVCWTPPETITPETVAAALAERGARPWQVEQTSAIITVAL +LDPDPARDR +>PROKKA_01238 +MTDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTGPVAVDAERASGIRY +GQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQDLPCLAEQGLRPDR +LFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPEAMLTYAALDVELLV +PLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQTLRRPVQRAVLKRL +WEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHGRAASREAPRWIAAI +RAGVEDAERGDAPAAQIRTGDGPPPPRAWKDRDPVADRRLRTAKARVARRAEQLGMPTEN +LLTPDTLRRICWTPPAPITPETVDAFLTERGARPWQVENVGAIVTVALLDPDPAGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001080.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001080.fa new file mode 100644 index 0000000000000000000000000000000000000000..6de3c96601582655368cee3bd7c94e499f1c55b4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001080.fa @@ -0,0 +1,16 @@ +>PROKKA_01284 +MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML +LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE +>PROKKA_01003 +MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML +LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE +>PROKKA_01601 +MGGAAAAALAAAANPLMPTPVEAVLGWGLSLAVGALWIAGFVSLSRGPLDARGRLPWAGA +MLLLPVLGALIWFWWRHRYYPARRREQPGWDPNDRGAVVVPPRRGRPVPSGIGRPDPNAG +VAAPKGLAPRRRYGAERD +>PROKKA_01497 +MEPWLGWTLSAVVGTIWVAGLVSLLRGPLDERRRLPWALAMVVLPVIGAGAWFWWRHRHY +PARKAAEPGWDPNRRDPVVLPPARSGRAAPTAIGRPDPWAGHAPHPDRLPTRRYGAPED +>PROKKA_01242 +MAGALTGAAAATPLVPTPGEAALGWTVSVVAGALWVAGFVSLGRSPLDARARLPWVGLML +LLPVLGALIWFWWRHRYYPARRREQPAWDPNDRSAVVVPPRRRYGAPEE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001082.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001082.fa new file mode 100644 index 0000000000000000000000000000000000000000..fc46e48ecd1d4d08a91fd89f134166ca50b045d3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001082.fa @@ -0,0 +1,65 @@ +>PROKKA_01287 +MEHLPPTSPGAPLLPQIARPADLSALTEDQLTALAAEIRAYLIAHVSKTGGHLGPNLGVV +ELTLAVHRVFESPKDAVIFDTGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRTESEHDVV +ESSHASSSLSWADGIARAWAQTGQGDRTVVAVIGDGALTGGMAWEAVNNIAAGRDRRVVI +VVNDNGRSYAPTVGGVAEHLGGLRRGVLDKVRTHHRYEQTLDYLKRRLQEAGLAGELVYR +PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLTAMEEALEDARAYGGPVIVHAMTEK +GHGYAPAVAHEADQFHAIGVIDPSTGEPITSSTAQSWTSVFGEEMVAIADERPDVVAITA +AMQNPVGLAPMALAHPDRVFDVGIAEQHAVTSAAGMAFGGLHPVVAVYATFLNRAYDQVL +MDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRISAPRDADTLREELREA +VAVEDAPTVVRFAKGSVGESVRALERLSDGTDVLARRGEAGGRDGAERDVLIVAVGAMAE +LGLDVAERLERHGISATVIDPRWVLPVARSVIDTAARHRIVVCLEDGVRAGGVGSRIRQE +MRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRITQDTVAQVLGAKVPYARPVPE +DAAAPHHQEQA +>PROKKA_01006 +MEHLPPTSPGAPLLPQIARPADLSALTEDQLTALAAEIRAYLIAHVSKTGGHLGPNLGVV +ELTLAVHRVFESPKDAVIFDTGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRTESEHDVV +ESSHASSSLSWADGIARAWAQTGQGDRTVVAVIGDGALTGGMAWEAVNNIAAGRDRRVVI +VVNDNGRSYAPTVGGVAEHLGGLRRGVLDKVRTHHRYEQTLDYLKRRLQEAGLAGELVYR +PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLTAMEEALEDARAYGGPVIVHAMTEK +GHGYAPAVAHEADQFHAIGVIDPSTGEPITSSTAQSWTSVFGEEMVAIADERPDVVAITA +AMQNPVGLAPMALAHPDRVFDVGIAEQHAVTSAAGMAFGGLHPVVAVYATFLNRAYDQVL +MDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRISAPRDADTLREELREA +VAVEDAPTVVRFAKGSVGEPVRALERLSDGTDVLARRGEAGGRDGAERDVLIVAVGAMAE +LGLDVAERLERHGISATVIDPRWVLPVARSVIDTAARHRIVVCLEDGVRAGGVGSRIRQE +MRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRITQDTVAQVLGAKVPYARPVPE +DAAAPHHQEQA +>PROKKA_01598 +MEHLPPTSPGAPLLPQIASPADLADVSEEQLTALAAEIRDYLIAHVSKTGGHLGPNLGVV +ELTLAVHRVFESPKDAVLFDTGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRAESEHDVV +ESSHASSSLSWADGIARAWHQTGQGDRTVVAVIGDGALTGGMAWEAVNNIAAGRDRRVVI +VVNDNGRSYAPTVGGIADHLDGLRRGVLDKVRTHHRYEQTLDFLKRRLQEAGTAGEMVYR +PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLGELEEALEDAKAYGGPVIVHALTEK +GHGYAPARAHEDDQFHAIGVIDPSTGEPVTSSTAQSWTSVFGEEMLAIAEERPDVVAITA +AMRNPVGLAPMALAHPDRVFDVGIAEQHAVASAAGMAFGGLHPVVAVYATFLNRAYDQVL +MDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRIAAPRDAETLREELREA +VAVEDAPTVVRFAKGSVGEPVRAIERLADGTDVLARRGEAGARDGAERDVLIVAVGALAE +LGLDVAERLERHGISSTVVDPRWVLPVAESVIEAAARHRIVVCLEDGVRAGGVGSRIRQE +MRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRVTQDTVAQVLGAKVPYARPVPQ +DEAARHPQEHA +>PROKKA_01494 +MSDTSRAPLGAPLLPGIHSPEDLALLSDAQLRALAAEIRAFLIQHVSQTGGHLGPNLGVV +ELTLAIHRVFDSPRDAVVFDTGHQSYVHKLLTGRQDFSRLRQQGGLSGYGDRAESEHDVV +ESSHASSSLSWADGISRAWKQTGQGDRTVVAVIGDGALTGGMAWEAVNNIAADRDRRVVI +VVNDNGRSYAPTVGGIADHLGGLRRGVLDKVRMHHRYEQTLDYLKRRLQEAGTAGEMVYR +PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDEHALEEALEDAKAYGGPVIVHAMTEK +GHGYGPATSHEDDMFHAIGRIDPETGRPISSPTAQSWTSVFGEEILDIARERPDVVAITA +AMQNPVGLGPMAAEFPDRVFDVGIAEQHAVTSAAGMAFGGLHPVVAVYATFLNRAFDQVL +MDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRIAAPRDADTLREELREA +VAVDDAPTVLRFAKGSVGEPVRALERLSDGTDVLARLGAPTGADGAERDVLIVAVGSFAE +LGLDVARRLGQHGITATVVDPRWVLPVARSVIELAGRHRIVVCLEDGVRAGGVGSRIRQE +MRAAGVDTALNEVGLPVEFLAHATRDQVLERVGLTAQRITQDTVAQVLGAKVPYARALPR +DAEHPEASAHPAGAPTTSAQAARPEEQA +>PROKKA_01245 +MEHLPPTSPGAPLLPQIARPADLSALTEDQLTALAAEIRAYLIAHVSKTGGHLGPNLGVV +ELTLAVHRVFESPKDAVIFDTGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRTESEHDVV +ESSHASSSLSWADGIARAWAQTGQGDRTVVAVIGDGALTGGMAWEAVNNIAAGRDRRVVI +VVNDNGRSYAPTVGGVAEHLGGLRRGVLDKVRTHHRYEQTLDYLKRRLQEAGLAGELVYR +PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLIAMEEALEDARAYGGPVIVHAMTEK +GHGYPPAVAHEADQFHAIGVIDPSTGEPITSSTAQSWTSVFGEEMVAIADERPDVVAITA +AMQNPVGLAPMALAHPDRVFDVGIAEQHAVTSAAGMAFGGLHPVVAVYATFLNRAYDQVL +MDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRISAPRDADTLREELREA +VAVEDAPTVVRFAKGSVGEPVRALERLSDGTDVLARRGEAGGRDGAERDVLIVAVGAMAE +LGLDVAERLERHGISATVIDPRWVLPVARSVIDTAARHRIVVCLEDGVRAGGVGSRIRQE +MRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRITQDTVAQVLGAKVPYARPVPE +DAAAPHHQEQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001087.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001087.fa new file mode 100644 index 0000000000000000000000000000000000000000..6dc8e9a16bd7c912e8e1fbf61b7c2098752b36b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001087.fa @@ -0,0 +1,26 @@ +>PROKKA_01299 +MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC +GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP +SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV +RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS +>PROKKA_01022 +MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC +GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP +SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV +RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS +>PROKKA_01593 +MRAVIAGAGAVGASVARELHAHGHEVVVVEIRPDAAHKADVGGAKLVLGDACDLALLERC +GAMEADVLVAATGDDRANLVCSLLGRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP +SIMTALVEEAVETGDLVRLLRLEAGGAVLSEFRVPAEHWLAGRRVGTVSWPQDAPLVAVV +RDGVPRHATADEMLEAGDELFFLAAAAADAALRRLLVGEDRAQARPGAGSSSAAGRRPSS +SPGAGALTDQASQSPRA +>PROKKA_01489 +MRVVIAGAGAVGSSIARELHAHGHEVSVVESRADAAARSDLAGARTVLGDATDLGVLGRA +GALGADVLVAATGDDRANLVASLLARSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP +SIMTALVEEAVESGDLVRLLRLEAGGAALTEFRIPSGHWLRGRRVGTVSWPAAAPLVAIV +RDGAPRSSTPDEVLEESDELFFLADAEAEGALRRLLVG +>PROKKA_01257 +MRAVIAGAGAVGASIARELHAHGHEVVVVEARTDAARKADVGGARLVLGDACDLTVLEQC +GALEADVLVAATGDDRVNLVCSLLSRSEFGVGRTVARVNNPLNDWLFDESWGVDVAVSTP +SIMTALVEEAVETGDLVRLLRLEAGGAALSEFRVPAKHWLEGRRIGTVSWPQEAPLVAVV +RDGAPRQASADEVLEVGDELFFLAAGSAEPALRRLLVGEGRAQGRSEAAESAGTPSS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001089.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001089.fa new file mode 100644 index 0000000000000000000000000000000000000000..f07e7fe788e7890f555f4baa345fc885a412b737 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001089.fa @@ -0,0 +1,15 @@ +>PROKKA_01301 +MSPAVAARPTGAAGRIERRGVIASVTLPGADEATVFRAVLADRLPAPGSMAPAETLQLVW +HGRRRVPGVMPGEWLTVRGRVTQMDGVPTLHNPEFDLVDAPEATR +>PROKKA_01024 +MSPAVAARPTGAAGRIERRGVIASVTLPGADEATVFRAVLADRLPAPGSMAPAETLQLVW +HGRRRVPGVMPGEWLTVRGRVTQMDGVPTLHNPEFDLVDAPEATR +>PROKKA_01591 +MSPAAGERADAGPGDLIERRGVVASVTLPGADDATVFRAALADRLPEPGSVTPAESLQLV +WHGRRRVPGVMPGQWLAVRGRLTRPDGVLTLHNPAFDLIDAPEAALRARPPREESP +>PROKKA_01487 +MSPRRTPAPAGERPAGERVGVVVAVTFPGADDATVFRAALADDLPAPGRPEPQEVLHLVW +HGRHRVAGVMPGAWMRVLGHPVAVAGEPTLFNPEFHLIDDEGGPA +>PROKKA_01259 +MSPAVAARPTGAAGRIERRGVIASVTLPGADEATVFRAVLADRLPAPGSMAPAETLQLVW +HGRRRVPGVMPGEWLTVRGRVTQMDGVPTLHNPEFDLVDAPEATR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001091.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001091.fa new file mode 100644 index 0000000000000000000000000000000000000000..107790c79ff2fa59f7abd1007bf8381e6570788b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001091.fa @@ -0,0 +1,20 @@ +>PROKKA_01303 +MTDSAELPVPLHALDPGLAPPAYAQPGDAGADLRTAVDVTLAPGERALVPTGVALAIPEG +HAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPIVLRRGDRIAQLVL +QPVVRARFEPVDALPDSERGAGGFGSTGGFTADNTPGRTS +>PROKKA_01026 +MTDSAELPVPLHALDPGLAPPAYAQPGDAGADLRTAVDVTLAPGERALVPTGVALAIPEG +HAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPIVLRRGDRIAQLVL +QPVVRARFEPVDALPDSERGAGGFGSTGGFTADNTPGRTS +>PROKKA_01589 +MTDSAELPVPLHALDPDLAPPAYAQPGDAGADLRAAVDVTLAPGERALVPTGVALAIPEG +FAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTDAVELRRGDRIAQLVI +QPVVRARFAPVDALPGSERGAAGFGSTGGFGTENAPGRTS +>PROKKA_01485 +MNGPREIDVPLRALDPQLPPPEYARPDDAGADLRAAEDVTLAPGERALVPTGVALAIPAG +FAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPVVLRRGDRIAQLVV +QPVVQARFMAVDRLADSERGEAGFGSTGGFTPAAHDDAPGRTA +>PROKKA_01261 +MTDSAELPVPLHALDPGLAPPAYAQPGDAGADLRTAVDVTLAPGERALVPTGVALAIPEG +HAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPIVLRRGDRIAQLVL +QPVVRARFEPVDALPDSERGAGGFGSTGGFTADNTPGRTS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001093.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001093.fa new file mode 100644 index 0000000000000000000000000000000000000000..acaa4cff152d8f9f5be334df0bfc9886d29022da --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001093.fa @@ -0,0 +1,15 @@ +>PROKKA_01305 +MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDEAEAAEGFELPGADLSGEELMV +RVLPAQSDEFTCASCFLVRHRSQAAREKNGLIYCTDCEG +>PROKKA_01028 +MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDEAEAAEGFELPGADLSGEELMV +RVLPAQSDEFTCASCFLVRHRSQAAREKNGLIYCTDCEG +>PROKKA_01587 +MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDETEAAEGFELPGADLSGEELMV +RVLPAQSDEFTCASCFLVRHRSQAAREKNGMTYCTDCEG +>PROKKA_01483 +MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDETEAAEGFELPGADLSGEELMV +RVLPAQSDEFTCASCFLVRHRSQAAREEGGLVYCTDCEG +>PROKKA_01263 +MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDEAEAAEGFELPGADLSGEELMV +RVLPAQSDEFTCASCFLVRHRSQAAREKNGLIYCTDCEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001095.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001095.fa new file mode 100644 index 0000000000000000000000000000000000000000..ed28ccbbea0a361652ac4ec188b72e9287c12ea7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001095.fa @@ -0,0 +1,25 @@ +>PROKKA_01308 +MGDMSPFRRSHEPGRPDHRSGTPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA +VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS +TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD +HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT +>PROKKA_01031 +MGDMSPFRRSHEPGRPDHRPDAPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA +VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS +TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD +HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT +>PROKKA_01584 +MEPMSPFRRSHESGRPEHRPGAPASGEHRHEARTLEGAGGLGASLARAGFYPELVAHAIA +VELGERTPDAHLVHVDTHFDYEEIHRHITVLVLAQDALLAVHLDDHAADAAGQAVLAQVS +TEMVPVRALGSVVLTTGHADPARFSPADPVAEMTLALIWAGGQRLDLQPAGCADPQCDLD +HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATA +>PROKKA_01480 +MEGMTPLRWNNHDDSASDGRRPAGEVRRTRQTVDATGTLEQALARAGYYPELVSHAVALE +LEGRTVHAHLVHVDTHFDYEEIHRHITVLVVADDVMLAVHLDDHAADPAGHSVLAQVATE +MVPLRAIESVLITTGHATPERYRPTDPVAEVTLGVQWAGGQRLDLQPAGCADPQCDADHG +YTGTSVREDLVIRVAADAEGQGAVDAALAFARTLRRVHLAAVA +>PROKKA_01266 +MGDMSPFRRSHEPGRPDHRPDAPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA +VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS +TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD +HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001097.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001097.fa new file mode 100644 index 0000000000000000000000000000000000000000..4b96909b55109a892394311a1be8495925a157fd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001097.fa @@ -0,0 +1,80 @@ +>PROKKA_01310 +MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK +PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV +VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY +PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI +VGLDGVRDAYATGRGTFRMRAAVDVEQVTARRTGLIVTELPYGVGPEKVIERIKAGVDAK +KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ +TLGLLPLLRVYVDHRLDVVRRRTAHRLQRRQDRLHLVEGLLLALVDIDEVIEIIRSSDDT +AAARTRLMGVFDLTQVQADHILELRLRQLTKFSRIELEAERDELQAAIAELEAILGSEAR +LREVVSAELQAVADEFGDDRRTVLLEAETVAAPAASNAGGPTPAGAAQAGADLMVPDTAC +WAVLTTSGRLLRTADRTPIASQGRRRKHDAFASVVATTARGEIGALTSTGALHRIQAVDL +PAAPEPSAAPAMTGSVPAKELVPLGKGESLVALVPLDAVIALGTAQGVVKRVRPEWPLNR +EVAEAIALKDGDAVVGAAPAVDDEDQLVFLTRAGQLLRYAASAVRPQGPAAGGVAGLRVA +ADDAVLAFGVAPAASLTGPGDDAAAHPRPAVVVTVTDGEGDLLGSAGGSVKVTPLGEYPA +KGRGTGGVRAHRLLKGETSLVLGWVGAGPALAASKAGVARALPVEYGRRDGSGVPVDQRI +EAVGAGASPELLSAPPVADDPVTVSAD +>PROKKA_01033 +MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK +PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV +VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY +PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI +VGLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYGVGPEKVIERIKAGVDAK +KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ +TLGLLPLLRVYVDHRLDVVRRRTGHRLGKHRDRLHLVEGLLLALVDIDEVIEIIRSSDDT +TAARTRLMGVFDLTQVQADHILELRLRQLTRFSRIELEAERDELQAAIAELEAILASDAR +LREVVSAELQAVADEHGDDRRTVLLEAETAAAPAAGPAPSGPTPAGAAEAGADLMVPDTA +CWALLSTSGRLLRTADRTPIAPQGRRRKHDAFASVVPTTARGEIGALTSAGALHRLQAVD +LPVAGEPSAAPAMTAAVPAAELVPLAKGETLVALVPLDAVLALGTAHGVVKRVRPEWPLN +RQVVDAVALKDGDAVVGAAPAPDEADQLVFLTRTGQLLRYAASAVRPQGPAGGGVAGIRL +AAGDTVLAFGVAPAASLTETGADAAAHPRPAVVVTVTDGEADVLGSAPGSVKVTPLGEYP +AKGRGTGGVRAHRLLKGESGLELGWIGAAPALAASRAGVARALPIEYGRRDGSGVPVDQR +IEAVGAGASPDLVSAPPAEDDAVAVSAD +>PROKKA_01582 +MSRSSRSRPSEQDVARPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLKP +VQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPVV +DGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEDTVDFVPNYDNQFQQPAVLPAAYP +NLLVNGTTGIAVGMATNMAPHNLREVVAAARHLLADPEADLEAIMAHIPGPDLPSGGRIV +GLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYAVGPEKVIERIKAGVDAKK +LSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQT +LGLLPLLRVYVDHRLDVVRRRTAHRLQRRQDRLHLVEGLLLALVDIDEVIEIIRSSDDTA +AARTRLMGVFDLTQVQADHILELRLRQLTKFSRIELEAERDELQAAIAELEAILGSEARL +REVVSAELQAVADEFGDDRRTVLLEAETVAAPAASTVGGPTPAGAAQAGADLMVPDTACW +AVLTTSGRLLRTADRTPIASQGRRRKHDAFASVVATTARGEIGALTSTGALHRIQAVDLP +AAPEPSAAPAMTGSVPAKELVPLGKGESLVALVPLDAVIALGTAQGVVKRVRPEWPLNRE +VAEAIALKDGDAVVGAAPAVDDEDQLVFLTRAGQLLRYAASAVRPQGPAAGGVAGLRVAA +DDAVLAFGVAPAASLTGPGDDAAAHPRPAVVVTVTDGEGDLLGSAGGSVKVTPLGEYPAK +GRGTGGVRAHRLLKGETSLVLGWVGAGPALAASKAGVARALPVEYGRRDGSGVPVDQRIE +AVGAGASPELLSAPPVADDPVTVSAD +>PROKKA_01478 +MTTRSSRSRTAEADAPAPLPVEQENIVDVDVSQEMEASFLEYAYSVIYSRALPDARDGLK +PVQRRILFMMSQMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV +VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEDTVDFVPNYDNQFQQPAVLPAAY +PNLLVNGAAGIAVGMATNMAPHNLREVVAAARHLLAHPDADLEALMAHVPGPDLPSGGRI +VGLDGIRDAYATGRGTFRMRATASIEQVSSRRTGIVVTELPYAVGPEKVIEKIKDGVRGG +RLQGISDVVDLTDRKHGLRLVVELKSGFNAQAVLAALYRHTPMEESFGINNVALVDGRPR +TLGLRELLQVYVDHRMDVVRRRTVHRLGERRDRLHLVEGLLLALVDIDEVIEIIRSSDDT +AAARTRLMQVFDLSQVQAEHILELRLRQLTKFSRIELEAERDELAAAIAELEAILASDAR +LREVVSAELQAVADEFGDDRRTELVTADAAASVVSAPGEPALPAGTGPSDGGELMIPDTA +CWALLTTTGRLLRTVDRTPLAPQGRRRKHDAFVSVVPTTARGEVGALTSTGRVLRLQAVE +LPAAEESSPAPALTAARPAKDLVPLAKGESLVALVPLDAVLALGTAHGVVKRVRPEWPLN +RDELTAIALKDGDSVVGAAPAPDDGDHLVFVTRAGQLLHFAASQVRPQGPAGGGVAGLRV +GAEDAVIAFGVAPAASMTAEGEDPAAHPRPAVVVTVTDGDADLLGSAGGSVKVTPLGEYP +VKGRGTGGVRAHRLLKGETHLTLAWVGASPALAASKAGVARALPVEYGRRDGSGVPVDQR +VEAVGAGASPELVAAAPVDDSGVEVSAD +>PROKKA_01268 +MMARSSRSRPAEQDAPRPLPLEQENIVDVDVSEEMEASFLEYAYSVIYSRALPDARDGLK +PVQRRILYMMSRMGLRPDRGHVKSARVVGEVMGKLHPHGDAAIYDAMVRLAQPFSLRLPV +VDGHGNFGSLDDGPAAPRYTEARMAPAALALTADLDEGTVDFVPNYDNQLQQPAVLPAAY +PNLLVNGTTGIAVGMATNMAPHNLREVVAGARHLLADPEADLEAIMAHIPGPDLPSGGRI +VGLDGVRDAYATGRGTFRMRAAVAVEQVSARRTGLVVTELPYGVGPEKVIERIKAGVDAK +KLSGIADVVDLTDRKNGLRLQIELKSGFNPQAVLAALYRHTPLEETFGINNVALVDGQPQ +TLGLLPLLRVYVDHRLDVVRRRTGHRLGKHRDRLHLVEGLLLALVDIDEVIEIIRSSDDT +TAARTRLMGVFDLTQVQADHILELRLRQLTRFSRIELEAERDELQAAIAELEAILASDAR +LREVVSAELQAVADEHGDDRRTVLLEAETAAAPAAGPAPSGPTPAGAAEAGADLMVPDTA +CWALLSTSGRLLRTADRTPIAPQGRRRKHDAFASVVPTTARGEIGALTSAGALHRLQAVD +LPVAGEPSAAPAMTAAVPAAELVPLAKGETLVALVPLDAVLALGTAHGVVKRVRPEWPLN +RQVVDAVALKDGDAVVGAAPAPDEADQLVFLTRTGQLLRYAASAVRPQGPAGGGVAGIRL +AAGDTVLAFGVAPAASLTETGADAAAHPRPAVVVTVTDGEADVLGSAPGSVKVTPLGEYP +AKGRGTGGVRAHRLLKGESGLELGWIGAAPALAASRAGVARALPIEYGRRDGSGVPVDQR +IEAVGAGASPDLVSAPPAEDDAVAVSAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001098.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001098.fa new file mode 100644 index 0000000000000000000000000000000000000000..3ea4fbde3b868cbbb3d4ff271f376c5943f7d79f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001098.fa @@ -0,0 +1,107 @@ +>PROKKA_01311 +MTDDGAPRGPGRGHDDGPRRRRGPDLSPAARRAVAAMLGLAALRAAGWILLAESLARLLT +RMAGTLDPEGTAQLFEMLFLPPAPVGPVGAASSFAGALALGAAGVGLRALADAGQRVWGR +RAALGVQVGVRRDLVAHRLASADGSRPRSGADAVLVTHGLQGLDDYYTEVLPALASAAVV +PPVLGAWILTRDPLSALVVLLTVPLVPFFMVLIGRHTQERIDAAQDGLDRLSGHLVELAR +GLPVLVGLRRAGVQRRALERASQRYHAATLGTLRTAFVSGMALELIASLSVAVMAVFIGL +RLVYGQMDLGAGLVVLVLAAEVYLPLRDVGSAYHASEDGREAEGRARAAARAPVPEAARD +ALADPTAAPARAAGPAAAPPGAVHLEDVGVAFGDRRVLQGVDLRAAPGTLTVLGSASGTG +KSTLLHLLAGLLRTTDARVQGSVSGVDPDRTVWVGQHPRLLEPTVGEELDAAAGRALADS +ERAAVLAAVALDGAAHRRPVELSPGELRRVALARALARLSTAGADRRPWLVLLDEPTAHL +DDAAAAAVRAGVVALARAGVPGLALPPCIVVAASHDPALQRAADALVDAQGTPLAPGAAD +GPADPEAAAPAGPEPASPAAVASPVEAEPVPASATSTAPSPAAARRARTRAALRILPWRS +GRLWAGVAWATGTHLSAALLAGLSGWLIVTAAGRPPVLYLLSVIVLVRAFGLSRAVFRYL +DRLATHDAVLGWASRLRLRLWDALGRRPALWGRLSRADGALSVLVADVDALRDAAPRVMV +PVPAAVLAWLVSAGAVALLAPELAAAALVPGALGLVAIPVVVAALDRRQTQAAVRHRAGL +LDRVAAVLAAAPDLHGLGRARAAADRLAEADAALQAPQRRAAWAAGAGRALAVLVSGGTA +LAVALTATQTGTAAAVAAFAVLLVLSWAEPYGALAQSAQELGTLASQARAAADLMGEDEP +GTAVPDAADPGRASATPDPTSAPMSADPEPAAPVRVTGLALRGAAVRFEGADAPLWSGVD +LCVEPGQTAVVTGPSGAGKSTLLAVLLGFQPLAEGAYLLRTEADGRRVEAPADAAALARV +AWTPQDALLFDSSLRGNLALARDPEDAPDDAELTAVLGRVGLGPWLAAAPEGLDTPVGAG +GRVLSGGQRQRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRAALAGRIAVVVTH +DERLAAEADVRLRLGVSPPRPSRGRPRPAAR +>PROKKA_01034 +MTPAALRALPALLALAVLRALGWILLAESLARLITGLAMTLDPEDSARLLDLLFHPPAPV +GPVPAAQTLSGPVLLGAAGVALRALAEAGQRVVGRRAALGAQQQVRAAVVAQRLAAADGG +RPRSGADAVVVTHGLKSLDDHYTEALPALAATAVVPAALGVWILTHDLVSAVVAAITLPL +VPLFMILVGRHTQERIDAAQDGLDRLAGHLLELARGLPVLVGLHRAGVQRRALQEVSQRH +HAATMVTLRTAFLSGLALELIASLSVAVMAVFIGLRLVNGQMALLDGLVVLILAAELYLP +LREVGAAFHASEDGREAESRARAAADAPVPAPVLDTLGPASGPDRDGGVLVQDLSVRMAG +RQVLEGLDLTAPPGHLTALAGPSGTGKSTVLRLLAGLLRQDAAEATGRVAGVDTERTLWI +GQHPVLTERTVAGELDLAAGGALPGPVRSAVLAAVALEGLQERDPADLSPGECRRVAVAR +LLARLHAADGTGPWLVLLDEPTAHLDGAVAAVVVETLAALPSGAVPGLSTPQCTVLAASH +DPTLLTAADAIVRLAPGAGPTAGSPATAMPVAAAQGRARPEPVTPRQVSLRAGLRLLPWR +QPKLWAGIGWAAGTHVSAALLAALSGWLIVTASTRPPVLYLLAVIVLVRGFGLSRAVFRY +LDRLTTHDAVFGWATELRLRLWDALGRQPRLWGRVGRTDGALSLLVSDVDAFRDAVPRVL +VPAPAALLAWLATAALTWALAPELAVVALVPGAVALVVIPALVAVLDRRQTAAQVRGQGA +LVDRVAAVLNAAGDLRGLGLTEPALRGLAVLDDRLQRPRRRAAWAAGGGRALAVAASGGI +AVAAAAAAAHTGTSAPVAALVVLLALSWAEPYGALAAAAQHWGTLADRARATGELLGPEE +GGAAAAPPEPAEAAEPEARVCRLRLVEAAFAHPGAPPLWTDLELDLAPGDVAVVTGPSGS +GKSTLLAVLLGFLPLTAGRYTLETVPPTPQPDPVRPDATALARVAWTPQDALIFDSTARG +NLALARGVADAPSDAELTAALELVGLGPWLAAAPQGLDTRVGPGGQRLSGGQRQRLAVAR +ALVARADVVLLDEPTAHVDADEARALITDLRRALADRIVVIVTHDGRLLEDGDVPVRVGC +>PROKKA_01581 +MTDDGAPRGPGREHDDGPRRRRGPDLSPAARRAVAAMLGLAALRAAGWILLAESLARLLT +RMADTLDPEGTAQLFEMLFLPPAPVGPVGAASSFAGALALGAAGVGLRALADAGQRVWGR +RAALGVQVGVRRDLVAHRLASADGSRPRSGADAVLVTHGLQGLDDYYTEVLPALASAAVV +PPVLGAWILTRDPLSALVVLLTVPLVPFFMVLIGRHTQERIDAAQDGLDRLSGHLVELAR +GLPVLVGLRRAGVQRRALERASQRYHAATLGTLRTAFVSGMALELIASLSVAVMAVFIGL +RLVYGQMDLGAGLVVLVLAAEVYLPLRDVGSAYHASEDGREAEGRARAAARAPVPEAARD +ALADPTAAPARAADPAAAPRRAVVLEDVGVAFGDRRVLQGVDLRAAPGTLTVLGSASGTG +KSTLLHLLAGLLRTTDARVQGSVSGVDPERTVWVGQHPRLLEPTVGEELDAAAGRALADS +ERAAVLAAVALDGAAHRRPVELSPGELRRVALARALARLSTAGADRRPWLVLLDEPTAHL +DDAAAAAVRAGVVALARAGVPGLALPPCIVVAASHDPALQRAADALVDAQGTPLAPGAAD +GAADPEAAAPAGPEPASPAAVASPVEAEPVPASATSTAPSPAAARRARTRAALRILPWRS +GRLWAGVAWATGTHLSAALLAGLSGWLIVTAAGRPPVLYLLSVIVLVRAFGLSRAVFRYL +DRLATHDAVLGWASRLRLRLWDALGRRPALWGRLSRADGALSVLVADVDALRDAAPRVMV +PVPAAVLAWLVSAGAVALLAPELAAAALVPGALGLVAIPVVVAALDRRQTQAAVRHRAGL +LDRVAAVLAAAPDLHGLGRARAAADRLAEADAALQAPQRRAAWAAGAGRALAVLVSGGTA +LAVALTATQTGTAAAVAAFAVLLVLSWAEPYGALAQSAQELGTLASQARAAADLLGEDEP +GTAVPDAADPGRASATPDPTSAPMSADPEPAAPVRVTGLALRGAAVRFEGADAPLWSGVD +LRVEPGQTAVVTGPSGAGKSTLLAVLLGFQPLAEGAYLLRTEADGRRVEAPADAAALARV +AWTPQDALLFDSSLRGNLALARDPEDAPDDAELTAVLERVGLGPWLAAAPEGLDTPVGAG +GRVLSGGQRQRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRAALAGRIAVVVTH +DERLAAEADVRLRLGVSPPRPSRGRPRPAAR +>PROKKA_01477 +MTDRPPRRRGRVRAGRGPGPGLDRRARRAVGVMALLAGVRALGWILLAESLARLLTSLAM +TLDPEASAQLFQLLFMPPAPVGPVGPVADVAGVVVLGAAGVVLRALADQGQHVAGRRAAL +GAQVGIRRELVAHRLAATDGTRPRSGADAVLVTHGLAGLDDYYTEVLPALASAAVVPPML +GVWILTRDGVSAAVVLLTVPLIPFFMVLIGRHTQERIAAAQDGLDRISGQLLELARGLPV +LVGLRRAGVQRRALEKASERYHAATLGTLRTAFVSGLALELIASLSVAIMAVFIGVRLVY +GQMDLYSGLVVLVLAAEVYLPLREVGSAYHSSEDGRAAAERAAAAVAEPVPTPALASLAW +PGPETGQDHGTDGGMDDGMDDRTPAAGTVLLRDVSVSRGPRPVVRGADLTLRPGGLTVLG +SASGAGKSTLLHLLAGVLRTPDVAVSGTVAGVDSDRTLWVGQHPRFLEATVDAELDAAAG +GALAAPVRREVLRAAALADFGARAPHELSPGEQRRVALARAMSRLAADRTAVETRPWLVL +LDEPTAHLDDASAAVVRATVGALARGAVPGLPTPPAAVLAASHDPVLQRAADALVDVEGR +PLAPGADAAPYADPDAAGPPLAAGAPDDAGPGDAPDAPRGEGSEGRPSLRAVLAVLPWGA +PRLWAGVGWATLTHLAAALLAGLSGWLIVTAAGRPPILYLLSVIVLVRGFGLFRAVFRYA +DRLATHDAVLRWASELRLRLWDAMGRRPALWSRLSRADGALSVLLSDVDALRDAAPRVLV +PVPAAVLAWAVTALLIGGLAPELAVTALVPGAVGLLVIPVVVAALDRRDTLLTARRRAAL +LDRVSAVLGAAPDLHGLGRTREAAAALTAWDEDLQRPQRRAAWVAGLGRALAVLASGGAA +LAAALTATQTGTSTPVAAFVVFLALSWAEPLGALAQAAQQTGTLVDQARQAAGLLGVEDE +AASGATSAAPDEAAASAAGSSAPAGRITGVRLEDAAYAYPGSTRVLWSGLDVALESGQTA +AVTGPSGAGKSTLLAVLLGFLTPTAGRHLLTVERDGVSREAPADPAALARVAWTPQDALV +FDSTVRGNLALARDADDAPTDAELADTLRLVGLGRWLDAAPDGLDTPVGPGGDRLSGGER +QRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRRALAGRIAVVATHDPRVAAAAD +VRVRLGGDAAGHP +>PROKKA_01269 +MSPSRPAAPAVERSASAAGPHPGRTRRARPPMTPAARRALPALLALAVLRALGWILLAES +LARLITGLAMTLDPEDSARLLELLFHPPAPVGPVPAAQTLSGPVLLGAAGVALRALAEAG +QRVVGRRAALGAQQQVRAAVVAQRLAAADGGRPRSGADAVLVTHGLKSLDDHYTEALPAL +AATAVVPAALGVWILTHDLVSAVVAAITLPLVPLFMILVGRHTQERIDAAQDGLDRLAGH +LLELARGLPVLVGLHRAGVQRRALQEVSQRHHAATMVTLRTAFLSGLALELIASLSVAVM +AVFIGLRLVNGQMTLLDGLVVLILAAEVYLPLREVGAAYHASEDGREAESRARAAADAPV +PAPVLETLAPASGPDRDGGVVIRDLSVRLAGRQVLGGLDLSALPGRLTALAGPSGTGKST +VLRLLAGLLRQDAAEATGRVAGVDTERTLWIGQHPVLTERTVAGELDLAAGGALPGPVRS +AVLAAVALEGLQERDPADLSPGECRRVAVARLLARLHAADGTGPWLVLLDEPTAHLDGAV +AAVVVETLAALPSGAVPGLSTPQCTVLAASHDPTLLTAADAIVRLAPGAGPTAGSPATAM +PVAAAQGRARPEPVTPRQVSLRAGLRLLPWRQPKLWAGIGWAAGTHVSAALLAALSGWLI +VTASTRPPVLYLLAVIVLVRGFGLSRAVFRYLDRLTTHDAVFGWATELRLRLWDALGRQP +RLWGRVGRTDGALSLLVSDVDAFRDAVPRVLVPAPAALLAWLATAALTWALAPELAVVAL +VPGAVALVVIPALVAVLDRRQTAAQVRGQGALVDRVAAVLNAAGDLRGLGLTEPALRGLA +VLDDRLQRPRRRAAWAAGGGRALAVAASGGIAVAAAAAAAHTGTSAPVAALVVLLALSWA +EPYGALAAAAQHWGTLADRARATGELLGPEEGGAAAAPPEPAEAAEPEARVCRLRLVEAA +FAHPGAPPLWTDLELDLAPGDVAVVTGPSGSGKSTLLAVLLGFLPLTAGRYTLETVPPTP +QPDPVRPDATALARVAWTPQDALIFDSTARGNLALARGVADAPSDAELTAALELVGLGPW +LAAAPQGLDTRVGPGGQGLSGGQRQRLAVARALVARADVVLLDEPTAHVDADEARALITD +LRRALADRIVVIVTHDGRLLEDGDVPVRVGC diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001099.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001099.fa new file mode 100644 index 0000000000000000000000000000000000000000..d60e4878846b0c1dbd34fe1ad145e5ee636703e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001099.fa @@ -0,0 +1,35 @@ +>PROKKA_01312 +MAEALPVFWYVIIAVLWLGYLALEGFDLGAGMLMQAWARDERRRRVLLNVIGPVWEGNEV +WLITAIGAMFAAFPFWYASLLSTLYLPMLLLLLALILRAVSIEYRGKARTDRTRAVWTWC +LALGSFTAAFVVGAFLALTTTGLPIDANGDRVGGPFAWLNGWAVLGGLAVVGFSIAQAWA +FIGLKTDGAPRQAAARFLSRWTPVALAPLLVWAGAVLLRGDRPWTWALLAAGVAAAAGSV +VAARRGREGLALAGLTLFLVAAWSAVMIVQFPVLQPSTVDPAFDLTAEIAASGPYTLGIM +AVVSLVFVPIVLAYSAWSYWVFRRRVRETHIPEPHAVEPV +>PROKKA_01035 +MAEVLPVYWYVIIAVLWLGYLALEGFDLGVGMLVRFWARDEPRRRVLLNIIGPVWEGNEV +WLITAVGAMFAAFPFWYAAVFSTLYLPMLVMLFGLILRAVSIEYRGKAATDAGREIWTWT +LGIGSFLAAFMAGVLLVLTTTGLPLDANGDRVGGPFVWVTGPALLGGLAVVGFSLAQAWA +FIGLKTDGAPRRSAARFLSTWTPLAVLPLLVWAGLVVARGDRPWTWALLVLAVVAVAASV +VAARAGREGLAFTSLTLVLVLAWTAIMVTQYPVVLPSTVDPQFSLTAQLASSGPYTLGLM +AVISLIFVPIVLAYTGWSYWMFRRRLADTHIPEAHLVEPL +>PROKKA_01580 +MAEALPVFWYVIIAVLWLGYLALEGFDLGAGMLMQAWARDERRRRVLLNVIGPVWEGNEV +WLITAIGAMFAAFPFWYASLLSTLYLPMLLLLLALILRAVSIEYRGKARTDRTRAVWTWC +LALGSFTAAFVVGAFLALTTTGLPIDANGDRVGGPFAWLNGWAVLGGLAVVGFSIAQAWA +FIGLKTDGAPRQAAARFLSRWTPVALAPLLVWAGAVLLRGDRPWTWALLAAGVAAAAGSV +VAARRGREGLALAGLTLFLVAAWSAVMIVQFPVLQPSTVDPAFDLTAEIAASGPYTLGIM +AVVSLVFVPIVLAYSAWSYWVFRRRVRETHIPEPHAVEPV +>PROKKA_01476 +MTEALPVYWFVIIAVLWLGYLALEGFDLGVGMLMQAWARDERRRRVLLNIIGPVWEGNEV +WLITAIGAMFAAFPFWYAALLSTLYIPMLLLLFALILRAVSIEYRGKAQTDRVRGIWTWC +LAVGSFLAAFIVGAMLALTTTGLPLDAHGDRVGGPSAWLNGWAVLGGLAVVGFSIAQAWA +FIGLKTDGAPRVAAARFLRTWTPVAVLPMLVWALAVLVRGDRPGAWILLLLALAAVLVSV +LAARAGREGVALAGLTGFAAATWSAVMVAQFPVLTPSAVDRAYDLTAQVSSSGSYTLGVM +AVVSLVFVPIVLAYSAWSYWVFRHRVKETHIPESHIVEPV +>PROKKA_01270 +MAEVLPVYWYVIIAVLWLGYLALEGFDLGVGMLVRFWARDEPRRRVLLNIIGPVWEGNEV +WLITAVGAMFAAFPFWYAAVFSTLYLPMLVMLFGLILRAVSIEYRGKAATDAGREIWTWT +LGIGSFLAAFMAGVLLVLTTTGLPLDANGDRVGGPFVWVTGPALLGGLAVVGFSLAQAWA +FIGLKTDGVPRRSAARFLSTWTPLAVLPLLVWAGLVVARGDRPWTWALLVLAVVAVAASV +VAARAGREGLAFTSLTLFLVLAWTALMVTQYPVVLPSTVDPQFSLTAQLASSGPYTLGLM +AVISLIFVPIVLAYTGWSYWMFRRRLADTHIPEAHLVEPL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001101.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001101.fa new file mode 100644 index 0000000000000000000000000000000000000000..21500015b46039d723c0fa6b901d296a98ff0bad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001101.fa @@ -0,0 +1,35 @@ +>PROKKA_01316 +MTNVSGNASYEYSRAALLAVTEVEAPLEVTSDDLDERLADVLRRLKLPPHLLQRVAGVRA +RRNWDASQDFQEAAAQAGTAALAAAGIGPERVGLLINTSVTRATLEPSVAVRIHHMMGLP +TSATNFDITNACLGFVNGLMLASTLVDAGQVDYAVVVASEDASKVQDATVENLHASTTNR +GNFMEQFASLTLGCGAAAAVVGSIEDHPDAHRIVRGITRAGTDHHDLCVGDHRGMYTDST +ALLNDGLELVMDAWNDTPAEWAWKDADRFITHQVSQLHTNAISESAGLPLDRIPTTFPVL +GNVGPASLPITLVREMDELSAGDTVVCLGVGSGLNTAMLEIQW +>PROKKA_01037 +MTNVSGNASYEYSRAALLAVTEVEAPVEVTSQDLDDQLAEVLTRLRLPGSLLERVAGVRS +RRNWDETEDFQEAAARAGVAALEQAGVPRERVGLLVNTSVTRATLEPSVAVRIHHLMGLP +TSATNFDITNACLGFVNGLMLASTLVDAGQIDYAVVVAAEDASKVQAATVANLHAETTHR +GNFMEQFASLTLGSGAAAAVVGRIEDHPDAHRIVRGITRAGTDHHGLCVGDHHGMYTDST +ALLKDGLELVMDAWHDVPAEWAWPQADRFITHQVSQMHTDAIAESAHLDPARIPTTFPTL +GNVGPASLPITLVREMDALEDGDTVVCLGVGSGLNTAMLEIEW +>PROKKA_01576 +MTNVSGNASYEYSRAALLAVTEVEAPLEVTSDDLDERLADVLRRLKLPPHLLQRVAGVRA +RRNWDASQDFQEAAAQAGTAALAAAGIGPERVGLLINTSVTRATLEPSVAVRIHHMMGLP +TSATNFDITNACLGFVNGLMMASTLVDAGQVDYAVVVASEDASKVQDATVENLHASTTNR +GNFMEQFASLTLGCGAAAAVVGSIEDHPDAHRIVRGITRAGTDHHDLCVGDHRGMYTDST +ALLNDGLELVMDAWNDTPAEWAWKDADRFITHQVSQLHTNAISESAGLPLDRIPTTFPVL +GNVGPASLPITLVREMDELSAGDTVVCLGVGSGLNTAMLEIQW +>PROKKA_01472 +MVQVPHVSGNASFEFSRAALLSVTEVQAPLEVTSDDLDEQLADVLTRLRLPRHLLERVAG +VKVRRAWDAQKDFQQAAAEAGTAALAAAGVAPGQVGLLVNTSVTRATLEPSVAVRIHDLM +GLPTSATNFDITNACLGFVNGLMLASTMVDAGQIDYAVVVAAEDASKVQASTVANLHAET +TVRGNFMEQFASLTLGSGAAAAVVGRTDEHPDAHRILRGITRAGTDHHQLCVGDHNGMFT +DSNALLKDGLELVMDAWHDVPAEWGWDHAARYVTHQVSQMHTDAISESAGIPLEKLPTTF +PVLGNVGPASLPITLVREQDSLRRGDAVVCLGVGSGLNTAMLEIQW +>PROKKA_01272 +MTNVSGNASYEYSRAALLAVTEVEAPVEVTSQDLDDQLAEVLTRLRLPGSLLERVAGVRS +RRNWDETEDFQEAAARAGVAALEQAGVPRERVGLLVNTSVTRATLEPSVAVRIHHLMGLP +TSATNFDITNACLGFVNGLMLASTLVDAGQIDYAVVVAAEDASKVQAATVANLHAETTHR +GNFMEQFASLTLGSGAAAAVVGRIEDHPDAHRIVRGITRAGTDHHGLCVGDHHGMYTDST +ALLKDGLELVMDAWHDVPAEWAWPEADRFITHQVSQMHTDAIAESAHLDPARIPTTFPTL +GNVGPASLPITLVREMDALEDGDTVVCLGVGSGLNTAMLEIEW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001102.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001102.fa new file mode 100644 index 0000000000000000000000000000000000000000..d278abf9b876b64d54a397b753ba9b1616925449 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001102.fa @@ -0,0 +1,89 @@ +>PROKKA_01317 +MPQIPAAPAVLPPADRLPGWDPAWSRLVEIRSAADPEGTVRTLHVADTGPVLAAAGAEIV +GTIVAVHGNPTWSWLWRSLLAETVRRARRGMAAWRVVAPDQLDMGFSERLAHTGSPSASS +MGRADDTYRTLGGRIADLDALLAALGLRDLAATGHPLITLGHDWGGVVSLGWAARHPELV +AGVATLNTAVHQPEGAPIPAPLQAALAGPVLPASTVTTDAFLSVTTSLATPALDRETRAA +YHLPYDTAARRGGVGGFVADIPADPGHGSHPELQRVGEDLAALGRTDVPALILWGADDPV +FLDRYLDDLRDRLPHARVHRYEGAGHLLVDDRDITAPLLQWAQLLRAGQLSDPASGLPGP +VPHATADPGLEVDLGEEPGAREPGMVRLWDHLRDWGAPGSDHREYTALVDMAGAQAGRSL +VGTARRPVAVTWGELQEMVSAIATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLRVGAV +AVVADQGLGVKGMTRAMKSARPRWIIGRTPGLTLARAQSWPGTRISVTEPGAAQRRLLDV +SDSLYAMVDRHRDPATGDAVDEHGTVLPEPALDADAAVLFTSGSTGPAKGVVYTHERLGR +LVAMISRTLGIRPGGSLLAGFAPFALLGPALGAASVSPDMDVTKPATLTARSLADAAIAG +QSTVLFASPAALANVVATADGLDAARRDALDAVRLVLSAGAPVHPQLMRQVRDLMPNAEV +HTPWGMTEGLLLTDIDGETVQRLRGADDEGVCVGTALPTVSLAIAPLLEDGTAEDLILDP +AQGHGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADIGHFDAEGRVW +LEGRLQHVITTPEGPLGPGGPEKTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVPATRP +ARRAGQHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRARVAR +WAEGVLAGGRAGAL +>PROKKA_01038 +MPQIPAAPAALPPADRLPGWDPAWSRLVEIRSAADPEGTVRTLHVADTGPVLAAAGAEIV +GTIVAVHGNPTWSWLWRSLLAETVRRARRGMAAWRVVAPDQLDMGFSERLAHAGYPSAAS +MGRAGDTYRTLGGRIADLDALLAALGLRDLAATGHPLITLGHDWGGVVSLGWAARHPELV +AGVATLNTAVHQPEGAPIPAPLQAALAGPVLPASTVTTDAFLSVTTSLATPALDRETRAA +YHLPYDAAARRGGVGGFVADIPADPGHGSHPELQRVGEDLASLGRTDVPALILWGADDPV +FLDRYLDDLRDRLPRARVHRYEQAGHLLVDDRDITAPLLQWAQLLRGGQLSDPASGLPGP +VPHATTDAAADPGLEVDLGEEPGARDPGVVRLWDHLRDWGAPGSDHREYTALVDMAGAQA +GRSLVGTARRPVAVTWGELQEMVSAIATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLR +VGAVAVVADQGLGVKGMTRAMKSARPRWIIGRTPGLTLARAQSWPGTRISVTEPGAAQRR +LLDVSDSLYAMVDRHRDPAAGDAVDEHGTVLPEPALDADAAVLFTSGSTGPAKGVVYTHE +RLGRLVALISRTLGIRPGGSLLAGFAPFALLGPALGAASVSPDMDVTQPATLTAQKLADA +AIAGQSSVLFASPAALANVVATADGLDAPQREALDAVRLVLSAGAPVHPQLMRQVSDLMP +NARVHTPWGMTEGLLLTDIDGDEVQRLRTADDAGVCVGSALPTVSLAIAPLLEDGSADDV +ILDPARGHGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADVGHFDAE +GRVWLEGRLQHVITTPEGPVGPGGPEKTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVP +ATRPARRPGHHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRA +RVADWAEAVLAGGKAGAL +>PROKKA_01575 +MEIRSAADPEGTVRTLHVADTGPVLAAAGAEIVGTIVAVHGNPTWSWLWRSLLAETVRRA +RRGMAAWRVVAPDQLDMGFSERLAHPGHPAAASMGRDGDTYRSLGARIEDLDALLETLGL +RDLAATGHPLITLGHDWGGVVSLGWAGRNPELVDGVATLNSAVHHPEGAPIPAPLQAALA +GPVLPASTVLTDAFVSVTTSLAKPALASDVRAAYHLPYETADRRGGVGGFVADIPAEPSH +GSHAELRRVWEGVSALGRAGTPALILWGADDPVFLDRYLDDLRDRLPQARVHRYEEAGHL +LVDDRDVTAPLLQWAQLLRAGQLDDPGSGLPGPVPHAPAASPADEDGLHVDLGEHAAPAG +DDVARLWDHLRDWGAPGSEHREYTALVDMAGAQTGRSLVGGARRPVAVSWGELQETVSAI +ATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLRVGGVAVVADQGLGIAGMTRAMKSARP +RWIIGRTPGLTLARAQSWPGARISVTEPGAAQKRLLDVSDSIYAMIERHRDPAVGEPVDE +HGSPLPEPALAADAAVLFTSGSTGPAKGVVYTHERLGRLVAMISRTLGIRPGGSLLAGFA +PFALLGPALGAASVSPDMDVTKPATLTARSLADAAIAGQSTVLFASPAALANVVASADGL +DAARRDALDAVRLVLSAGAPVHPQLMRQVRDLMPNAEVHTPWGMTEGLLLTDIDGETVQR +LRGADDEGVCVGTALPTVSLAIAPLLEDGTAEDLILDPAQGHGVLGEIVVSAPHLKDRYD +ALWHTDQQSKRDGLWRRDGRVWHRTADIGHFDAEGRVWLEGRLQHVITTPEGPLGPGGPE +KTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVPATRPARRAGQHRDGRPKQGLAPTALA +SAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRARVARWAEGVLAGGRAGAL +>PROKKA_01471 +MPRIPAAPAALPPFDQLPGWDPDWSRLVTIRSAADLPGVERTLHVADNGPQLAALGAELA +GTILAVHGNPTWSYLWRALLAETTRRARRGQQAWRVVAPDQLDMGYSERLEHPASPTPSE +MGRARSTYRSLGDRLDDLDALTAALGLTDLAATGHPLITLGHDWGGVVSLGWAGRHRDVV +AGVSTLNTAVHQPPQAKIPAPLQAALAGPVLPASTVSTDAFIAVTTSLAKPSLAPEVRAA +YHLPYPSAERRGGVGGFVADIPVDASHGSHAALEEVSSGVSALGAQGTPALIQWGADDPV +FLDRYLDDLRDRLPAARVHRYEEAGHLLIDDRDVVTPLLTWAQLLTAGLLADPASGLPGP +RPHADDAAPRTSALPLLPEASRGVHVDIADHASEAGSPAGLPRLWDRLEDWGAPDSPMRE +YTALVDMAGAETSRALFGGARRPVAVSWGEFQETVSAIATGLWEAGMRPGDRVSMLVPPG +RDLSAALYAVLRVGAVAVVADQGLGVSGMTRAMKSARPRWVIGKTAGLTLARAQNWPGTR +LSVSTLAAPQRALLDVSDSLYAMVDRHRAPELGVPRDAAGAPLPVPELGADAAVLFTSGS +TGPAKGVVYTHERLGHLVRLIARTLDIRPGASLLAGFAPFALLGPALGAASVSPVMDVTK +PATLTAAALADAAIAGQSSVLFASPAALANVVATAGDLSGEQRTALRQVRQVLSAGAPVH +PALLRQVSALMPEAEVNTPYGMTEGLLLANIDGETIHALRRADDAGVCVGSPLPTVEFRI +APLAEDGTPEEVTLDPAAGHGVLGEFVVSAPHLKDRYDALWFTDHQSKRDGLIRRDGRVW +HRTADVGHFDAEGRVWIEGRAQHVLTTPDRPLAPGGPEGVVDALGPVARSAVVGVGPAGT +QAVVVVVEAAVPAARPPRRAGHHRDGRPKQGLAPTALAASVRSALEPLPVAAVLVADHIP +TDIRHNSKIDRPRVARWAEGVLAGGTVDGL +>PROKKA_01273 +MPQIPAAPAALPPADRLPGWDPAWSRLVEIRSAADPEGTVRTLHVADTGPVLAAAGAEIV +GTIVALHGNPTWSWLWRSLLAETVRRARRGMAAWRVVAPDQLDMGFSERLAHAGSPSAAS +MGRAGDTYRTLGGRIADLDALLAALGLRDLAATGHPLITLGHDWGGVVSLGWAARHPELV +AGVATLNTAVHQPEGAPIPAPLQAALAGPVLPASTVTTDAFLSVTTSLATPALDRETRAA +YHLPYDTAARRGGVGGFVADIPADPGHGSHPELQRVGEDLAALGRTDVPALILWGADDPV +FLDRYLDDLRDRLPHARVHRYEQAGHLLVDDRDITAPLLQWAQLLRGGQLSDPASGLPGP +VPHATADAAADPGLEVDLGEEPGAREPGVVRLWDHLRDWGAPGSDHREYTALVDMAGAQA +GRSLVGTARRPVAVTWGELQEMVSAIATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLR +VGAVAVVADQGLGVKGMTRAMKSARPRWIIGRTPGLTLARAQSWPGTRISVTEPGAAQRR +LLDVSDSLYAMVDRHRDPAAGDAVDEHGTVLPEPALDADAAVLFTSGSTGPAKGVVYTHE +RLGRLVALISRTLGIRPGGSLLAGFAPFALLGPALGAASVSPDMDVTQPATLTAQKLADA +AIAGQSSVLFASPAALANVVATADGLDAPRREALDAVRLVLSAGAPVHPQLMRQVSDLMP +NARVHTPWGMTEGLLLTDIDGAEVQRLRAADDEGVCVGSALPTVSLAIAPLLEDGSAEDV +ILDPARGHGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADVGHFDAE +GRVWLEGRLQHVITTPEGPVGPGGPEKTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVP +ATRPARRPGHHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRA +RVADWAEAVLAGGKVGAL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001106.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001106.fa new file mode 100644 index 0000000000000000000000000000000000000000..ef91c3263852cc8fcb3d11f71ced0bee79cabb86 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001106.fa @@ -0,0 +1,50 @@ +>PROKKA_01321 +MDCKDPRVAADETERPRVTTSTTSGVQDGKETTASEATTTRTRSTAAKKSAATKSATTKG +ATTKGATTRTTATKSAATKTAATPTAKKKATRKPTAAKTTATAKTTAAAKTTAAVKTTAT +KKTATTRGKKATASAASAEQAEDDEEFVEARERTEAADAVEEDVVEDETATEDSDDEDAD +GSDAPERPAMDAEAVTGTKAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDY +LKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHL +LEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAI +TRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQK +YGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVV +AMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD +>PROKKA_01042 +MDCKDPRVAADETERPRVTTSTTSGVQDGKETTASEATTTRTRSTAAKKSAAKKSAATKS +ATTKGATTRTTATKSAATKTAATPTAKKKATRKPTAAKTTATAKTTAAKKTATTGGKKAT +ASAASAEQAEDDEELVQARERTEAADAVEEDVVADETATEDSDDEDADGSDAPERPAMDA +EAVTGTTAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNA +EQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHLLEANLRLVVSLA +KRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIR +IPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPL +GEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPK +TLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD +>PROKKA_01570 +MTTSTTNGAQDAPETTDSGAATTRSRSTAAKKTTAAKSTTAKGTAARKTASSTTAAKSTA +KSAAAKGAATKAAAKTAAADGEAPAKTTTRRTAASKTTAAKSTPTKPAAKTTTRKKAAPA +ATAKGKKATASAAAQAEQDEELADAVERTDAADAVDPDVADVVDGEAKAATEDSDDEDAD +GSDAPDAPAMDQEAVTGTKAGSGQAVAQTKGAFVMDDSEDDAPVQQVVVAGATADPVKDY +LKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQAEASDDYRERRDIQLIIADGRKAKNHL +LEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAI +TRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQK +YGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADVVSFTLLQEQLHSVLDTLSEREAGVV +AMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD +>PROKKA_01466 +MTAGTPTERPRVTTSTTSGKQDGKETAASTTTAAAAKKTTTAAKKKTTAAAAKKPAAAKT +ASGASTAAKKTTAKSTAAQATTTRGATTKKAAADAETEAAPAAAPRKRTSTATSTAKAAP +KKTTRAPKKTASKAVAEEELVEEEDLELDADDVAEQASQDGDDADADGSDAPAAEDLVAT +TEKPAETAAKGAFVMDNSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNAEQEVDLAM +RIEAGLYAEHHFAENPPEDYRLRRDVELIIADGRRAKNHLLEANLRLVVSLAKRYTGRGM +LFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEV +INKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGDSEF +GDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKV +YGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD +>PROKKA_01277 +MDCKDPRVAADETERPRVTTSTTSGAQDGKETTASGATTTRTRSTAAKKSTATKSATTKG +ATTRTTATKSAATKTAATPTAKKKAARKPAAAKTTATAKTTATKKTATTRGKKATASAGS +AEQAEDDEEFVEARERTEAADAVEEDVVEDETATEDSDDADADGSDAPERPAMDAEAVTG +TKAATGQKVAQSKGAFVMDDSEDDAPVQQVVVAGATADPVKDYLKQIGKVALLNAEQEVD +LAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGRKAKNHLLEANLRLVVSLAKRYTG +RGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHM +VEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQKYGREPISLHTPLGEDGD +SEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEI +GKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001108.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001108.fa new file mode 100644 index 0000000000000000000000000000000000000000..4fd6e70ad08e3ce2b9618108dedcc460960438c9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001108.fa @@ -0,0 +1,35 @@ +>PROKKA_01323 +MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM +FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL +AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPQADIVAGLLQMLELR +AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE +RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG +SAPAQEDGPGRPSTGDGD +>PROKKA_01044 +MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM +FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL +AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPEADIVAGLLQMLELR +AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE +RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG +SAPAQEDGPGRPSTDDGD +>PROKKA_01568 +MQDAAPIYTRHDAEAVPPGLALLVTLTGHMDAGRVSRQVRTALREHLEHRTVASFDVDSM +FDYRARRPRMRFDRDRYRDLRLPTLEVQLVEDLIGHPFLLLAGPEPDFRWQAVVEAVLGL +AEEWQVDSLTFLDAAPLPVPHTRRIGVTTHGTRAEAVEGLSTWSPEAEIVSGLLQMLELR +ADEAGIPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASREIEAELE +RQVSGSEEVQQMIAGLERNFDQNAEDQERSLLETEEGLPDGDELASAVEAYLAGRAGPDG +SAPAQEDGPPRPSTDDER +>PROKKA_01464 +MQDPTQLYTRHDAAPGDAVPDGLGVLVTLTGHLDAGHVGRQVGAGLRERLAHRTVARFDV +DQLHDYRARRPRIRFDRERYTDLRMPALDVELMEDLLGHPFLLVAGPEPDMQWGRFTAAL +LGLLQEWEASSATFLDAAPLPVPHTRRIGVTTHGSRADALEGLSTWSPEADVVAGLVQVL +ELRAEEAGLPTAGYTVHVPHYVAEAGYPQAAVAALEYAGASLDLMLPTDELRDAAREVDA +ELERQVAGSPEVQTMITGLEKNYDQNSEGQERSLLESHGELPDGDELASAVEAYLAERDE +SVQPRPTTPAQDDEGPAPSPDPQV +>PROKKA_01279 +MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM +FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL +AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPQADIVAGLLQMLELR +AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE +RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG +SAPAQEDGPGRPSTGDGD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001109.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001109.fa new file mode 100644 index 0000000000000000000000000000000000000000..47dabe8871b232464089d335d21c0c15f92ebfc7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001109.fa @@ -0,0 +1,50 @@ +>PROKKA_01324 +MITLDRPTLTARALEDLTASALVVGVGTGPDGPVLLTDALPAEAATALEASFELLGVRGA +ADEVHRLPGLGGVPVPLLVLAGVGGLDDDGEAADESLRRAAGAAVRSLAGTDAVALALPA +DTPARLAAVAEGAVLGAYAFTAQKSERARAETDTSRPVREVEVVTPLAAADADPVLRRAA +VVGDAVCAVRDLVNTAPSHLYPATFADAVAEDLADSSVSVDVWDEDRLRAEGFGGILAIG +QGSSRPPRLVRIEHAPADAAAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFA +VVRAAAALDVPVKVTGWLALAENMPSGTAIRPSDVITMYGGKTVEVMNTDAEGRVVMADA +LVAATDERPDAVLDVATLTGAQLVALGVRHTGVMGDDALRDEVVAAADAAGELAWGMPLP +EQLRASLTSRVADISNMGDRFGGMMTAATFLREFVDAGRSEGDAAARTPWAHLDIAGPSF +NESAAYGYTPQDATGVMVRTLVGLIEGRAR +>PROKKA_01045 +MITLDRPTLTARALEDLTASALVVGVGTGPDGPVLLTDALPAEAATALEASFELLGVRGA +EDEVHRLPGLGGVPVPLLVLAGVGGLDDDGEASDESLRRAAGAAVRSLAGTDAVALALPA +DTPARLAAVAEGAVLGAYAFTAQKSERARAEADSSRPVRELEVVTPLAAADADPVLRRAA +VVGDAVCAVRDLVNTAPSHLYPATFADAVAEDLADSSVSVDVWDEDRLRAEGFGGILAIG +QGSSRPPRLVRIEHAPADAAAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFA +VVRAAAALDVPVKVTGWLALAENMPSGTAIRPSDVITMYGGKTVEVMNTDAEGRVVMADA +LVAATDERPDAVLDVATLTGAQLVALGVRHTGVMGDDALRDEVVAAADAAGELAWGMPLP +EQLRASLNSRVADISNMGDRFGGMMTAATFLREFVDAGRPQDDDAARTPWAHLDIAGPSF +NESAAYGYTPQDATGVMVRTLVGLIEGRAR +>PROKKA_01567 +MITLDRPTLTARTLEDVSASALVVGVGTGPDGPVLLTDALDAPAASALEASFDLLGVRGA +QDEVHRLPGLGGSPVPMLVLVGVGPLDDDGEVSDEALRRAAGAAVRSLAGTDAVALALPA +DTAQRLSAVAEGASMGAYAFTALKSEKAREEAEKSRPVRGLEFVTALGAEEAEAALRRAA +VLGDAVCAVRDLVNTAPSHLYPGTFADAVAQDLSGSSVSVDVWDEERLTAEGFGGILAIG +QGSSRPPRLVRIEHAPAEAKAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFA +VVRAAAALDVPVKVTGWLALAENMPSDTAIRPSDVVTMYGGKTVEIMNTDAEGRVVMADA +LVAATDERPDAVLDVATLTGAQMVALGTRYTGVMGDDALRTEVVEAADRVGELAWAIPIP +ENQRASLNSRVADISNMGDRFGGMMTAAAFLREFVDAGRTGEEDAPRTPWAHLDIAGPSF +NESAAHGYTPQDATGVMVRTLMGLIEGRGR +>PROKKA_01463 +MISQERPTLIARSLAEVTAPAVVVGVGAGPDGPLLLTDALPDEAAVALESSLELLEVKGR +PDEVHRLPGLSGSRWPLLVLVGLGDLDQDGGADDEALRQASGAAVRSLAGTESVALALPA +DTPSRLAAVAEGAALGAYAFTAFTSAGDTPGRAPVSTVELVTPLPASASEPVLRRAAVIG +DAVCAVRDLVNTPPSHLYPASFADAVVGDLEGTDVDVRVWDEAQLAAEGFGGIVGIGQGS +SRPPRLVRVEHAPAGARAHVALVGKGITFDTGGISLKPPASMMTMKSDMAGAATVFAVVR +AAAALEIPVRVTGWLAMAENMPSDTALRPSDVLTMHGGKTVEVMNTDAEGRVVMADALVA +ATDERPDAVLDVATLTGAQLVALGVRHTGVMGDEALRNEVVAAAGAAGELAWPMPIPEQL +RPSLDSRVADISNMGERFGGMMTAAAFLREFVDAGRPAAERAESPTPWAHLDIAGPSFNE +SAAYGYTPRDATGTMVRTLVGLIAGRAG +>PROKKA_01280 +MITLDRPTLTARALEDLTASALVVGVGTGPDGPVLLTDALPAEAATALEASFELLGVRGA +EDEVHRLPGLGGVPVPLLVLAGVGGLDDDGEAADESLRRAAGAAVRSLAGTDAVALALPA +DTPARLAAVAEGAVLGAYAFTAQKSERARAEADTSRPVRELEVVTPLAAADADPVLRRAA +VVGDAVCAVRDLVNTAPSHLYPATFADAVAEDLADSSVSVDVWDEDRLRAEGFGGILAIG +QGSSRPPRLVRIEHAPADAAAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFA +VVRAAAALDVPVKVTGWLALAENMPSGTAIRPSDVITMYGGKTVEVMNTDAEGRVVMADA +LVAATDERPDAVLDVATLTGAQLVALGVRHTGVMGDDALRDEVVAAADAAGELAWGMPLP +EQLRASLNSRVADISNMGDRFGGMMTAATFLCEFVDAGRPEGDAAARTPWAHLDIAGPSF +NESAAYGYTPQDATGVMVRTLLGLIEGRAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001110.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001110.fa new file mode 100644 index 0000000000000000000000000000000000000000..e874000929680611a3f497cf92b3a867f43496ee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001110.fa @@ -0,0 +1,45 @@ +>PROKKA_01325 +MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH +AAEVADETRNAAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK +LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG +VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE +TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI +YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA +EEEFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL +IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS +>PROKKA_01046 +MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH +AAEVADETRNAAKFGINATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK +LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG +VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE +TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGSI +YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA +EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL +IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS +>PROKKA_01566 +MADSATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKLGGTCLHWGCIPTKAYLH +AAEVADETRNSAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLTGLLKMRKVQVIEGEGK +LVSKNEVEVDGTRYKAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG +VIGSEFASLWNSFGVEVTIIEGLETLVPNEDPAIIKVLAREFKKKGIKTNLGTFFDKVEE +TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGITMDRGFVITDERLHTGVGSI +YAVGDIVPGLQLAHRGYQQGIFVAEEIAGNSPMVVEDINIPKVTFTEPEIMSVGYTQPKA +EEKFGKDNVEVVEYNLAGNGKSSILGTGGIIKMVRQKNGPIVGVHGIGKRIGEQIGEAQL +IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHG +>PROKKA_01462 +MADSATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH +AAEVADETRNAAKVGVNATLESVDMAKVRDYKDGIVSGKHKGLAGLLKMRKVQVIEGAGK +LVSKNEVEVDGTRYTAENIVLASGSVSKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG +VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE +TDSGVKVTLADGKVFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI +YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA +EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMVRQKNGPIVGVHGIGKRIGEQIGEAQL +IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS +>PROKKA_01281 +MADKATAQEFDVLVLGGGSAGYAAALRSVQYGKSVALVEKSKVGGTCLHWGCIPTKAYLH +AAEVADETRNAAKFGVNATLESVDMAKVRDYKDGIVAGKHKGLAGLLKMRKVQVIEGEGK +LVSKNEVEVDGTRYTAENIVLASGSVAKTMGLPISKKIMTSTEALELDYTPKSAIVLGGG +VIGSEFASLWNSFGVDVTIIEGLKTLVPNEDPAIIKVLEREFKKKGIKTNLGTFFDKVEE +TDSGVKVTLADGKEFEAEVCLVAVGRGPNTEGLGYEEQGVKMDRGFVLTDERLHTGVGNI +YAVGDIVPGLQLAHRGFQQGIFVAEEIAGNKPMVVEDINIPKVTFTEPEIMSVGYTQPKA +EEKFGKDNVEVAEYNLAGNGKSSILGTGGIIKMIRQKNGPIVGVHGIGKRIGEQIGEAQL +IVNWEAYPEDVAQFVHAHPTQNEALGEAAMALFGHPLHS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001112.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001112.fa new file mode 100644 index 0000000000000000000000000000000000000000..000afa0aa960b94263990bcc310e31020b3afa44 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001112.fa @@ -0,0 +1,15 @@ +>PROKKA_01327 +MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN +HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ +>PROKKA_01048 +MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN +HMKLGVKFLIGVIVFVAALTGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ +>PROKKA_01564 +MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN +HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ +>PROKKA_01460 +MEILHNVVVAIHIVSAAAIVGGWFAHFKNPTVTVSQWWGALGMILSGVVLFGWAMTGEPN +HMKLGIKFLIGVIVFIAALLGRRKANRGEVVPKGLAHAVGGMGLVNILVAVLWS +>PROKKA_01283 +MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN +HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGMAHAVGGLGLVNILVAVLWQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001122.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001122.fa new file mode 100644 index 0000000000000000000000000000000000000000..ed75294a5269d60c2e9fccc43d2811e323f8cc81 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001122.fa @@ -0,0 +1,15 @@ +>PROKKA_01339 +MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNETADAWDERDDD +WDSRPVDDAS +>PROKKA_01059 +MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNEAADAEDARDDD +WDSRPVDDAS +>PROKKA_01553 +MSEKSEYWYNVRTQQVEEGAQSDWSQLLGPFGTREEAQGAMSRVQANNEAADAADERDDN +WDNNPFNDAD +>PROKKA_01449 +MTDTHEPGSGYWFNVRTHQIEEGPQSDWKELLGPYQTRQDAENALARVQARNEAADAEDA +HDDAWDASPLNDAS +>PROKKA_01294 +MTETSEFWYNVNTHQVEVGAQSDWSQLLGPFGTREEAQAAMDRVRANNEAADAEDARDDD +WDSRPVDDAS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001125.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001125.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a191f130519a309257737f8bd96502f75162159 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001125.fa @@ -0,0 +1,105 @@ +>PROKKA_01343 +MTVSADARPDAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG +AYDFWSKAKAAGVKPIIGLEAYVAPGQQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL +SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ +YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH +EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT +LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE +LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF +ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV +MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA +KGLEGLKRQWGVHAAGVIMSSVPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG +LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM +MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL +IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA +LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE +CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREEKGSYTGFGD +FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD +LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD +VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY +APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV +MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG +>PROKKA_01063 +MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG +AYDFWSKAKAAGVKPIIGLEAYVAPGHQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL +SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ +YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVVTDLRRLAKDLGLPFVATNDLHYTH +EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT +LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE +LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF +ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV +MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA +KGLEGLKRQWGVHAAGVIMSSAPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG +LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM +MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL +IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA +LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE +CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGRENEGSYTGFGD +FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD +LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD +VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY +APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV +MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG +>PROKKA_01549 +MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAERLGMDSLAITDHGYLFG +AYDFWSQAKSAGIRPIIGLEAYVTPGHQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL +SENTAGMHNLFRMSSIASLDSVYAKWPRLDRELLSQYSSGLIATTGCPSGEVQTRLRLGQ +YDEAVAAAAEFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH +EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT +LLIAERCDVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE +LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF +ERFLNPDRVSMPDFDVDFDDRRRPEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV +MDQPFSLGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA +KGLEGLKRQWGVHAAGVIMSSEPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG +LRNLTIISDAIENVKANQGVELDLETLDVDDAASYDLLARGDTLGVFQLDGGPMRSLLKM +MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL +IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA +LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE +CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREDKGAYTGFGD +FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVSQKRKEDHGEFTFD +LFALGGPQEDESDAADGVAVPDLPEWAKKEKLAYEREMLGLYVSDHPLQGLDGVLAQHAD +TQITRVLDDDGPADGSQVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY +APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRISMPSFKATEQV +VGQLADVLRTHEGSSEVRLSLVGQRGTQEFQLGPQFRVNPNPALFGDLKILLGPACLS +>PROKKA_01445 +MSVQQETTAEATRDGGFVHLHTHTEYSMLDGAAKLDELFAEANRLGMDSLAITDHGYLFG +AFDFWKKATDAGIKPIIGLEAYLTPGQQHRSDKEKIRWGEPHQRGDDVSGGGAYTHMTML +AESTQGMHNLFRMGSIASLDSVYAKWPRIDRELLSQYSSGLIATTGCPSGEVQTRLRLGQ +YKEAVEAAAEFRDIFGRDNFYCEVMQHGLDIEKRVVEDLRRLAKDLGLPFVATNDLHYTH +EHDAKAHEALLAIQSGSKLNEPTYDQGGSRFAFSGTDYYLKSPRQMRELFAELPEACDNT +LLIAERCETSFDTSANYMPRFPTPEGEDETSWLIKEVAKGLAYRYPEGVPDHVRKQADYE +LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLRHGLIF +ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV +MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPEAKRYAEAGEFRELVAADPVAKQVFETA +KGIEGLKRQWGVHAAGVIMSSHPVIDVIPIMRRLQDGQVITQFDYPTAEGLGLIKMDFLG +LRNLTIISDAIENIRANRGVDLDLEHLDVDDAESYALLARGDTLGVFQLDGGPMRALLKM +MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGLQEITPIHPELAEPLKDILDTTYGL +IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEGAVKA +LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE +CRHMGITVLPPDVNESFLNFTPVGDDIRFGMGAVRNVGGNVVKGMVQAREEKGLYTGFGD +FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVQQKRKEDHGEFTFD +LFALGGAADAADDSDASDGVAVPDLPEWPKKERLAFEREMLGLYVSDHPLQGLDGVLSQF +ADTQITRILDDDGPADGAHVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSLDVMFFGQ +VYAPIAMMLAEDLVVAVKGRVQRRDDGSVVLSAMELAIPELTDATGGPVRITMPAFKATE +RVVGQLGDVLRTHEGSTEVRLSLTGQRGVQEFQLGPQYRVTPNPALFGDLKILLGPSCLG +>PROKKA_01298 +MTVSADARADAVKDGGFVHLHTHTEYSMLDGAAKLDDLFAEAQRLGMDSLAITDHGYLFG +AYDFWSKATAAGVKPIIGLEAYVAPGQQHRTDKEKTRWGEPHQRGDDVSGGGAYTHMTLL +SETTEGMHNLFRMGSIASLDSVYAKWPRLDRELLSQYSKGLIATTGCPSGEVQTRLRLGQ +YREAMQAASDFRDIFGKDNYYCEIMHHGLDIERRVMTDLRRLAKDLGLPFVATNDLHYTH +EHDAKAHEALLALQSGSKLNEPSYDQGGSRFAFSGTEYYLKSPRQMRELFAELPEACDNT +LLIAERCEVEFDTKANYMPVFPTPEGEDETSWLIKEVASGLAYRYPDGVPDHVRKQADYE +LDVIISMGFPGYFLVVADFINWAKENGIRVGPGRGSGAGSMVAYALRITDLDPLKHGLIF +ERFLNPDRVSMPDFDVDFDDRRRSEVIDYVTRKYGDERVTMIVTYGTIKTKQALKDSARV +MDQPFSMGESLTKALPPAVMAKDIPLKDIEDPAAPRYGEAAPFRELIATDPVAKEVFETA +KGLEGLKRQWGVHAAGVIMSSVPVIDVIPIMRRLQDGQVITQFDYPMAESLGLIKMDFLG +LRNLTIISDALENVKANQGVDLDLETLDVDDPAAYELLARGDTLGVFQLDGGPMRSLLKM +MRPDNFEDISATIALYRPGPMGANSHTNYALRKNGQQEITPIHPELEEPLREILDTTYGL +IVYQEQVMAIAQKVAGYSLGQADILRRAMGKKKKSELDKQYEAFHQGMLDRGYSEAAVKA +LWDILLPFSDYAFNKAHSAAYGLVSYWTAYLKAHYPAEYMAALLTSVGDDKDKLAMYLNE +CRHMGITVLPPDVNESHLTFTPVGRDIRFGMGAVRNVGANVVKGMVQGREEKGSYTGFGD +FLAKVPLVVCNKRTIESMIKAGAFDSLGYARRALLAVHEEAVDATVAQKRKEDHGEFTFD +LFALGGGDEDDSDAADGVAVPDLPEWAKKEKLAFEREMLGLYVSDHPLQGLDGVLAQHAD +VQITRVLDDDGPADGAIVTIAGLITTLERRIAKSSGNAYARCEIEDLGGSMDVMFFGQVY +APIAMMLAEDLVVAVKGRVQRRDDGSVSLSAMELTIPELSDGPGGPVRITLPAFKATEQV +MGQLADVLRTHEGSSEVRLSLVGQRATQEFQLGPQFRVSPNPALFGDLKILLGPACLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001127.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001127.fa new file mode 100644 index 0000000000000000000000000000000000000000..ebffe193a064160b3daeb9df292cf73b8f19d36a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001127.fa @@ -0,0 +1,21 @@ +>PROKKA_01345 +MLTALIVAVLAYALDQLTKYAVESTMQLGDSVAVIPGVLRWHYILNPGAAFSIGEDHTWV +FTIIQAVVAVAALVGIARVRSTPWALALGGLAGGVLGNLTDRLFRPPAFGRGHVVDMISV +PHFAIFNVADSFIVCSVIGVALLVMTGRRLDGTREA +>PROKKA_01065 +MLTALVVAVLAYALDQLTKYAVESTMQLGDSVAVIPGVLRWHYILNPGAAFSIGEDHTWV +FTVIQAVVAVAALVGIARVRSTPWALALGGLAGGVLGNLTDRLFRPPAFGRGHVVDMISV +PHFAIFNVADSFIVCSVIGVALLVMTGRRLDGTREA +>PROKKA_01547 +MSAAVEAPAPAAGPGARRRAVLAALLVAVLAYALDQLTKLWVETTMELGDSVTVVPGLLR +WHYILNPGAAFSIGEDHTWVFTVIQAVVAVAAVVGIVRARSLPWALALGGLAGGVLGNLT +DRLFRPPSFGQGHVVDMISVPRFAVFNVADSFIVCSILAIAFLVMTGRRLDGTREA +>PROKKA_01443 +MSPAAPQDALTDHRDAPARPGRGVVGAALGVATLAYALDQGTKLLVERTMELGESIVVIP +GLLRWHYILNPGAAFSIGTDVTWLFTLIQAVVAVVALVALLRSRSRAWSVALGGLLGGVM +GNLTDRLFRPPSFGQGHVVDMVSVPNFAIFNVADSFIVCSILTLCLLLMSGRRLDGTRES +DAAAEA +>PROKKA_01300 +MLTALIVAVLAYALDQLTKYAVESTMQLGDSVAVIPGVLRWHYILNPGAAFSIGEDHTWV +FTVIQAAVAVAALVGIARVRSMPWALALGGLAGGVLGNLTDRLFRPPAFGRGHVVDMISV +PHFAIFNVADSFIVCSVIGVALLVMTGRRLDGTREA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001129.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001129.fa new file mode 100644 index 0000000000000000000000000000000000000000..8bbcac0ecca4d1e2337551af7355c65fa4be75a6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001129.fa @@ -0,0 +1,15 @@ +>PROKKA_01347 +MQLLLALAYIALTVVLAALTVRIVLDVTQSFVRHWRPTGAALMLASGVYGATDPLLRPVR +RAVPPVNLGGIGLDVAFLIVFLGVVLLRVLVLSLAGVA +>PROKKA_01067 +MQLLLALAYIALTVVLAALTVRIVLDVTQSFARHWRPTGAALVLASGVYGATDPLLRPVR +RAVPPVNLGGIGLDVAFLIVFLGVVLLRVLVLSLAGVA +>PROKKA_01545 +MQLILALVYIVLTVVLAALTVRIVLDVTQSFARHWRPTGAALVAASAVYAVTDPLMRPVR +RAVPPVNLGGIGLDVAFLVVFLGVVLLRVLVLVLAGNL +>PROKKA_01441 +MQLVFALLYFVLTAYMAVLTVRIVLDVTRSFARSWRPSGPVLVAASGVYALTDPPLRALR +RRIPPLTLGGVGLDVAFLVVFLGVVLLRVLVLTLA +>PROKKA_01302 +MQLLLALAYIALTVVLAALTVRIVLDVTQSFARHWRPTGAALVLASGVYGATDPLLRPVR +RAVPPVNLGGIGLDVAFLIVFLGVVLLRVLVLSLAGVA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001130.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001130.fa new file mode 100644 index 0000000000000000000000000000000000000000..e0ce1786acee9c8fb494f60ede646cd84eee4e5c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001130.fa @@ -0,0 +1,25 @@ +>PROKKA_01348 +MAGALKKTMIYLGLADGDEYDEQPRAAERETAPRHEVVEARRPAEPDTDPHMEAVRPAAV +RDPEPAERPEPVTPSGSTAADPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT +LSTVHPRSYNDAKAIGEAFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS +KVFLLTPATVDVVGAEQGESGAADSPFDGD +>PROKKA_01068 +MAGALKKTMIYLGLADGDEYDEQPRAAEREAAPRHEVVEARRPAEPDTDPHMEAVRPAAV +RDPEPAERPEPVTPSGSTAAEPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT +LSTVHPRSYNDAKAIGESFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS +KVFLLTPATVDVVGAEQGESGVADSPFDGD +>PROKKA_01544 +MAGALKKTMIYLGLADGEEYDEQQRAAERDAAERRDVVEARRAAEPDTDPSMEPVRSATV +VRPESIERAESPAPSGSTAAAPAEPAELRRSSRPEPVDPGYRAPVTPIKRAAASSAEGAP +VSTLSTVHPRSYNDAKAIGEAFRSGMPVIMNVTELGENEAKRLVDFAAGLVFGLHGSISR +ITSKVFLLTPANVDVVGAEQGDAEESGDPYDGD +>PROKKA_01440 +MAGGLKKTMIYLGLADGDEYDDDPRHEAVDAAPRREPVEARRVAEPAPRLEPEDEEFDEP +STPSHAGSTAAAAAEPAPRRAASRPETADPGHRAPVTPIKRAAAPSAEGDAVRTLSTVHP +RSYNDAKRIGEAFRTGTPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITSKVFLLT +PSSVEVVGEEPPAGRDGDAPYDND +>PROKKA_01303 +MAGALKKTMIYLGLADGDEYDEQPRATEREAAPRHEVVEARRPAEPDTDPHMEAVRPAAV +RDPEPAERPEPVTPSGSTAADPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT +LSTVHPRSYNDAKAIGEAFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS +KVFLLTPATVDVVGAEQGESGAADSPFDGD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001134.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001134.fa new file mode 100644 index 0000000000000000000000000000000000000000..68b68abec35ed4a12979529a2ba5c475bcb3590f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001134.fa @@ -0,0 +1,30 @@ +>PROKKA_01352 +MRLGRGTPPVAPAGADASTVVRFPGRTARRRRATRWGVAAAVLAVLGALGWVVFFSPVLA +VDRVEVTGTRHVSAAEVQERLEPVYGVPLSRVGAGRVGELVGGLPGVAEVQTVPRLPTGL +EVVVREHETRARRDGDDGVQLLLADGTVLTGVPEERLEGEDLPAFSEELAQRAQEERAEV +AEVLAALPEAVADRVETADSRGPGQVRLALEGGVTLVWGDAQDAGLKGPVAEAFLADERH +GSAEGGVAEIDVSVPTRPITR +>PROKKA_01072 +MRLGRGTPPVAPAGADASTVVRFPGRTARRRRATRWGVAAAVLAVLTALGWVVFFSPVLA +VDRVEVTGTRHVSATDVQERLAPVYGVPLSRVGAGRVGELAGGLPGVAEVQTVPRLPTGL +EVVVREHEARARRDGGDGVQLLLADGTVLTGVPEERLEGEDLPAFSEELAQRVQEERAEV +AEVLAALPESVADRVETADSRGPGQVRLALEGGVTLVWGDAQDAGLKGSVAEAFLADERH +GSAEAGVAEIDISVPTRPITR +>PROKKA_01540 +MTPGRGGRPPRPAGPAQPPAGSTVVPFPGRSVRRRRAVRWAVAGAVAALLGALAWVLLFS +PVLAVDEVDVTGTRHVSAEAVQERLAPLHGVPLPRVGSSAVRELVGDLPGVAEVRVVAHP +PTRVEAAVREHEARARRGGEAGVDLLLDDGTVLAGVPAERVEGESLPEFSEELSAGPRRD +REEVAAVLAGLPAPVAERVESVDSSRAGQVRLGLRDGVVLVWGDAEDAELKGTVATAFLE +GDQHGSRAGGVREVDVSVPTRPITR +>PROKKA_01436 +MVAFPGRSARERRRRRAGMLAAVFAALALAAWAVFASPLLAVDRIDVTGTRLVDRAAVEE +RVAPLRGVPLPRIGSSSAGDLLSGMPGVASARTVAVPPTALEVRIEELAPVARSAGGDRA +QVLLEDGSVLGSVPVSALPGEGEEGGALPSAPEALLTAGPDVRASAATVLRALPDGVRDR +VRGVDAGSPEQVRLDLGGGRTLVWGDASEPERKAAVAQALLDGLEDARGVREVDVSVPDR +PVTR +>PROKKA_01307 +MRLGRGTPPVAPAGADASTVVRFPGRTARRRRATRWGVAAAVLAVLTVLGWVVFFSPVLA +VDRVEVTGTRHVSATDVQERLEPVYGVPLSRVGAGRVGELVGGLPGVAEVQTVPRLPTGL +EVAVREHEARARRDGDDGVQLLLADGTVLTGVPEERLEGEDLPAFSEELPQRAQEERAEV +AEVLAALPESVADRVETADSRGPGQVRLALEGGVTLVWGDAQDAGLKGSVAEAFLADERH +GSAEGGVAEIDVSVPTRPITR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001135.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001135.fa new file mode 100644 index 0000000000000000000000000000000000000000..075ce745e6c3221699a93e6ffbd9066e7dcff79a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001135.fa @@ -0,0 +1,50 @@ +>PROKKA_01353 +MSRDESTRPAAEGRFADLGRVHLLGIGGVGVSGVARILQEQGVAVSGSDAKDLPVMRELA +AGGARITVGYDAAHLGRDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR +VLAVAGTHGKTTTSSMAAMAFSDAGWDPTFAVGAAVAGLGTNARAGRGEWFIAEADESDG +TLVNYPSTIGIVTTVEADHLDHYGTEEAVHQVFRDFAGGLPAAAQGGVLVACLDDAGAAD +LAAWAREHAAADVVTYGSAPRDGVAPDLLVTDLAVEPGETGVGQRATFRMAGGPERTLHL +QVPGRHNALNAAAVVLAAVRAGMAFEAAVRGVEAFRGTARRFEFRGAARGVRVFDDYAHH +PTEVAAAVSAGRAVAGDARVHVLFQPHLFSRTRDFAAEFAAALSGADAVRVLPVYAAREE +PMPGVDSSLIASRLTTGAAEDRVVAEDRAEAVRSLAAGATAGDVVLTMGAGDVTALGADL +LAELGRDAAPGVAHP +>PROKKA_01073 +MSRDESTRPAAEGRFADLGRVHLLGIGGVGVSGVARILQEQGVAVSGSDAKDLPVMRELA +AGGARITVGYDAAHLGRDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR +VLAVAGTHGKTTTSSMAAMAFSDAGWDPTFAVGAAVAGLGTNARAGQGEWFIAEADESDG +TLVNYPSTIGIVTTVEADHLDHYGTEEAVHQVFRDFAGGLPAAAQGGVLVACLDDAGAAD +LAAWAREHAAADVVTYGSAPRDGVAPDLLVTDLAVEPGETGVGQRATFRMAGGPERTLHL +QVPGRHNALNAAAVVLAAVRAGMAFEAAVRGVEAFRGTARRFEFRGAARGVRVFDDYAHH +PTEVAAAVSAGRAVAGDARVHVLFQPHLFSRTRDFAAEFAAALSGADAVRVLPVYAAREE +PMPGVDSSLIASRLTTGAAEDRVVAEDRAEAVRSLAAGATAGDVVLTMGAGDVTALGPDL +LAELGRDAAPGVAHP +>PROKKA_01539 +MSRDESTRPVAEGRFDELGRVHLLGIGGVGVSGVARILQDQGVAVSGSDAKDLPVMRELA +AAGARITVGYDAAHLGEDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR +VLAVAGTHGKTTTSSMAAMAFASAGWDPTFAVGAAVAGLGTNARAGQGEWFIAEADESDG +TLVNYPTTIAVVTTVEADHLDHYGTEEAVHQVFRDFAAGLPDAASGGVLVACLDDDGAAG +LAAWAREHAAARVLTYGTGPRDGVAPDLLVADLAVEPGESGVGQRATLRLASGPEATLHL +QVPGRHNALNAAAVALAAVQAGMGFEDAVRGLEAFRGTARRFEFRGAGRGVKVFDDYAHH +PTEVTAAVSAGRAVAGDGRVHVLFQPHLFSRTREFAAEFAAALSAADVVRVLPVYAAREE +PMEGVDSSLIAGRLTTAADADRAVAEDRAVAVRELAAGAESGDVILTMGAGDVTALGADL +VAALGPDAAPGAAGR +>PROKKA_01435 +MTTQQTPEGRARRERVAALGRVHLLGIGGVGVSGVARILQDQGVAISGSDAKDLPVMHDL +AAGGARITVGYDAAHVGDDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMEGH +RVLAVAGTHGKTTTSSMAAMAFTDAGWDPTFAVGAAVAGLGTNARAGAGEWFVAEADESD +GTLVNYPTTIAVVTTVEADHLDHYGTEEAVHEVFRVFAGQLPAAEDGGALVACLDDEGAA +GLAAWAHEHARAAVVTYGTGPRDGVEPDLLVDGVTVEPGESGVGQRARFTLADGTSAEVR +LQVPGRHNALNAAAVALAAVRAGMSLREAVHGLEQFRGTARRFEFRGAERGVRVFDDYAH +HPTEVVAAVSAARAVAGEGRVHVLFQPHLFSRTRDFAAEFAAALSGADRVRVLPVYAARE +EPMEGVDATLITRALTTPDPADRTVAVDRAAAVRELAAGAREGDVILTMGAGDVTALGPD +LVAALAADPSVDA +>PROKKA_01308 +MSRDESTRPAAEGRFADLGRVHLLGIGGVGVSGVARILQEQGVAVSGSDAKDLPVMRELA +AGGARITVGYDAAHLGRDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR +VLAVAGTHGKTTTSSMAAMAFSDAGWDPTFAVGAAVAGLGTNARAGQGEWFIAEADESDG +TLVNYPSTVGIVTTVEADHLDHYGTEEAVHQVFRDFAGGLPAAAQGGVLVACLDDAGAAD +LAAWAREHAAADVVTYGSAPRDGVAPDLLVTDLAVEPGETGVGQRATFRMADGPERTLHL +QVPGRHNALNAAAVVLAAVRAGMAFEAAVRGVEAFRGTARRFEFRGAARGVRVFDDYAHH +PTEVAAAVSAGRAVAGDARVHVLFQPHLFSRTRDFAAEFAAALSGADAVRVLPVYAAREE +PMHGVDSSLIASRLTTGAAEDRVVAEDRAEAVRSLAAGATAGDVVLTMGAGDVTALGPDL +LAELGRDAAPGVAHP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001138.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001138.fa new file mode 100644 index 0000000000000000000000000000000000000000..c9a67735ae8a5d1d5611b3128a30325ab25f3760 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001138.fa @@ -0,0 +1,50 @@ +>PROKKA_01356 +MTGPASDAAPAPVRRPRADTARTADLTSWDAPGWAGLRVVVTGLGLTGFSVADTLAELGA +AVVVVEGDDGPENRARAETLRIVGVREVLLDRAATQALPEVDGAAADLVVTSPGWRPDQP +LLMAAHAAGLPIWSDVELAWRLRERAGRKTADWVCLTGTNGKTTTVTMVEAILRADGRRA +VACGNVGTPVLDAIRDPQGFDVLALELSSFQLHWTHGLAPASSAVLNLAEDHVDWHGSME +EYAAAKGKVYANTRVACVFNEQDPLTRTLVERADVQEGCRAIGFTTDTPGLSDIGVVDGI +LVDRAFLDNRRHEAIALAERADLGPVAPRHTVANAAAAAALTRAVGVSPAAVAEGLRSYD +RGEHRIQLVATSRDVMWVNDSKATNPHAADASLAAFSSVVWLAGGLPKGVTYHELVAAHA +HRLRAVVLLGRDTSALRAALAAHAPEVPVHAPLAAADGTGPADGAAVMAEAVRVADGLAR +PGDIVLMAPAAASMDQFRSYAARGDAFIEAVAGLMREHGWDVHDDAAPDAD +>PROKKA_01076 +MTGPASAAAPAPVRRPRADTARTADLTSWDAPGWAGLRVVVTGLGVTGFSVADTLAELGA +AVVVVDGDDGPENRARAETLRIVGVREVLLDRAATQVLPEVDGAAADLVVTSPGWRPDQP +LLMAAHAAGLPIWSDVELAWRLRERAGRKTADWVCLTGTNGKTTTVTMVEAILRADGRRA +VACGNVGTPVLDAIRDPQGFDVLALELSSFQLHWTHGLAPASSAVLNLAEDHVDWHGSME +EYAAAKGKVYANTRVACVFNEQDPVTRTLVERADVQEGCRAIGFTTDTPGLSDIGVVDGI +LVDRAFLDNRRHEAIALAERADLGPVAPRHTMANAAAAAALTRAVGVSPAAVAEGLRSYD +RGEHRIQLVATSRDIMWVNDSKATNPHAADASLAAFSSVVWLAGGLPKGVTYHELVAAHA +HRLRAVVLLGRDTSALRAALAAHAPDVPVHAPLAAADGTGPADGAAVMAEAVRVADGLAR +PGDTVLMAPAAASMDQFRSYAARGDAFIEAVAGLMREHGWDVHDDAAPDTD +>PROKKA_01536 +MSASENTALVPVRRPLADTGRTAALTSWDAEGWAGLRVVVAGLGVTGFSVADTLAELGAV +VVVVDGNDGPENQARAETLRIVGVHEVLLDAEATQSLPEVDGAPAELVVTSPGWRPDQPL +LMAAHAAGLPIWSDVELAWRVRERAGRPTADWVCLTGTNGKTTTVTMVEAILRADGRRAI +ACGNVGTPVLDAIRDPEGYDVLALELSSFQLHWTHRVAPASSAVLNLAEDHVDWHGSMEE +YAAAKGKVYENTRVACVFNEHDPVTRTLVERADVQDGCRAVGFTTDTPGLSDVGVVDGIL +VDRAFTENRRHEAIALAERTDLGPVAPRHTMANAAAAAALTRAVGVAPAAVAEGLRSYDR +GEHRIQLVATSRDVMWVNDSKATNPHAADASLAAFTSVVWIAGGLPKGVTYEELVGAHAH +RLRAVVLLGTDASALRSALAAHAPDVPVHAPLADADGTGPADGAAVMAEAVRVADGLARP +GDTVLMAPAAASMDQFRSYAQRGEAFIDAVAALMREHGWDTDAGTAAP +>PROKKA_01432 +MSAPVMRPHADTDRTRGLRTWDDAGWAGLRVVVTGLGVSGFSAADTLAELGARVVVVDGR +DSPENRAKADTLRIVGVADVLLSEDATHSLPEVDGERPDLVVTSPGWRPDQPLLMAAHEA +GLPIWSDVELAWRLRERAGRRTADWVCLTGTNGKTTTVTMVEAILRADGRRALACGNVGT +PVLDAVRDPEGFDTLAVELSSFQLHWTHSIVPASSAVLNLAEDHVDWHGSMEEYAAAKGK +VYERTTVACVFNEADALTRTLVERADVAEGCRAVGFTTDTPGLSDVGVVDGIIVDRAFLE +NRRHEAIALAERSDLGAVAPRHTVANACAAAALTRAVGVSPEAVAEGLRSYDRGEHRIQL +VATSRDVMWVNDSKATNPHAADASLAAFSSVVWIAGGLPKGVTYDELVSAHAGRLREVIL +LGTDTSELRRALAAHAPEVPVHAPLADADGHGSPDGRAVMAEAVRLADAHACPGDTVLMA +PAAASMDQFRSYAERGDAFIAAVAELMREHGWDVDSEADAPA +>PROKKA_01311 +MTGPASDAAPAPVRRPRADTARTADLTSWDAPGWAGLRVVVTGLGLTGFSVADTLAELGA +AVVVVDGDDGPENRARAETLRIVGVREVLLDRAATQVLPEVDGAAADLVVTSPGWRPDQP +LLMAAHAAGLPIWSDVELAWRLRERAGRKTADWVCLTGTNGKTTTVTMVEAILRADGRRA +VACGNVGTPVLDAIRDPEGFDVLALELSSFQLHWTHGLAPASSAVLNLAEDHVDWHGSME +EYAAAKGKVYANTRVACVFNEQDPLTRTLVERADVQEGCRAIGFTTDTPGLSDIGVVDGI +LVDRAFLDNRRHEAIALAERADLGPVAPRHTMANAAAAAALTRAVGVSPAAVAEGLRSYD +RGEHRIQLVATSRDIMWVNDSKATNPHAADASLAAFSSVVWLAGGLPKGVTYHELVAAHA +HRLRAVVLLGRDTSALRAALAAHAPDVPVHAPLAAADGTGPADGAAVMTEAVRVADGLAR +PGDTVLMAPAAASMDQFRSYAARGDAFIEAVAGLMREHGWDVHDDAAPDTD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001139.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001139.fa new file mode 100644 index 0000000000000000000000000000000000000000..562b3d8f2789bd2d00d01cd168c894243ce83fb6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001139.fa @@ -0,0 +1,56 @@ +>PROKKA_01358 +MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA +ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRVRGHSPTTVIGITGS +AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA +YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPEGVAVLNLDDERVAGMA +ARTAAPITWFTADERGVARAAEDVAAGRASGLVAARDVRADDQERPVFDLQVGTEEAAVR +HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII +NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA +QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA +ALGERLATADAVAAPSASPKESRP +>PROKKA_01078 +MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA +ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRVREHSPTTVIGITGS +AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA +YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPDGVAVLNLDDERVAGMA +ARTAAPITWFTADERGVARAAEDVAASRASGLVAARDVRSDDQERPVFDLQVGTDEAAVR +HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII +NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA +QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA +ALGERLATADAVAAPSASPKESRP +>PROKKA_01535 +MIALTAAQIAEAVSGTLSPALDPQTVLVHVTPDSREVAAEGTLYVAKPGERADGHDFIDA +ALAAGAVAVLAERPTQAPDGAEHPSIVVEDAVLAMGALAREVVSRIREHSPTTVIGITGS +AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELETRYLVVEMGADHVGNIA +YLCDIVRPDVGVVLMVGTAHAGSFGGVANIAATKGELAEAVGPEGAVILNLDDDRVAAMA +SRAQAPVTWFTADEAGAARAAQDVAAGRAAGLVAARALHADDHERAAFDLQIGADADAPR +HPLTSGLTGLHHAHNVLAAAAAAHAAGMAPADVARVLDGLGPTSRFRMERTDRPDGVTII +NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA +QLLVVGAGARPLYIGALNEGSWGDEAHFVEDVAQAEEFLAEHLAPGDLVLVKSSNGVGLA +ALGERLATAGASDPAPRPVRLPEGVPTVIGLLIGGVLGLVLSAAGTPLFIRFLVKRGYGQ +FVRDDGPTTHKTKRGTPTMGGAVIIGAFVLAYLLTHGILALLGVGFGGPTASGLILLFLT +VGMAFVGFVDDFTKITKQQSLGLTPRGKIILQGLIGTAFAVLALNFPDDRGLTPASTAIS +FARDVPWLDLAFAGPVVGLILFVIWSNLITTATTNAVNLTDGLDGLATGATAMITGAYVL +MSIFQSSQACSLVDEPGCYEVRDPMDLALLGAILTGSLLGFLWWNTSPAKIFMGDTGSLG +LGGALAGFAILSRTELLVVLLAGLMVAITVSVIVQVGWFRISGGKRVFLMAPLQHHFELK +GWAEVTVVVRFWLVSLMCVTAGLAVFYGEWIVRQGGLAGVTP +>PROKKA_01430 +MIALTAAQIAEAVSGTLSSTLDPETVLVHVTPDSREVVGEGTLYVAKPGEHADGHDYIDA +ALAAGASAVLAERPTQDADGAAHPAILVADAVLAMGALAREVVRRIREHSPTTVIGITGS +AGKTTTKDLLAALLSTQGPTVAPVGSFNGEVGVPLTVFRAALDTRYLVVEMGADHVGNIA +YLCDVVTPDIGVVLMVGTAHAGSFGGVENIAKTKGELVEALGPDGVAVLNRDDGRVAAMA +SRTQAPVVWFSTEESGAAAAAEDVAAGRASGLSVARALTADAEERPVFDLQLGADLDAPR +HAVRAGLTGLHHAHNMLAAAAAAQAAGMDPADIARGLDGLGPTSRHRMERSERADGVSII +NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARIREHTLVGESVVRLNIS +QLLVVGAGARPLYIGAMNEGSWGDEAHFVDDVEQAEAFLAEALQPGDIVLVKSSNGVGLA +ALGDRLAAADVTPSTASPSDTTKETRP +>PROKKA_01313 +MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA +ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRIRGHSPTTVIGITGS +AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA +YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPDGVAVLNLDDERVAGMA +ARTAAPITWFTADERGVARAAEDVAAGRASGLVAARDVRADDQERPVFDLQVGTDEAAVR +HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII +NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA +QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA +ALGERLATADAVAAPSASPKESRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001144.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001144.fa new file mode 100644 index 0000000000000000000000000000000000000000..47a4afbe0fc4f1da4c29e6435fb79b36501f4dc8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001144.fa @@ -0,0 +1,20 @@ +>PROKKA_01363 +MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCIYVFSAREFERVHEQMRSAPL +SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW +NTYLAEQEAAFSETDEDVLPGVF +>PROKKA_01083 +MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCVYVFSAREFERVHEQMRSAPL +SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW +NTYLAEQEAAFSETDEDVLPGVF +>PROKKA_01530 +MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCVYVFSAREFERVHEQMRSAPL +SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW +NAYLAEQEAAFSETDEDVLPGVF +>PROKKA_01425 +MFLGTYTPRLDEKWRLILPAKFREELADGLVLTRGQERCVYVFSAAEFERVHEQLRSAPL +SSRQARDYIRVFLSGASDETPDKQGRITVPSPLRQYAGLDRDVTVIGAGTRAEIWDTAAW +AAYLAEQEAAFSETDEDVLGGIL +>PROKKA_01318 +MFLGTYTPRLDEKSRLILPAKFREELAEGLVLTRGQERCIYVFSAREFERVHEQMRSAPL +SSRQARDYIRVFLSGASDEVPDKQGRVTVPAPLRQYAGLDRDVTVIGAGTRVEIWDSESW +NTYLAEQEAAFSETDEDVLPGVF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001148.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001148.fa new file mode 100644 index 0000000000000000000000000000000000000000..c03e49764d3ed77114b072eca4c3bec34208d9b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001148.fa @@ -0,0 +1,20 @@ +>PROKKA_01367 +MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAEHLDQRVTRVHNLVHDRRLLAVRRPEP +AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK +TEIRRRAQALAW +>PROKKA_01087 +MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAEHLDQRVTRVHNLVHDRRLLAVRRPEP +AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK +TEIRRRAQALAW +>PROKKA_01526 +MGRESAAPTRRSLAHVSTSSSDTPVPADAIPAELDALVGDWLTMPDVAERLDQRVTRVHN +LVKDHRLLAVRRPDPAVRAVPALFLTETGLLEPLQGTLVLLADAGYSDEESLRWLFTEDP +SLPGRPIDALRDGRKTEVRRRAQALAW +>PROKKA_01421 +MTTEHPVDRVPSDAVSPELDALVGDWLTLPDVAERLDLRVTRVHNLINDRRLLAVRRPEP +SVRAVPAAFLTERGLLEPLHGTLVLLQDAGFDDEEALRWLFTPDESLPGRPIDALRDGHK +TEVRRRAQALGW +>PROKKA_01322 +MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAERLDQRVTRVHNLVHDRRLLAVRRPEP +AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK +TEIRRRAQALAW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001151.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001151.fa new file mode 100644 index 0000000000000000000000000000000000000000..0b65238a5ef34847a1da65735b215ed871ce04c2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001151.fa @@ -0,0 +1,25 @@ +>PROKKA_01371 +MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGPAILASNHLSVSDSVFMPAMLDRQV +HFLAKHEYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP +EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDRVQPIGHVLPRIRRLGMIFGEPL +DFSDRAEAVGDPRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRTAAPPRARD +>PROKKA_01091 +MSTFYWSAKTFAVAPATRLLFRPWVKGLANVPAEGPAILASNHLSVSDSVFMPAMLDRQV +HFLAKHEYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLAALREGRLLGIYP +EGTRSPDGRLHRGKIGVAKLALASGVPVVPIAMIGTDRVQPIGHVLPRIRRLGMIFGEPL +DFSGRAAAADDRRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRVAAPPRAGD +>PROKKA_01521 +MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGAAILASNHLSVSDSVFMPAMLERQV +HFLAKKDYFTGAGPKGWITRKFFEATNQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP +EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDQAQPIGRTLPRIRRIGMIFGEPL +DFSDRAEGVTDARVLRAVTDEIMEAIRRLSGQEYVDAYAADVKSGRVPAPPRARD +>PROKKA_01417 +MSAFYWSAKTFVVAPATRLLFRPWVKGLSHVPAEGPAILASNHLSVSDSVFMPAMLDRQV +HFLAKQEYFTGRGAKGWATKKFFEATNQLPMDRSGGAASLRSLEAGLECLREGKLLGIYP +EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDRVQPIGRILPTLRRLGMIFGEPL +DFSHLQGREGDHRALRQVTDEIVEAIRRLSGQDYVDVYAADVKSGRVAVPPRAGRD +>PROKKA_01326 +MSTFYWSAKTFAVAPATRLLFRPWVKGLGNVPAEGPAILASNHLSVSDSVFMPAMLDRQV +HFLAKREYFTGPGVKGWVTRRFFEAANQLPMDRSGGEASLRSLDAGLEALREGRLLGIYP +EGTRSPDGRLHRGKIGVAKLALASGAPVVPIAMIGTDQVQPIGHVLPRIRRLGMIFGEPL +DFSDRAEAVGDPRVLREVTDEIMEAIRRLSGQEYVDTYAADVKAGRTAAPPRARD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001153.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001153.fa new file mode 100644 index 0000000000000000000000000000000000000000..8ed959d749d8b7f8b1bec6c8c9dc553f2ebaa40b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001153.fa @@ -0,0 +1,60 @@ +>PROKKA_01373 +MHEISEPYHHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRAL +AKGLIAAGIQPGETVGLLASTRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSDV +RAVVTGNEDLAKTVRDAVQREGLPELIGLWTMDPADGAPGSGLEALVALGADVTDEELET +RRSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVREDTSTVLFIP +LAHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQ +SGGKEKIFRRGADVAIRWSRALDSGQMTAPLRLQRAFYSALVYRRIRTAMGGRLAYAVSG +GGPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRLKIGTVGHPLGGNQVRIAEDG +EILTRGTSLMRGYHNRPEANEEAFEDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGKN +VAPAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAAR +EDAVRRHIQEAVDKANSLVSRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQ +IADIYGEPAPQN +>PROKKA_01093 +MHEISEPYHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRALA +KGLIAAGIQPGETVGLLASTRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSHVR +AVVTGNENLAKTVRDAVQREGLPELIGLWTMDPADGAPGSGLEALVALGTDVTDEELETR +RSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVRQDTSTVLFIPL +AHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQS +GGKEKIFRRGADVAIRWSRALDSGQMTAPLRLQRAFYSALVYRRIRTAMGGRLAYAVSGG +GPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRLKIGTVGHPLGGNQVRIAEDGE +ILTRGTSLMRGYHNRPEANEEAFEDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGKNV +APAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAARE +DAVRRHIQEAVDKANSLVSRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQI +ADIYGEPAPHN +>PROKKA_01519 +MREISEPYHPRLSPESNITDFLERQAEERPDHGLFAVADEQDQWTDVSARDARERVRALA +KGLIAAGVGAGDRVGLIAATRLEWTLVDFAIWYAGAVTVPIYETSSATQVAWIVEDADVC +AVVAGDESLVKTVRDAVHREHLPELRGVWVMDVAGGEPGSGLDELAALGADVSDEDLEAR +RSAANLEDLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGEVVRPDTSTVLFIPL +AHVFARFVSVLTVAAGARCGHVTDLKRLSNSLQTFQPSFVLAVPRVFEKIYNAALLNAQS +GGKDKIFRRGADVAVRWSRALDSGKMTAPLRLQRAFYSALIYRRIRAAMGGRLEYAVSGG +GPLSPDLAHFFRGVGLTILEGYGLTETTAPITVGRPGRLKIGTVGLPLGGNAVRIAEDGE +ILTRGTSLMRGYHDRPEANEEAFEDGWFRTGDLGSLDEDGFLTITGRKKELIVTAGGKNV +APAMLEDAIRSDALISQVMVVGDAKPFIAAIVTLDADTLPSWLAAHGLPKDLDVAAAAKE +ERVRRHVQEIVDKASSAVSRAEGIREFRILDRDFSMEEGHMTPSLKMKRAVIMQDFAAEI +ADIYGEAPAQG +>PROKKA_01414 +MRQISEPYLPRLSPDAAITDFLRDQAVQHPERALFAVPREDGSWDDVTAAEAWDRVRALA +RGLVAAGVGPGDRVAIVSATRLEWTLADFAIWTAGAVTVPVYETSSASQIAWIFEDAGVG +AAIADTPARAKSVSDAVHREGLPELKGLWVMDEDGGAPGAGLDRLTDAGADVPADELDAR +REGVTLESLATIIYTSGTTGRPKGCELTHGNFAELVNQTLRSSLGEVVDEGASTLLFIPL +AHVFARFVSVLTVAAGARCGHVPDLSRLATSMDTYHPTFLLAVPRVFEKIYNASLLKAQA +GGKEKIFRRGADVAVRWSRALEEGRMTAPLRLQRAFYSALLYRRIREAMGGHLKYAVSGG +GPLSPDLAHFFRGVGVTILEGYGLTETTAPITVGRPGKLKIGRVGQPLGGNEVRIDDDGE +ILTRGTSLFRGYRNRPEANAEAFTEDGWFRTGDLGELDDDGFLKITGRKKEIIVTAGGKN +VAPAQLEDAIRSDALVSQVMVVGEAKPFVAAIVTLDADTLPSWASAHGLDPQISMAEAAR +EPQVIAHVQKAVDRANDTVSRAEGIREFRILDRDFSADEGHMTPSLKMRRTAILKDFQPV +LDEIYGAGPARG +>PROKKA_01328 +MHEISEPYHHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRAL +AKGLIAAGIQPGETVGLLASTRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSHV +RAVVTGNENLAKTVRDAVQREGLPELIGLWTMDPADGAPGSGLEALVALGTDVTDEELET +RRSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVRQDTSTVLFIP +LAHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQ +SGGKEKIFRRGADVAIRWSRALDSGQMTAPLRLQRAFYSALIYRRIRTAMGGRLAYAVSG +GGPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRLKIGTVGHPLGGNQVRIAEDG +EILTRGTSLMRGYHNRPEANEEAFEDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGKN +VAPAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAAR +EDAVRRHIQEAVDKANSLVSRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQ +IADIYGEPAPHN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001154.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001154.fa new file mode 100644 index 0000000000000000000000000000000000000000..7e30d49867725007ae94380213d49fa3c9e8ef34 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001154.fa @@ -0,0 +1,50 @@ +>PROKKA_01374 +MSPPPAGRPTGPDATASGPVPILGGMATTAEHHDLLIIGSGSGNSLVSEHWKGRSVVIAD +SGPFGGTCLNVGCIPTKMYAYPASLAALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGI +SRDGLRHRRDDLDYTSVIQEEVRFVGPRRVRTASGREITADQVVVAAGSRPTLPEIPGLD +LPSVHTSDTVMRLDRLPRRLLVVGGGFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSV +STTFTKIAARRWDLRTGWTPAGIEPVEDAERAADGWVRVRLDRAEGQEQTGIVEEAIEAD +AVLIAVGRTPNTDRLDPAAAGLDVTDDGILASDEHQRALSDGAPVEGVYVLGDVANTWQL +KHVANHEARVVAHNLEHPDDLRANTLGPVPAAVFTHPQAASVGLTVEQALADYGADAITV +KTQPFGDVAYGWAMEDTEGVCTVVAEKATGRILGGHILGHEAANLIQPLVTGMAFGIDAH +RLARGQYWPHPALTEVVENALLGLDVPDSGLL +>PROKKA_01094 +MATSAEHHDLLIIGSGSGNSLISEHWKGRSVVIADSGTFGGTCLNVGCIPTKMYAYPAGL +AALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGISRDGLRYRRDDLDYTSVIQEEVRFV +GPRRVRTASGREITADQVVVAAGSRPTLPEIPGLDLPSVHTSDTVMRLDRLPRRLLVVGG +GFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSVSTTFTKIAARRWDLRTGWTPAGIEP +VEDAERAADGWVRVRLDRAGGQEQTGIVEEAIEADTVLIAVGRTPNTDRLDPAAAGLDVT +DDGVLASDEHQRALSDGAPVEGVYVLGDVANTWQLKHVANHEARVVAHNLEHPDDLRANT +LGPVPAAVFTHPQVASVGLTVEQALADYGADAITVKTQSFGDVAYGWAMEDTEGVCTVVA +EKATGRILGGHILGHEAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGLD +VPDSGLL +>PROKKA_01518 +MATSTEHHDLLIIGSGSGNSLVTEHWEGRSVAIADSGVFGGTCLNVGCIPTKMYAYPAGL +AASAGAESERLGVGLEFTGADFPAIRDRIFQRIDAISEGGLRYRRDELEHTSVIQEEVRF +VGPRRVRTASGREVTADQVVIAAGSRPTLPRIPGVDLPSVHTSDTVMRLPRLPRRLLVIG +GGFIACEFASIFAALGSEVIHVNRGHRLLKAHDLSVSTAFTEIAARQWDVRTGWTPAGVE +PVADPDRAAQGWVRVRLDRAEGQEQTGTVEEVVEADAVLMAIGRTPNTDRLDVDAAGLDV +TEDGVLATDRHQRVLSGGAPVEGVYALGDVANTWQLKHVANHEARVVAHNLEHPEDLRSA +VLAPVAAAVFTRPQVAAVGLTVEQALAEHGADAITVKTQAFGDVAYGWAMEDSEGLCTVV +AEKATGRILGGHILGHDAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGL +DVPDSGLL +>PROKKA_01413 +MSPDPAASSAGDEVDGPDDPHVRAVSYADAMATTERFDLIILGSGSGNSLVTDHWEGRRV +AIVDAGVFGGTCLNVGCIPTKMYAYPAQLAASGAEAERLGVGLDFTGADFEGIRDRIFGR +IDAISEGGLRYRRDQLEHTEVVAEEAWFSGPKELTTASGRVLAGEQVVVAAGSRPTVPDV +PGVGLPSVHTSDTIMRLPRQPKRLVILGGGYIASEFAAIFSGLGTEVVQVNRGARLLKAH +DSSISTRFTALAARQWDVRTGWTLAGVEPVGDQRRADEGWVRVRLDAVEGQEQMVEREET +LEADAVLLAVGRTPNTDRLRPEAAGFDVTAAGVLAVDEHQRVLSSGVPVEGVYALGDVAN +AWQLKHVANHEARVVAHNLEHPEDLRANTLGPVPAAVFTRPQIASVGLTQDEARELLGED +AVTVKEQAFGDVAYGWAMEDAEGVCTIVAERATGRILGAHLMGHDAANLIQPLVTAMSFG +IDAHRLARGQYWPHPALTEVVENALLGLDVPDSGLL +>PROKKA_01329 +MATSAEHHDLLIIGSGSGNSLISEHWKGRSVVIADSGTFGGTCLNVGCIPTKMYAYPAGL +AALPPEARSLGVGLEFTGADFPAIRDRIFTRIDGISRDGLRYRRDDLDYTSVIQEEVRFV +GPRRVRTASGREITADQVVVAAGSRPTLPEIPGLDLPSVHTSDTVMRLDRLPRRLLVVGG +GFIACEFASVFAGLGTEVVQVNRGHRLLKQHDMSVSTTFTKIAARRWDLRTGWTPAGIEP +VEDAERAADGWVRVRLDRAGGQEQTGIVEEAIEADTVLIAVGRTPNTDRLDPAAAGLDVT +DDGVLASDEHQRALSDAAPVEGVYVLGDVANTWQLKHVANHEARVVAHNLEHPDDLRANT +LGPVPAAVFTHPQVASVGLTVEQALADYGADAITVKTQSFGDVAYGWAMEDTEGVCTVVA +EKATGRILGGHILGHEAANLIQPLVTGMAFGIDAHRLARGQYWPHPALTEVVENALLGLD +VPDSGLL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001155.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001155.fa new file mode 100644 index 0000000000000000000000000000000000000000..eadec1594463de88e6e87adbbc5c61686e344d79 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001155.fa @@ -0,0 +1,105 @@ +>PROKKA_01375 +MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN +SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE +NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK +AVAGGGGRGMRRVERREDLRGSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE +GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV +DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVSAQLRIAAGATLPELGITQDALQVR +GFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT +CRGRDYATAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFLSGDVATDFIDKHPELATV +NRSQDRGSKALQYLVDVTVNQPHGPRVEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED +AVPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV +AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY +PTEVTDAFVAEAAASGVDVFRIFDALNDVEQITPAIEAVRATGTAVAEAALCYTGNMTDP +KETLYTLDYYLGLARRMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFDLPVHLHTHD +TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM +EPYWESVRSAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA +ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKEFAERPQEFDIPDSVIGFLRGELGDPP +GGWPEPFRTKALQGRREGAGMVEISAEDSSALGEAGQTRRGVLNRLLFPGPTKEFEAHRE +EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR +QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQAVATIEAMKME +AAITAQVAGTVRRVVTEGITPVNGGDLLLVIE +>PROKKA_01095 +MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN +SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE +NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK +AVAGGGGRGMRRVERREDLRGSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE +GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV +DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVGAQLRIAAGATLPELGITQDALQVR +GFAIQCRITTEDPANGFRPDIGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT +CRGRDYATAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFVSGDVATDFIDKHPELATV +NRSQDRGSKALQYLVDVTVNQPHGPRIEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED +AAPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV +AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY +PTEVTDAFVAEAAASGVDVFRIFDALNDVEQITPAIEAVRATGTAVAEAALCYTGNMTDP +KETLYTLDYYLGLARRMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFDLPVHLHTHD +TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM +EPYWESVRSAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA +ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKEFAERPQEFDIPDSVIGFLRGELGDPP +GGWPEPFRTKALQGRREGAGMVEISAEDSTALAEAGQTRRAVLNRLLFPGPTKEFEAHRE +EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR +QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQAVATIEAMKME +ATITAQAAGTVRRVVTEGVTPVNGGDLLLVIE +>PROKKA_01517 +MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN +SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE +NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK +AVAGGGGRGMRRVERREDLRGSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE +GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV +DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVGAQLRIAAGATLPELGITQDALQVR +GFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT +CRGRDYATAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFVSGDVATDFIDKHPELATV +NRSQDRGSKALQYLVDVTVNQPHGPRVEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED +AVPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV +AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY +PTEVTDAFVAEAAASGVDVFRIFDALNDVSQITPAIEAVRATGTAVAEAALCYTGNMTDP +AEKLYTLDYYLGLARQMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFELPVHLHTHD +TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM +EPYWESVRAAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA +ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKQFAERPQEFDIPDSVIGFLRGELGDPP +GGWPEPFRTKALQGRREGAGMVEISAEDSTALGEAGQTRRAVLNRLLFPGPTKEFEAHRE +EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR +QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQPVATIEAMKME +AAITAQVAGTVRRVVTEGVTPVNGGDLLLVIE +>PROKKA_01412 +MSLPLDPDTTRNGAGRPAHAAAPAFSKVLVANRGEIAVRAFRACHELGARTVAVFPHEDR +NSIHRQKADEAYRIGQEGHPVRAYLDVDEILRVAKDVGADAIYPGYGFLSENAGLARAAA +EAGITFVGPPADVLELTGNKVEALRAAKRAGIPTLKSSDPSSDVEWLLGQAEEIGFPIFV +KAVAGGGGRGMRRVERPEDLKDSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQVLADA +EGNVVHLFERDCSLQRRHQKVIEMAPAPHLDEEIRQALHRDAVAFAKEMGYVNAGTVEFL +VDTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVAAQLRIAAGATLEELGIRQEDLHV +RGFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKL +TCRGRDYETAVRRVRRALAEFRVRGVTTNIPFLMNVMDDPQFVAGDVATDFIDKHPELAM +VNRSQDRGSKALQYLADVTVNKPHGERVDGIDPRDRLPGHPSDKRHEPDRSPFDGPSRNP +GAVPPAGWRQVLAEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPA +VAHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTP +YPTEVTDAFVQEAAATGVDVFRIFDALNDVEQIIPAIAAVRATGTAVAEAALCYTGNMTD +PAEELYTLEYYLGLARRMVDAGAHVLAIKDMAGLLRPAAAKELVGALRAEFDLPVHLHTH +DTAGGQLATLLAASEAGVDAVDVAVASMAGTTSQAPMSALVAALEHTERDTGLTLEAAAA +MEPYWESVRAIYAPFEAGLKAPTGRVYQHEIPGGQLSNLRTQAIALGLGERFEQVEAMYA +AADDILGHLVKVTPSSKVVGDLALQLVGGGVDPDQFRERPEDFDIPDSVVGFLRGELGDP +PGGWPEPFRTRALKGRREGSGMVQVSEEDAAALAEAGQGRRDVLNRLLFPGPTKEYEAHR +EEFGDISTLHTRDFLYGLVPGREHVVSLGRGVRLIATLQSVSEPDEKGMRTAMLTLNGQL +RQIQVRDRSVESSVRQAEKADAAVPGQVPAPFAGSVTVQAAVGDVVEQGAPVATIEAMKM +EAAITAPVSGTVTRVVTQGVTPVQGGDLLLVIE +>PROKKA_01330 +MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN +SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE +NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK +AVAGGGGRGMRRVERREDLRGSLQAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE +GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV +DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVGAQLRIAAGATLPELGITQDALQVR +GFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT +CRGRDYAMAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFVSGDAATDFIDKHPELATV +NRSQDRGSKALQYLVDVTVNQPHGPRIEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED +AAPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV +AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY +PTEVTDAFVAEAAASGVDVFRIFDALNDVEQITPAIEAVRATGTAVAEAALCYTGSMTDP +KETLYTLDYYLGLARRMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFDLPVHLHTHD +TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM +EPYWESVRSAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA +ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKEFAERPQEFDIPDSVIGFLRGELGDPP +GGWPEPFRTKALQGRREGAGMVEISAEDSSALAEAGQTRRAVLNRLLFPGPTKEFEAHRE +EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR +QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQAVATIEAMKME +ATITAQAAGTVRRVVTEGVTPVNGGDLLLVIE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001156.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001156.fa new file mode 100644 index 0000000000000000000000000000000000000000..4c1f4f5685f9da5da76be5c3729676ba969d30ab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001156.fa @@ -0,0 +1,25 @@ +>PROKKA_01376 +MTPTAGPGRPPALGAQGTLFDEGRTQGDDVGFRGPTACKAAGITYRQLDYWARTDLVAPT +VRSASGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVGHLRERGVEDLAQITLMSD +GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVVGAPEPGDELAGR +RRARRSA +>PROKKA_01096 +MTPTAGPGRPPALGAQGTLFDEGRTQGDDVGFRGPTACKAAGITYRQLDYWARTDLVAPT +VRSASGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRAAVGHLRERGVEDLAQITLMSD +GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVVGAPEPGDELAGR +RRARRSA +>PROKKA_01516 +MTPTAGSGRPPALGAQGTLFDEDVTPGDDVGFRGPTACKAAGITYRQLDYWARTDLVVPT +VRGAAGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVGHLRERGVEDLAQITLMSD +GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVIVAPEPGDELAGR +RRARRSA +>PROKKA_01411 +MTPHAGPGLPLGIDGRQGRLFDVDALAPGGDVGYRGPTACKAAGITYRQLDYWARTDLVV +PTVRGASGSGTQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVAHLRERGVDDLAQITLM +SDGASVYECTSPDEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPGEVLGDDHAPEDELS +ARRRARRPARTAS +>PROKKA_01331 +MTPTAGPGRPPALGTQGTLFDEGATRGDDVGFRGPTACKAAGITYRQLDYWARTDLVVPT +VRSASGSGSQRLYSFRDILVLKVVKRLLDTGVSLQQIRTAVGHLRERGVEDLAQITLMSD +GASVYECTSADEVVDLVQGGQGVFGIAVGRVWREVEGSLAELPRESVVGAPEPGDELAGR +RRARRSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001157.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001157.fa new file mode 100644 index 0000000000000000000000000000000000000000..68860969449903f9372c1aab92c68f5d840bc463 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001157.fa @@ -0,0 +1,20 @@ +>PROKKA_01377 +MTEPRPVPADDAGDVPLSVLGVRVELPEQHHVILLVDPPGRTMIPLWVGAPEAAAAALAL +EGVRAPRPLTHELLLAAVDALGAEVVRVRLTEVRDEVVHAELVLSTGARVDARASDAVVV +ALRADAPVLGSPAVLADAGMPARTGEEDAGQERAVEDFRDFLDTVRPEDFA +>PROKKA_01097 +MTEPRPVPADDAGNVPLSVLGVRVELPEQHHVILLVDPPGRTMVPLWVGAPEAAAAALAL +EGVRAPRPLTHELLLAAVDALGAEVVRVRLTEVRGEVVHAELVLSTGARVDARASDAVVV +ALRADAPVLGSPAVLADAGMPARTGEEDAGQERAVEDFRDFLDTVRPEDFA +>PROKKA_01515 +MTEPRPEDAPEAGDVPMSVLGVRVELPEQHHVILLVDPPGRIMVPLWVGAPEAAAAALAL +EGVSAPRPLTHELLLSTVAALGAEVVRVRLTEVRNDVVHGELELSTGARVDARASDAVVL +ALRANAPVLASPAVLAEAGMSARSGEEDGQERTVEDFRDFLDSVRPEDFA +>PROKKA_01410 +MAEPPEPAGDVPLTVLGVRVELPEQQHVILLLDPPGEIVLPLWVGSPEAAAAALALEGAP +SPRPGTHALLLAALAAAGSRLRGVRLTRIEDETVHAALLLDGGAEVDARASDAVVLAVRA +QVPVLCAAEVIAAAGMAARDAAAGDEDEVDDFRAFLDSVDPEDFA +>PROKKA_01332 +MTEPRPVPADEVGDVPLSVLGVRVELPEQHHVILLVDPPGRTMVPLWVGAPEAAAAALAL +EGVRTPRPLTHELLLAAVDALGAEVVRVRLTEVRDEVVHAELVLSTGARVDARASDAVVV +ALRADAPVLGSPAVLADAGMPARTGEEDAGQERAVEDFRDFLDTVRPEDFA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001161.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001161.fa new file mode 100644 index 0000000000000000000000000000000000000000..a09487d76eea723ae03ee7996fbb57a656d4b134 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001161.fa @@ -0,0 +1,50 @@ +>PROKKA_01381 +MENPQNPLAGRVPDVEPSARVAASTATRPDDATPDWRGRPFLGQPGPLANLFSVELWERF +SFYGMQAMLVYYMSWTAAEGGLGIDPAVATGIVGAYGGMVYVFCILGGWVADRLLGSERT +MFVSAVGIMLGHIALALVPGVPGLTLGLVLVAVGSGGLKANATNLVGSLYSREDPKRDAG +FSIFYMGVNIGALFGPLLTGLARDTMGFHVGFGLAAAGMAIGLTQYALTRKNLPTDVHRV +PDPLPRSQYGRWGLIGLGMVAVVVALFLTDVITLDNLSDAVVVLAAVAAIAIFAVLLTST +KVSEEERSRVKAFIPLFIGTSVFFALFQQQFTVIALYSEHRLDRNLFGWLMPMEWVNSIN +PIFIIVFAPVFAALWTKLGTRQPATPVKFGIGIVLIGIAFLLFIPVADVAAVPLLWLTLI +LFVCTMGELLVSPVGLSLATKVAPRSFPVMMVSLYNLSVALGTALAGSLAGSYSEQNEVG +YFGTIGAVTLGVGLIVLAIAKPVRRGMRGVL +>PROKKA_01101 +MENPQNPLAGRVPDVEPSARVAASTATRPDDATPDWRGRPFLGQPGPLANLFSVELWERF +SFYGMQAMLVYYMSWTAAEGGLGIDPAVATGIVGAYGGMVYVFCILGGWVADRLLGSERT +MFVSAVGIMLGHIALALVPGVPGLTLGLVLVAVGSGGLKANATNLVGSLYSREDPKRDAG +FSIFYMGVNIGALFGPLLTGLARDTMGFHVGFGLAAAGMAIGLAQYALTRKNLPTDVHRV +PDPLPRSQYGRWGLIGLGMVAVVVALFLTGVVTLGNLSDAVVVLAAVAAIAIFAVLLTST +KVTEEERSRVKAFIPLFIGTSVFFALFQQQFTVIALYSENRLDRNLFGWLMPMEWVNSIN +PIFIIVFAPVFAALWTKLGTRQPATPVKFGIGIVLIGIAFLLFIPVADVVAVPLLWLTLI +LFVCTMGELLVSPVGLSLATKVAPRSYPVMMVSLYNLSVALGTALAGSLAGSYSEENEVG +YFGVIGAVTLGVGLLVLAIAKPVRRGMRGVL +>PROKKA_01511 +MHTPQNPPTGHEPAVEPSARVAAPTAAAPDPAAAPDWHGRPFLGQPGPLANLFSVEMWER +FSFYGMQAMLVYYMSWTLAEGGLGIDVAVATGIVGAYGGMVYVFCILGGWIADRLLGSER +TMFYSAVTIMLGHIALALVPGIPGLALGLILVAVGSGGLKANAANLVGALYSQQDPKRDA +GFSIFYMGVNIGALFGPLLTGLARDSWGFHFGFGLAAVGMAIGLVQYALTRKNLPSDVHR +IPNPLPRSQYGRWVLIALAAVAVGVVLFLTGIVTVANLADAVVVLAAVAAIGIFAVLLTS +KKVTEEERSRVKAFIPLFIGTAVFFALFQQQFTVIALYSENRLDRNLFGWEMPMEWVNSI +NPIFIIAFAPVFAALWTKLGPRQPGTPVKFGIGIVLIGLAFLLFIPVADVLAVPLLWLAL +ILFVCTMGELLVSPVGLSLSTKVAPRSFPVMMVSLYNLSVALGTALAGSLAGSYSEENEV +GYFGVIGAVTVGVGLLMLAIAKPVRRGMRGVL +>PROKKA_01406 +MTHSPDSGASVAPDADLGAAQAPAPDWHGRRFFGQPGPLANLFSVEMWERFSYYGMQAML +VYYMSWTAERGGLGIDEATATGIVGAYGGMVYVFCILGGWIADRLLGSERTMFFSAVGIM +LGHIALALVPGVPGLILGLVLVAVGSGGLKANAANLVGSLYAKGDQARDAGFSIFYMGVN +LGGLVGPLLTGWARQTWGFHVGFGLAAVGMAIGLTQYALTRKNLPSTVHGVPDPLPRSQY +GRWALIGLAGLAVVAVLLLTGVVNVGNLADAVVVLAALAAIAIFAVLLTSSKVSAEERSR +VKAFIPLFIGTAVFFALFQQQFTVVALYSENRLDRTLFGTEIPMEWVSSINPIFIIAFAP +VFAALWTRLGDRQPSTPVKFALGILLIGAAFLLFIPASGFLAVPLLWLTLILFVMTMGEL +MISPVGLSLSTKVAPAAFPVLMVALYNLSVALGTALAGSLAGSYTAENEAGYFGVIGGVT +IAVGVVMLLLAPAVRRGMRGVR +>PROKKA_01336 +MENPQNPLAGRVPDVEPSARVAASTATRPDDATPDWRGRPFLGQPGPLANLFSVELWERF +SFYGMQAMLVYYMSWTAAEGGLGIDPAVATGIVGAYGGMVYVFCILGGWVADRLLGSERT +MFVSAVGIMLGHIALALVPGVPGLTLGLVLVAVGSGGLKANATNLVGSLYSREDPKRDAG +FSIFYMGVNIGALFGPLLTGLARDTMGFHVGFGLAAAGMAIGLTQYALTRKNLPTDVHRV +PDPLPRSQYGRWGLIGLGMVAVVVALFLTDVITLDNLSDAVVVLAAVAAIAIFAVLLTST +KVSEEERSRVKAFIPLFIGTSVFFALFQQQFTVIALYSEHRLDRNLFGWLMPMEWVNSIN +PIFIIVFAPVFAALWTKLGTRQPATPVKFGIGIVLIGIAFLLFIPVADVAAVPLLWLTLI +LFVCTMGELLVSPVGLSLATKVAPRSFPVMMVSLYNLSVALGTALAGSLAGSYSEQNEVG +YFGTIGAVTLGVGLIVLAIAKPVRRGMRGVL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001162.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001162.fa new file mode 100644 index 0000000000000000000000000000000000000000..3bc4beabd9e7f65d501eeea9973ee6da5f41d82f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001162.fa @@ -0,0 +1,22 @@ +>PROKKA_01403 +MSLIRRRPAALSLATLAALALAASGCAVDDGETRAALQSAEDRLAQAEDRISELEADASD +RVDLGQLRQEAEDALEEADQRAAEVVEDLTRSLPSGSDIVDVEALREDGKVVIEYGQSLL +EADPQVLEDTMREAADRARDAIPDLEDVEFRVGDRTFTY +>PROKKA_01133 +MSLIRRRPAALSLATLAALALAASGCAVDDGATRAALQSAEDRLAQAEDRISELEADASD +RVDLGQLRQEAEGALEEADQRAAEVVEDLTRSLPSGSDIVDVEALREDGKVVIEYGQSLL +EADPQVLEDTMREAADRARDAIPDLEDVEFRVGDRTFTF +>PROKKA_01492 +MTTLRPRRPAVLSLAALAALSLALSGCGVDEGDAQAALESAEDRLAQAEDRISELEADAS +NRVDLGELQRQAEGALDGADQRVGELLEDLRGRAEPLREITEQDLRDLELPRIEGLDLEA +EAAVEDLMKSLPSGPDMADVEALREDGRVIVEYAESALEADPQVLEDTMREVAEQARNAI +PDLKDVEFRVGDQSFRF +>PROKKA_01404 +MVVPGWPASLALMTTTPRASRASRPAAALLTLAGAALALTGCAAGPDQETADALASADER +IASAEAEIADLKDRMDRVPDTAAMQSQASEAVSSAVAQATGAAGSLGADAARRAQEAVDG +VSGLPDAEAVQQVEDGGRVIVEYAQDALPKDPAELQARLDEAADAVRRQVPDSAGVEFKV +GDQTFTF +>PROKKA_01353 +MSLIRRRPAALSLATLAALALAASGCAVDDGATRAALQSAEDRLAQAEDRISELEADASD +RVDLGQLRQEAEGALEEADQRAAEVVEDLTRSLPSGSDIVDVEALREDGKVVIEYGQSLL +EADPQVLEDTMREAADRARDAIPDLEDVEFRVGDRTFTF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001163.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001163.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a33911eea9e971d82924adcba6a7be60ace0576 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001163.fa @@ -0,0 +1,55 @@ +>PROKKA_01404 +MTENPQHRSGEDEFVPAGDDQVAERLAAMTEEEAEARAASLRAGLADYELEEDDAALLDA +WQLGPDEDVDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDAEWN +GREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSMLRR +KDRPVIVAANKVDDMVQEADAATLWSLGFGYPYPVSAVHGRGVADLLDAALEALPEESAH +GGLVPRGGPRRIALVGRPNVGKSSLLNKLAGSDRVVVDDLAGTTRDPVDELVELGGRLWR +FVDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPQVISEQDVRILQMVLDSG +RALVIAFNKWDQVGEDRRLQLAKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDLALD +SWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDPGYR +RFIVRRLRETFGFEGTPLEIGMRVREKRGRRR +>PROKKA_01134 +MTENPQHRSGEDEFVPAGDDQVAERLAAMTEEEAEARAASLRAGLEDYELEEDDAALLDA +WQLGPDEDVDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDAEWN +GREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSMLRR +KDRPVIVAANKVDDMVQEADAATLWSLGFGYPYPVSAVHGRGVADLLDAALEALPEESAH +GGLVPRGGPRRIALVGRPNVGKSSLLNKLAGSDRVVVDDLAGTTRDPVDELVELGGRLWR +FVDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPQVISEQDVRILQMVLDSG +RALVIAFNKWDQVDEDRRLQLAKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDLALD +SWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDPGYR +RFIVRRLRETFGFEGTPLEIGMRVREKRGSRR +>PROKKA_01491 +MTEHTRDDVATTPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLNEGV +DLADADAVAAAAVAMELEQSTDPDVEAVRVGGTDVTEAIRGAEVTDTVSTVAVVIPVREE +LRRRQRETIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGEPGVD +AGTLHRQGGRAGRPRRHRVHVRPPRRGRGARGLHRARLRADRGGRPGRRRGPGRHPGREG +RPTMTDNPQHRSGDDEFVPAGEDQVAERLAAMTEEEAEARAASLRAGLADYELEDDDAAL +LDAWQLGPDEDLDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDA +EWNGREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSM +LRRKDRPVIVAANKVDDMVQEADAASLWSLGFGYPYPVSAVHGRGVADLLDAALEAMPEE +SAHGGLVPRGGPRRIALVGRPNVGKSSLLNRLAGSDRVVVDDLAGTTRDPVDELVELGGR +LWRFVDTAGIRRRQHMAHGADYYAALRTASALDRAEVAVVLLEAPSVISEQDVRILQMVL +DSGRALVIAFNKWDQVDEDRRHQLEKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDT +ALDSWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDP +GYRRFIVRRLRETFGFEGTPLEIGMRVREKRGLAPLSAAAADDDGVPRARRGSTDPAPAG +GRRRPTPSRGSSHGFLMFRA +>PROKKA_01403 +MTENTPLTEGEEYQPAGEDHLAERLAAISDEEADARAASLRAGLGDYELEEDDAALLADW +DGDDEFDLDLPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYEAEWNG +RVFTVVDTGGWEHDAKGIHKRVADQAELAVDVADAVVFVVDATVGMTATDEAVVTMLRRK +DRPVIVAANKVDDMVQEADAASLWSLGFGYPWPVSAVHGRGVADLLDAALEELPEESAHG +GLVPRGGPRRIALVGRPNVGKSSLLNKLAGADRVVVDDYAGTTRDPVDELVELGGRLWRF +VDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPSVISEQDVRIVQMALESGR +ALVLAFNKWDQMDEDRRPQLEKEIERDLAHVAWAPRVNISALTGWHKDRLVPALDTALES +WDRRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQASTRPPTFVLFTTGFLDPGYRR +FIVRRLRETFGFEGTPIEIGMRIRERRGRKR +>PROKKA_01354 +MTENPQHRSGEDEFVPAGDDQVAERLAAMTEEEAEARAASLRAGLEDYELEEDDAALLDA +WQLGPDEDVDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDAEWN +GREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSMLRR +KDRPVIVAANKVDDMVQEADAATLWSLGFGYPYPVSAVHGRGVADLLDAALEALPEESAH +GGLVPRGGPRRIALVGRPNVGKSSLLNKLAGSDRVVVDDLAGTTRDPVDELVELGGRLWR +FVDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPQVISEQDVRILQMVLDSG +RALVIAFNKWDQVDEDRRLQLAKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDLALD +SWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDPGYR +RFIVRRLRETFGFEGTPLEIGMRVREKRGRRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001165.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001165.fa new file mode 100644 index 0000000000000000000000000000000000000000..1bd16672a763c7b496ec5f351732ecb1f8c0dee8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001165.fa @@ -0,0 +1,35 @@ +>PROKKA_01407 +MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR +GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR +VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG +RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA +QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT +VRALNAQELGHLKALVGL +>PROKKA_01137 +MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR +GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR +VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG +RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA +QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT +VRALNAQELGHLKALVGL +>PROKKA_01489 +MNSRKPRGSGRTPSVGRRGGPFQERDFQRQLGARRGPAGPRDEAPFDEDAVPRTRGRRGR +GAGAARAKAANLDRIHDESGERLQKVLASAGVASRRVSEDLIAEGRVEVDGVIVTEPGVR +VDPARAVIRVDGISVQTDVTKQYYVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG +RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA +KVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGS +VRALSAQELGHLKALVGL +>PROKKA_01400 +MNSRKPRGSGRTPAAGKRGGPFSERDFQRNLGARRGPARPKDEPAFDEDAAERRVRSRRG +KGAGAARAKAQHLEEIHVEDGERLQKVLASAGVASRRVCEDLIAEGRVEVDGVVVTEPGV +RVDPVRSRIQVDGISVQTDVTKQYFVFNKPRGVISTMLDPEGRPSIATYLKPGQENLFHV +GRLDNETEGLLILTNDGELANRLTHPSWEVPKTYLVQTRGPLAKGVSNRLREGVELEDGL +AKVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQG +SVRAMTAQEQGHLKALVDL +>PROKKA_01357 +MNSRKPRGSGRTPAVGRRGGPFQERDFQRQIGARRGAAAPREEAPFDEDAVPRTRGRRGR +GAGAARAKAAHLDRIHDESGERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVR +VDPATAVIRVDGISVQTDVTKQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVG +RLDNETEGLLILTNDGELANRLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVA +QVDSFKLVDSTPGHVLVEVVLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGT +VRALNAQELGHLKALVGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001166.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001166.fa new file mode 100644 index 0000000000000000000000000000000000000000..e7dd62048478079746aedd1938b04b53f4266c93 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001166.fa @@ -0,0 +1,60 @@ +>PROKKA_01412 +MATHDAPAEDRPSGAYADAHARSLRDPEGFWLDAARAIDWTVAPTRALDDSAAPLYRWFP +DGELNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRYTYAELTDAVARLAGALAARGVG +KGDRVLVYLPMIPQAPIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGI +EPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADADGRGGASWEDWGEAVAAAE +PADCVPVRATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASD +VGWVVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIR +RADPEGELLKAHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANP +VGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGSLPTLWRDDQR +YIDSYLSAFPGHYATGDSGVVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALGSHPAVA +ECAVIGVADPLKGQRPSGYVVLKSGVETPEPGSEAEAALLDELRQAVRREVGPVADFRDV +VVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDPAVLEALAGVLRPAR +>PROKKA_01143 +MATHDAPAEDRPSGAYADAHARSLRDPEGFWLDAARAIDWTVAPTRALDDSAAPLYRWFP +DGELNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRYTYAELTDAVARLAGALAARGVG +KGDRVLVYLPMIPQAHIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGI +EPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADADGRGGASWEDWGEAVAAAE +PADCVPVQATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASD +VGWVVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIR +RADPEGELLKDHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANP +VGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGTLPTLWGDDQR +YIDSYLSAFPGHYATGDSGVVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALAAHPAVA +ECAVIGIADPLKGQRPSGYVVLKSGVETPEAGSEAEAALLDELRQAVRREVGPVADFRDV +VVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDPAVLEALAGVLRPAR +>PROKKA_01487 +MMPPPNPAPPAPTPPPTPAPLHDPEGFWLEAAEAIDWTVPPTRALDDSAAPLYRWFPDGE +LNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRFTYAELTDAVARLAGALAARGVGKGD +RVLVYLPMIPQAHIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGIEPK +RRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADVDGRGGASWEDWGEAVAAAEPAE +CVPVQATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASDVGW +VVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIRRAD +PEGELLQDHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANPVGL +EQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGTLPTLWRDDQRYID +SYLSAFPGHYATGDSGVVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALASHPAVAECA +VIGVADPLKGQRPSGYVVLKSGVPVPEPGSEAEAALLDELRQAVRREVGPVADFRDVVVV +DALPKTRSGKILRKTMRQMADGEEYAVPSTIEDASVLDALAPVLRPGA +>PROKKA_01394 +MATDTTAAPRSYADVHRRSLEDRESFWLAAAEAIDWTVPPTRALDDSAAPLYRWFPDGVL +NTAHNCLDRHVAAGRGEELALVHDSAMTGEVTRFTYAELTAEVARLAGALAERGVGKGDR +VLVYLPMIPQAPIAMLACARLGAVHSVVFGGFAPRELAARIDDATPDVVLTCTGGIEPKR +RVEYLPAVAEALEIAEHPVRTVLVHHREGFATAREDVADRGGAEWEDWAEAVADAAPAGC +VDVAATDPLYILYTSGTTGRPKGVVRDHGGHAVALRWTMENIYDVGPGQVMCTASDVGWV +VGHSYIVYGPLLAGATTVLYEGKPVGTPDAGAFWRLIQDHGVRSFFTAPTALRAVRKADP +EAALLAEYDVSSLRHFFAAGERLDPETQKWIEGVLGMPVIDHWWQTETGWAIAANPVGLE +ELPVKTGSSSVPSPGFDVVVVDGLGTPVAPGEEGNIAIRLPLPPGTLPTLWKADQRYVDS +YLTAFPGHYATGDSGIVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALASHPAVAECAV +IGVADTLKGQRPSGYVVLRAGVERPEPGGEAEEALLAELVQTVRREVGPVADFRDVAVVE +ALPKTRSGKILRKTMRQLADGEQVAVPSTIEDASVLEDLAAVLRPAG +>PROKKA_01362 +MATHDAPTEDRPSGAYADAHARSLRDPEGFWLDAARAIDWTVAPTRALDDSAAPLYRWFP +DGELNTAFNCLDRHVEAGRGDAVALIHDSAMTGEVTRYTYAELTDAVARLAGALAARGVG +KGDRVLVYLPMIPQAHIAMLACARLGAVHSVVFGGFAPRELASRIDDAAPDVVLTCSGGI +EPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADADGRGGASWEDWGEAVAAAE +PADCVPVRATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASD +VGWVVGHSYIVYGPLLAGATTVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIR +RADPEGELLQAHDLSSLRHFFAAGERLDPETQRWIEGLLGMPVIDHWWQTETGWAIAANP +VGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGTLPTLWRDDQR +YIDSYLSAFPGHYATGDSGLVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALAAHPAVA +ECAVIGVADQLKGQRPSGYVVLKSGVETPEAGSEAEAALMDELRQAVRREVGPVADFRDV +VVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDPAVLEALAGVLRPAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001167.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001167.fa new file mode 100644 index 0000000000000000000000000000000000000000..4a94464a6acad82f00607fb9ee4f7cc6589d5333 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001167.fa @@ -0,0 +1,26 @@ +>PROKKA_01413 +MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPLREALSRLVADGLAEQAPG +RGIVVADLSLEQADQLFDLRIALESLLARRAAQRATPEAAERFTVLAGRFQEAEAALRGG +TDPADYYAMTAELDSRLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLAASAAEHAD +IADAVGSGAADLAEATTRVHLHHAFHHLTRRGRAEETPTLLTPTEGDRP +>PROKKA_01144 +MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPLREALSRLVADGLAEQAPG +RGIVVADLSLEQADQLFDLRIALESLLARRAAQRATPEAAERFTVLAGRFQEAEAALRGG +TDPADYYAMTAELDSRLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLAASAAEHAD +IADAVGSGAADLAEATTRVHLHHAFHHLTRRGRAEETPTLLTPTEGDRP +>PROKKA_01486 +MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPVREALSRLVADGLAEQAPG +RGTVVADLSLEQADQLFDLRIALESLLARRAAQRATPETAARFTALAARFQEAGEALRAG +TDPADYYAMTAELDASLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLATSAAEHAD +IADAVGSGAADLAEATTRVHLHHAFHHLTRRTRADETPTLLSPTEGDRP +>PROKKA_01393 +MPPFTPAGVSVYSGAMRVSDRAYAALRGEILDWTLPPGTVLGEVELADRLGISRTPVREA +LARLVADGLAAQAPGRGVVVADVSLEEAEQLFELRIALESLLARRAAERADADQAAAMGA +LADRFLAAVPRLEAGDEPAGYYTLTDELDAGLDAAAGNPYLVSTLRTLRLHLARLRRLAA +HDPARLASSAAEHADIAAAVAAGAADLAEATTRVHLHHAATHLTRRARAAESTTLLTPTP +FEGAHQ +>PROKKA_01363 +MRASERAYQALRAEILDWSLPPGAGLGEVEQAERLGISRTPLREALSRLVADGLAEQAPG +RGIVVADLSLEQADQLFDLRIALESLLARRAAQRATPEAAERFTVLAGRFQEAEVALRGG +TDPADYYAMTAELDSRLDEAAANPYLVSTLRTLRLHLARLRRLAADDPARLAASAAEHAD +IADAVGSGAADLAEATTRVHLHHAFHHLTRRGRAEETPTLLTPTEGDRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001168.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001168.fa new file mode 100644 index 0000000000000000000000000000000000000000..8181efb89899dc04dc77db3520088f7ad49677b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001168.fa @@ -0,0 +1,50 @@ +>PROKKA_01414 +MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLRR +GPIVAARAQALSHPVSTGGEGASVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH +PGDNIPPILAVAQHAGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG +IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ +TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA +RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV +ALQDGSWHHVDSYAPERAQREDTVALWHKVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL +KDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP +GELDQLNILADPAFLSEADLAAAPKGLF +>PROKKA_01145 +MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLKR +GPIVAARAQALSHPVSTGGAGASVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH +PGDNIPPILAVAQHTGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG +IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ +TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA +RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV +ALQDGSWHHVDSYAPERAQREDTVALWHRVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL +KDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP +GELDQLNILADPAFLSEADLAAAPKGLF +>PROKKA_01485 +MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIVNRIIDNASVAVASLQR +GPIVAARAQALSHPVSTGGAGATVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH +PGDNIPPILAVAQHAGRSGKDLIRGIATGYEVQVDLVKSICLHKHKIDHVAHIGPSASAG +IGTLLGLDTETVFQAVGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAADRAMRGQ +TSPVPIYEGEDGVIAWMLDGPDASYEVPLPEAGEPKRGILDTYTKEHSAEYQAQAWIDLA +RKLNKEHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV +ALQDGAWHHVDSYAPERAAREDTVALWHKVTTVEDPEWTRRYHSNDLTEKAFGGAVEITL +TDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVTQEEQDRFLDAVQRVSELGP +GELDQLNVTADPAFLSQADLDNAPKGLF +>PROKKA_01392 +MKKHDVRVHPSADNLAREDQLAHKLAEVAVDPVEVLPEVEEMIINRIIDNASVAVASLKR +GPIVAARAQALSHPVSTGGAGATVFGVDQKVSPEWAAWANGVAVRELDYHDTFLAEEYSH +PGDNIPPILAVAQHAGRSGADLIRGIATGYEVQVDLVKSICLHKHKIDHVAHIGPSASAG +IGTLLGLDAETVFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAADRAMRGQ +TSPVPIYEGEDGVIAWMLDGKDAHYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA +RKLHSEHPEAMDPENVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSVPYIFTV +ALQDGAWHHVDSYAPERAARPDTVALWHKVTTVEDPEWTRRYHSNDLSEKAFGGAVEITL +TDGTVITDQIAVADAHPLGARPFAREQYIQKFRTLAEGVVTPEEQDRFLDAVQRLSELQA +GELDQLNVLANPAFLSEADLAAAPKGLF +>PROKKA_01364 +MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLKR +GPIVAARAQALSHPVSTGGEGASVFGVAQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH +PGDNIPPILAVAQHAGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG +IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ +TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA +RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV +ALQDGSWHHVDSYAPERAQREDTVALWHKVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL +KDGAVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP +GELDQLNILADPAFLSEADLAAAPKGLF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001169.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001169.fa new file mode 100644 index 0000000000000000000000000000000000000000..8acee9a3e9dca1a6cee445573d7d3d9cb6c4904d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001169.fa @@ -0,0 +1,35 @@ +>PROKKA_01415 +MLYSTKTAEQKRIDLRETLKQGGAQQFPGAFTPLSAKLIQEKGFPGVYISGGVLANELGL +PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ +FNPKRCGHLDGKNMVELDTAVKRIAAAVHARRDPNFLIMARTDLRAVEGLDAAIARMKAL +VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRRQLADAGVAMVI +YPVTLLRSAMGAAERVLNAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV +PTLDIGANHADL +>PROKKA_01146 +MLYSTKTAEQKRIDLRQTLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL +PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ +FNPKRCGHLDGKNMVELDTAVKRIAAAVHARRDPNFLIMARTDLRAVEGLDAAIARMKAL +VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRRQLADAGVAMVI +YPVTLLRSAMGAAERVLHAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV +PTLDIGANHADL +>PROKKA_01484 +MLYSTKTAEQKRVDLRAALAEGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL +PDVGLTTLTEVALRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ +FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL +VEAGADAIFPEALKDIGEFETVCRELAPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI +YPVTLLRSAMGAAERVLDAIKDEGTQASQVDQMLTRARLYELVDYEGYNAFDTGIFNFDV +PTLDIDENNANL +>PROKKA_01391 +MLYSKKTAAQKRIDLRETLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL +PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFEDAGLAGCHIEDQ +FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL +VEAGADAIFPEALKDIGEFETVCRELAPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI +YPVTLLRSAMGAAERVLDAIREEGTQQSQVDQMLTRARLYELVDYEGYNAFDTGIFNFDV +PTLDIDSNNANL +>PROKKA_01365 +MLYSTKTAEQKRIDLRQTLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL +PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ +FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL +VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI +YPVTLLRSAMGAAERVLDAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV +PTLDIGANHADL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001172.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001172.fa new file mode 100644 index 0000000000000000000000000000000000000000..316f85eef22a47585abc79d911397ed5a87aae17 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001172.fa @@ -0,0 +1,25 @@ +>PROKKA_01419 +MPEISASAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRLDPADKSREPLTRELMVH +PGAVAILAVRTKLTTTGPREQVALVRQYRHPVGMELWEIPAGLRDVDGEDLHQVAVRELA +EEADLRAREWHTLVDYYTTPGGSSEAIRVFLARQIEEIPDGERHTRQDEEAAMPLVWVGL +DEVTDAVLDGRVHNPSTVVAVLALGAHRAQGWRRLRPVDAPFVPDRQAPGADWPA +>PROKKA_01150 +MPEIPASAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRLDPADKSQDPLTRELMVH +PGAVAILAVRTKLTTTGPREQVALVRQYRHPVGMELWEIPAGLRDVDGEDLHQVAVRELA +EEADLRALEWHTLVDYYTTPGGSSEAIRVFLARQIEEIPDGERHTRQDEEAAMPLVWVGV +DEVTDAVLDGRVHNPSTVVAILALCAHRAQGWRRLRPVDAPFVPDRHGPGADWPA +>PROKKA_01480 +MPEISACAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRMDPEHKGQDPLTRELMVH +PGAVAVLAVRTQLSTVGPREQVALVRQYRHPVGMELWEVPAGLRDVDGEDLHQVAVRELA +EEADLRAREWHTLVDYYTSPGGSTEAIRVFLARQVEVIPEAERHARTDEEAAMPLAWVGL +DEVTDAVLDGRVHNPSTVVAILALCAHRAQGWRRLRPVDAPFVPDRHGPGADWPA +>PROKKA_01388 +MAEVPASAGRSPLRDLSLPRRVKKSKTVFEGRVWDIARESFRMDPDDKGQEPLTRELMVH +PGAVAVLALRTHLTTAGPVEQVALVRQYRHPVGMELWEVPAGLRDVAGEPLVETARRELR +EEADLEAAEWHTLADFFTTPGGSTEAIRVFLARQVSAVPEGARHEREGEEASMPLAWVNT +DEVLDAVLDGRIHNPSTVVAVLALHAHRAQAWRRLRPPDAPFVPDRRGPGADRPA +>PROKKA_01369 +MPEIPASAGRSPLRDLHVPRPVKKSKTVYEGRVWDIARESFRLDPADKSREPLTRELMVH +PGAVAILAVRTKLTTTGPREQVALVRQYRHPVGMELWEIPAGLRDVDGEDLHQVAVRELA +EEADLRAREWHTLVDYYTTPGGSSEAIRVFLARQIEEIPDGERHTRQDEEAAMPLVWVGV +DEVTDAVLDGRVHNPSTVVAVLALGAHRAQGWRRLRPVDAPFVPDRQAPGADWSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001183.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001183.fa new file mode 100644 index 0000000000000000000000000000000000000000..55ee379aad2358b08bdda3910f1e06b592303495 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001183.fa @@ -0,0 +1,20 @@ +>PROKKA_01433 +MAAPTTKIARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP +AGMVYALPAEGDDGAVPGRGSDAQLNRLASMARELLVSAEPTANLVVLRTPPGAAQFLAS +VIDQARVEHVMGTIAGDDTILLITTGTTSAPAVAAHLLGLAG +>PROKKA_01165 +MAAPTTKIARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP +AGMVYALPAEGDDGAVPGRGSDAQLNRLASMARELLVSAEPTANLVVLRTPPGAAQFLAS +VIDQARVEHVMGTIAGDDTILLITTGTTSAPAVAAHLLGLAG +>PROKKA_01465 +MAVPTTKTARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP +GGMVYALPAEGDDGALPGRGSDAQLSRLSSMARELLISAEPTENLVVLHTPPGAAQFLAS +VIDQARVENVMGTIAGDDTILLITTGVSAAPVVAAHLLGLAG +>PROKKA_01373 +MATPATKTARQAAIRDVLQTRAIRSQAELSDALAERGLSVTQGTLSRDLVDLGAVRLRGA +EGMVYAVPADGEEAVAGRSAESQTGRLASMARELLLSAEPTENLVVLRTPPGAAQFLASV +VDQARVEGIVGTIAGDDTVLLITAGTREAPAVAARLLGMAG +>PROKKA_01383 +MAAPTTKIARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP +AGMVYALPAEGDDGAVPGRGSDAQLNRLASMARELLVSAEPTANLVVLRTPPGAAQFLAS +VIDQARVEHVMGTIAGDDTILLITTGTTSAPAVAAHLLGLAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001185.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001185.fa new file mode 100644 index 0000000000000000000000000000000000000000..eb725537cc56ee1e14af23d05d4a1c8b830162c6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001185.fa @@ -0,0 +1,45 @@ +>PROKKA_01435 +MSTDQSALLERYHAALTGVFGRPTRVLVRGEGVHVWDADGRRYTDLLAGIAVNALGHGHP +ALVRAVSEQVATLGHVSNLFTSEPQIRLAERLLELAGAPAGSTVFFANSGTEANEAAFKL +ARRHGADDPSGRRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVKHVPGGDAAA +LRAALAPDDDGATVAAVILEPVQGEAGVHGWPAGYLAEVRAATREAGALMILDEVQSGVG +RTGTWFGFQNPAVTGAAEPVVPDAFTLAKGLGGGVPIGALVCVGPAVSGLLTAGQHGTTF +GGNPLATAAGLAVLQTVEDEGLLGHVRAAGEAVAALLEDLPEVAAVRGHGLWIGVDLADP +AGPAPAGGLAPAVVAAGLEAGWILNATGPSTLRLAPPLTVPVAELERFAAALPGLVAAAL +TPAEGDRP +>PROKKA_01167 +MSTDQSALLKRYHAALTGVFGRPTRVLVRGEGVHVWDADGRRYTDLLAGIAVNALGHGHP +ALVRAVSEQVATLGHVSNLFTSEPQIRLAERLLELAGAPAGSTVFFANSGTEANEAAFKL +ARRHGADDPSGRRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEHVPGGDAAA +LRAALAPDDDGATVAAVILEPVQGEAGVHGWPAGYLAEVRAATREAGALMILDEVQSGVG +RTGTWFGFQNPAVTGAAEPVVPDAFTLAKGLGGGVPIGALVCVGPAVSGLLTAGQHGTTF +GGNPLATAAGLAVLQTVEDEGLLGHVRAAGEAVAALLEDLPEVAAVRGHGLWIGVDLADP +AGPAPAGGLAPAVVAAGLEAGWILNATGPSTLRLAPPLTVPVAELERFAAALPGLVAAAL +TPAEGDRP +>PROKKA_01463 +MSTTQDALLARYADSLTGVFGRPARVLVRGEGVHVWDADGRRYTDLLAGIAVNSLGHAHP +AVVRAVREQIAGLGHVSNLFTSEPQIRLAEELLAVADAPAGSTVFFANSGTEANEAAFKL +ARRHGGQDPSGSRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEHVPGGDVDA +LRAALAPGASGATVAAVVLEPVQGEAGVHGWPVGYLAQVRALTREAGALMILDEVQSGMG +RTGTWFGFQNPSVTGSDDPVLPDAFTLAKGLGGGVPIGALVCVGPEVSGLLSAGQHGTTF +GGNPLATAAGLAVLETIRSEGLLEHVRAAGERAAKLLADLPEVAAVRAHGLWIGVDLAAP +RGPVPDGGLAPAVVAAGLEAGWILNATGPDTLRLAPPLVIAAEDLERFVELLPALVAAAT +TEGDPS +>PROKKA_01371 +MSTAPGTDPAAPQEELLARYAHALTGVFGAPARALVRGSGTSVWDADGREYTDLVAGIAV +NSLGHAHPAVVEAVSRQVATLGHVSNLFTSEPQVRLAEALLDRAGLPEGSSVFFCNSGTE +ANEAALKLARRHGTQDPTGRRTRVLALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEF +IAGGDAGALAAALAPDAEGRTVAAVVLEPVQGEAGVHGWPAAYLARVRDLTREAGALMIL +DEVQSGVGRTGTWFAFQNPQVTGSGAPVVPDAFTLAKGLGGGVPIGALVSVGPQVSRLLA +PGQHGTTFGGNPLATAAGLAVVETLEAEGLLDHVRTVGARVSERLETLAEVTAVRAYGLW +IGVDLADDAAASPTGGLAPAVVRAGLDAGWILNATGPRTLRLAPPLNVEAADLDRFADAL +PALVRAARAAAPTPHAPKEETA +>PROKKA_01385 +MSTDQSALLERYHAALTGVFGRPTRVLVRGEGVHVWDADGRRYTDLLAGIAVNALGHGHP +ALVRAVSEQIATLGHVSNLFTSEPQIRLAERLLELAGVPAGSTVFFANSGTEANEAAFKL +ARRHGADDPSGRRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEHVPGGDAAA +LRAALAPDDDGATVAAVILEPVQGEAGVHGWPAGYLAEVRAATREAGALMILDEVQSGVG +RTGTWFGFQNPAVTGAAEPVVPDAFTLAKGLGGGVPIGALVCVGPAVSRLLTAGQHGTTF +GGNPLATAAGLAVLQTVEDEGLLGHVRAAGEAVAALLEDLPEVAAVRGHGLWIGVDLADP +AGPVPAGGLAPAVVAAGLEAGWILNATGPSTLRLAPPLTVPVAELERFAAALPGLVAAAL +TPAEGDRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001186.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001186.fa new file mode 100644 index 0000000000000000000000000000000000000000..a24e4f1c780c667747dad4dc535320c906024ef7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001186.fa @@ -0,0 +1,35 @@ +>PROKKA_01436 +MTPHTDPATAAAPVLSTADRLDRAESKAEVLVEALPWIRRFAGTVMVVKYGGNAMVSEEL +RRAFAEDIVFLHHVGVHPVVVHGGGPQINAMLDRLGIASEFRGGLRVTTEEAMDVVRMVL +TGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGVDPTAI +LDVIESGRIPVVSSVAPEINDDGEPTGQVLNVNADTAAAALAAALGAAKLVLLTDVEGLY +ADWPDRDSLISSLTAAQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRPHSMLL +EVFTSAGVGTQVVPDAEPTAPTTPEEDA +>PROKKA_01168 +MSPHTDPATAAAPVLSTADRLDRAESKAEVLVEALPWIRRFAGTVMVVKYGGNAMVSEEL +RRAFAEDIVFLHHVGVHPVVVHGGGPQINAMLDRLGIASEFRGGLRVTTEEAMDVVRMVL +TGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGVDPTAI +LDVIESGRIPVVSSVAPEINDDGEPTGQVLNVNADTAAAALAAALGAAKLVLLTDVEGLY +ADWPDRDSLISSLTAAQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRPHSMLL +EVFTSAGVGTQVVPDAEPTAPTTPEEDA +>PROKKA_01462 +MSQSSSRQPDPVTTAAAPVLSAADRLDRAESKAEVLIEALPWIQRFAGSVMVIKYGGNAM +VSDELRRAFAEDVVFLHHVGVHPVVVHGGGPQINAMLDRLGIESEFRGGLRVTTEEAMDV +VRMVLTGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGV +DPTAILDVVRSGRIPVVSSVAPEIDEHGEPTGQVLNVNADTAAAALASALGAAKLVLLTD +VEGLYADWPDRESLISSLTAGQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRP +HSMLLEVFTSAGVGTPVVPDADTAGRPAPTTVQEDA +>PROKKA_01370 +MTGQPAPADPTTPSVPVLSTAQRLERAASKAEVLVEALPWVQRFAGATMVIKYGGNAMVS +DELRRAFAEDVVFLHHVGVHPVVVHGGGPQINAMLERLGIESEFRGGLRVTTPEAMEVVR +MVLTGQVGRELVGLINSHGAYAVGSSGEDAGLFRARRTGAVVDGETVDLGLVGEVTAVNP +EAIRDVIDAGRIPVVSSVAPEIGDDGEPTGEVLNVNADTAAAALAAGLGAAKLVLLTDVE +GLYADWPDRDSLISSLTASQLRGLLPGLQSGMIPKMAACLHAVDSGVHRAHVVDGRRPHS +MLLEVFTSDGVGTQVVPDPTPATRPASAPTTATAQEDA +>PROKKA_01386 +MSPHTDPATAAAPVLSTADRLDRAESKAEVLVEALPWIRRFAGTVMVVKYGGNAMVSEEL +RRAFAEDIVFLHHVGVHPVVVHGGGPQINAMLDRLGIASEFRGGLRVTTEEAMDVVRMVL +TGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGVDPTAI +LDVIESGRIPVVSSVAPEIDDDGQPTGQVLNVNADTAAAALAAALGAAKLVLLTDVEGLY +ADWPDRDSLISSLTAAQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRPHSMLL +EVFTSAGVGTQVVPDAEPTAPTTPEEDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001187.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001187.fa new file mode 100644 index 0000000000000000000000000000000000000000..0db0c4c8941e027df3edaec97ffd3d4b505d71f7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001187.fa @@ -0,0 +1,40 @@ +>PROKKA_01437 +MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNQGPRDAAAAVLTENRVAAAPVVWTRRAVR +DGRATAVVLNSGGANAATGAEGLEDARRTAEHAAAALGTAADDVLVCSTGLIGERLPMDT +LTAGVAEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM +LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPAAFA +AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP +NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLTAREVLVEVDLH +AGDAEATVWTNDLTHDYVHENSAYST +>PROKKA_01169 +MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNEGPRDAAAAVLTENRVAAAPVVWTRRAVR +DGRATAVVLNSGGANAATGAEGLEDARRPAEHAAAALGTSADDVLVCSTGLIGERLPMDT +LTAGVAEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM +LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPEAFA +AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP +NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLSAREVLVEVDLH +AGDAEATVWTNDLTHDYVHENSAYST +>PROKKA_01461 +MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNDGPRRAAAAVFTANRVAAAPVLWSRQAVS +DGRADAVVLNSGGANAATGAPGFQDAHATAEHAAEALGVSSGDVLVCSTGLIGERLDRER +LFAGVAAAAGALSADGGEDAAVAIKTTDTVAKTAQARGEGFIVGGMAKGAGMLAPGMATM +LCVITTDADVPAAVLDAALKDAVRTTFNRVDSDGCMSTNDTVILLASGAAGVAPDPEAFA +ATLHEVCADLSRQLVADAEGAAHDVAVRVHGAQTEDAAEAVARAVTRSNLFKAAIFGQDP +NWGRVIAAVGTVPEEVAAFDPYALDVSFNGVQVCRGSGVGEDRALVDLSAREVLVEVDLH +AGDAEATVWTNDLTHDYVHENSAYST +>PROKKA_01369 +MSVTAAQGFRAAGVTAGLKPSGKPDVAVVVNDGPSHTAAGVFTTNRVAAAPVRWSRQVLT +DGRADAVVLNSGGANAATGHAGFQDAHRTAEHAAEALGVSAGDVVVCSTGLIGERLPLDT +LLAGVDAAAAGLAEDGGADAALAIMTTDTVPKEAQASGEGWTVGGMAKGAGMLAPGMATM +LCVVTTDADLPAAALRAALEEAVRTTFNRVDSDGCMSTNDTVVLLASGASGVAPEPTQFG +AALHAVCADLARQLVGDAEGAGHDVLIRVVNASDEDAGEAVARAVSRSNLLKTAIFGQDP +NWGRVISAVGTVPEEVAPFDADALDVSFNGVQVCRAAGVGDSRAGVDLSGREVVIEIDLH +AGDAVVELWTNDLTHDYVHENSAYST +>PROKKA_01387 +MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNEGPRRAAAAVLTENRVAAAPVVWTRRAVR +DGRATAVVLNSGGANAATGAEGLADARRTAEHAAAALATAADDVLVCSTGLIGERLPMDT +LTAGVSEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM +LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPEAFA +AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP +NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLTAREVLVEVDLH +AGDAEATVWTNDLTHDYVHENSAYST diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001191.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001191.fa new file mode 100644 index 0000000000000000000000000000000000000000..3b8348592198338d6c48538a0c33f9c7beeb2e3b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001191.fa @@ -0,0 +1,24 @@ +>PROKKA_01442 +MSVATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACPRCGSAAH +GVPALTGLPPGRVALVSFTRVRMPGTEDRARIGAWWAPARPADGLGLGVDVERADAAAFA +DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV +PADVVLVDLTDRLPGGLLGALALRGR +>PROKKA_01174 +MSVATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACPRCGSAAH +GVPALTGLPPGRVALVSFTRVRMPGTEDRARIGAWWAPARPADGLGLGVDVERADAAAFA +DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV +PADVVLVDLTDRLPGGLLGALALRGR +>PROKKA_01456 +MPGGDGDGAEDAAGPDDGPAAAPGLGLDVERVDAPAFADRDALGEVGFSTAERAWVAALP +RSERPAARARLWTRKEALVKAAGTGFTGDPADVAALHPPPGVVLLDVAAGLPDGIVGSVA +LRRA +>PROKKA_01364 +MTTAPTSPTRGIEVGAVGVSRTEGTAQVLAALGTRLGLGPRALALAHSCPGCGATDHGAP +ALRRAGDGTTPGGAPGDDGGPVLPAVSLTHVDGPRPVTVLAWCTPSVAGTAWGIGVDAED +PTAPQTLRAFAAGADGAAEIDAVAFAAEERAALAGLSPEGALAERVRLWTVKEALVKARG +TGLDRDPAEVRPQLGEAVVPLADPRLPPGVVGTVAWRPAS +>PROKKA_01392 +MSAATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACAGCGSAAH +GVPALTGLPPGRVALVSFTHVRMPGAEDRARIGAWWAPARPADGLGLGVDVERADAAAFA +DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV +PADVVLVDLTDRLPGGLLGALALRGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001193.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001193.fa new file mode 100644 index 0000000000000000000000000000000000000000..9f53adf5db02d35ed46b31a6e95a8ef8200bcd24 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001193.fa @@ -0,0 +1,35 @@ +>PROKKA_01444 +MTPSPETGAEPTAPVAEISPVDAEAVEAAVQAALAAYEAAADLDELKAARLAHTGDRAPL +TLANKAIGALPKERKAEAGKLMGAARGRLGKALAARTEVLEAEQAARILREETVDVTTAV +RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF +FVDPAEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV +DKGLTMAHLRGTLEYFARQMFGAEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG +GCGMVHPNVLRAAGLDPEEYSGFAFGMGVERTLMFRNEVPDMHDMIEGDVRFSQHFGMEV +>PROKKA_01176 +MTPSPETGAEPTAPVAEISPVDAEAVEAAVQAALAAYEAAADLDELKAARLAHTGDRAPL +TLANKAIGALPKERKAEAGKLMGAARGRLGKALAARTEVLEAEQAARILREETVDVTTAV +RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF +FVAPAEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV +DKGLTMAHLRGTLEYFARQMFGAEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG +GCGMVHPNVLRAAGLDPEEYSGFAFGMGVERTLMFRNEVPDMHDMIEGDVRFSQHFGMEV +>PROKKA_01454 +MTPSPETGAEPTAPAAEISPVDAAAVDAAVQAALAAFDAATDLDELKAARLAHTGDRAPL +TLANKGIGALPKERKAEAGKLMGDARGRLNKALAARTEVLEAEQAERILREETVDVTAAV +RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF +FVEPSEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV +DRGLTMAHLRGTLEYFARQMFGEEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG +GCGMVHPNVLRAAGLDPEEFSGFAFGMGVERTLMFRNEVPDMRDMIEGDVRFSQHFGMEV +>PROKKA_01362 +MTSSPETGASEDAPQLSPVDGPAVDAAVAEALAAFEAAADLEELKAARLAHQGDRAPLTL +ANKAIGTLPKEQKAEAGKTMGAARSRIGKALAARTEVLEAEHAARMLAEETVDVTAAAAR +RLPGARHPLSLLQERVSDIFVGMGWEIAEGPELEHDWFNFNALNFPPDHPAREMQDTFFV +EPLESNLLLRTHTSPVQVRSMLERGAPVYVLCPGRTFRTDELDATHTPVFHQFEGLAVDR +GLTMADLRGTLEYFARQMFGPEAEIRLRPNFFPFTEPSAEMDIWHPQAKGGPRWIEWGGC +GMVHPNVLRSAGIDPEEFSGFAFGMGIERTLMFRNEVPDMRDMIEGDVRFSQHFGMEL +>PROKKA_01394 +MTPSPETGAEPTAPVAEISPVDAEAVEAAVQAALAAYEAAADLDELKAARLAHTGDRAPL +TLANKAIGALPKERKAEAGKLMGAARGRLGKALAARTEVLEAERAARILREETVDVTTAV +RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF +FVAPAEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV +DKGLTMAHLRGTLEYFARQMFGAEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG +GCGMVHPNVLRAAGLDPEEYSGFAFGMGVERTLMFRNEVPDMHDMIEGDVRFSQHFGMEV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001194.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001194.fa new file mode 100644 index 0000000000000000000000000000000000000000..669781dd445af5b669b6173eb763b99e50289f41 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001194.fa @@ -0,0 +1,20 @@ +>PROKKA_01446 +MTAAPSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEAHGWTHRFPG +GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSMWRTGDPA +SRNVFERRASLALGGYIERPVVRGLRRRR +>PROKKA_01178 +MTAAPSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEARGWTHRFPG +GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSTWRTGDPA +SRNVFERRAGLALGGYVERPVVRGLRPRR +>PROKKA_01453 +MTTPDSPAGVGAGPPPLRWRTRARGLWNLVNLSTPLGLVGAVVSGCALRPGPHGLIEARG +WRHSFPGGAAFTVGDVVFTRPGLRMTEDLWRHEAGHAAQYAGMLGLPFLPAYAAAAAWST +WRTGDPASRNPFERGAGLALGGYVERPVRRGPRRRR +>PROKKA_01357 +MSAAPARPTRPRGAARLRGLWNLLNLSTPLGVVGAVLAGCPLRPGPDGLLHAEGWRHRFP +GGAAFTVGDVVFTRPGLEMTERLWRHEGAHAAQYAACLGLPFLPLYGMSAAWSSWRTGDP +ASRNPFERGAGLERGGYVQAAVRRGPGRGALKPAGGDLRDARRA +>PROKKA_01396 +MTAARSRPSPPAHVRARGLWNLLNLATPLGLVGAVVAGCALRPGPHGLIEARGWTHRFPG +GAAFTVGDVVFTRPGLRMTPALWRHEAGHADQYALLLGLPFLPAYALAAAWSMWRTGDPA +SRNVFERRAGLALGGYVERPVVRGLRPRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001195.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001195.fa new file mode 100644 index 0000000000000000000000000000000000000000..165db53d9f3f661bfb324eae300e90a01070caef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001195.fa @@ -0,0 +1,26 @@ +>PROKKA_01447 +MFESTRKRVRVRAWRGRRDAPTVVAMTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDA +VGILADRGVTAEAVELPCAFGAAGPALTAALDRVRPEVAIAVGLAGGTATVRVERVAVNL +QDARIPDNAGEQPVDRPVRADGPAALFATLPAKRAVAAIREAGVAAEPSLSAGAFVCNHV +MYSLLDGPGTARAAGFIHVPWDTEHRPTPDTPALPAADLARAVAEAALTALAGGPDLDVP +GGTLH +>PROKKA_01179 +MTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDAVGILADRGVTAEAVELPCAFGAAGS +ALTAALDRVRPEVAIAVGLAGGTAAVRVERVAVNLQDARIPDNAGDQPVDRPVRADGPAA +LFATLPAKRAVAAIRAAGVAAEPSLSAGAFVCNHVMYALLDAPGTARAAGFLHVPWDAEH +RPTPDTPALPAADLARAVAEAALTALAGGPDLDVPGGTMH +>PROKKA_01452 +MTTPASASAVRVLLTGFEPFGGDGHNPSIVAARDAVALLAERGVAAEAVELPCAFAAAGP +ALAAALERTRPEAAVAVGLAGGTAAVRVERIAMNLQDARIPDNAGDQPVDRPVRAEGPAA +HFATLPVKRAVEAVRAAGVPAEPSLSAGAFVCNHVLYALLDAPGTARAAGFVHVPWDLAH +RPRPDAPALPAEDLARAVAEVALVALEGGADLDVPGGTLH +>PROKKA_01356 +MTDPVRVLLTGFEPFGGDDHNPSIEAARAAAAALTADGTPAVAVELPCVFAAAGPALAAA +LEAHRPEIAVAVGLAGGTAAVRVERVAVNLQDARIPDNAGDRPADRPVRSGGPAAHFATL +PVKRAVAAVREAGVPAEPSLSAGSFVCNHVMYSLLDAPAPARAAGFVHVPWSREHAPTPQ +TPALPAADLARAVAAVARAALVEGPDLDVPGGALH +>PROKKA_01397 +MTSRAPAPAARVLLTGFEPFGGDVHNPSIAAARDAVGILADRGVTAEAVELPCAFGAAGP +ALTAALDRVRPEVAIAVGLAGGTATVRVERVAVNLQDARIPDNAGEQPVDRPVRADGPAA +LFATLPAKRAVAAIREAGVAAEPSLSAGAFVCNHVMYALLDAPGTARAAGFIHVPWDTEH +RPTPDTPALPAADLARAVAEAALTALAGGPDLDVPGGTLH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001197.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001197.fa new file mode 100644 index 0000000000000000000000000000000000000000..5f10bf697756460c81c09f2a1fb34a172486b539 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001197.fa @@ -0,0 +1,20 @@ +>PROKKA_01449 +MGLALLDDVAAPTRLLAARRSAPAPLRGLWEFPGGKVEPGEGVQEALLRECREELGVAVR +LGPEVAAPEPDGWELANGARMRVFWGVLAEEGTTPRALQDHDLLAWLPLAGPGVRHLDWI +PADRPIVAEVLRGAATAFSAGR +>PROKKA_01181 +MGLALLDDVAAPTRLLAARRSAPAPLRGLWEFPGGKVEPGEGVQEALLRECREELGVAVR +LGPEVAAPEPDGWELANGARMRVFWGVLAEEGTTPRALQDHDLLAWLPLAGPGVRHLDWI +PADRPIVAEVLRGAATAFSAGR +>PROKKA_01450 +MVGLALLDDAAAPSRLLAARRSAPAVLRGLWEFPGGKVETGEGPREALAREVREELGVAV +RLGAEVPSPDPEGWELANGARMRVLWGVLAEEGAEPAALEDHDLLAWVPLSGAGAHHLDW +IPADRPIVSAVVAGAATAFAAAP +>PROKKA_01354 +MSPATPQTPPVPSAPRPVVGVALVDDAARPTALLAARRSAPASLAGLWEFPGGKVEPEEG +ADAALHRELVEELGVRVRLGTEVAAPEGPGWELANGARMRVWFGVLREDSGAPAALQDHD +RLEWTPLTAEALHALDWIPADRPIVDALLAAVEAGRLGL +>PROKKA_01399 +MTSATPARPAPAARPTTSPRDGARPRQVVGLALLDDVAAPTRLLAARRSAPAPLRGLWEF +PGGKVEPGEGVQEALLRECREELGVAVRLGPEVAAPEPDGWELANGARMRVFWGVLAEEG +ATPRALQDHDLLAWLPLAGPGVRHLDWIPADRPIVAEVLRGAATAFSAGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001198.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001198.fa new file mode 100644 index 0000000000000000000000000000000000000000..bf06e38b028dd6453717482b4faf0b36792506a1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001198.fa @@ -0,0 +1,15 @@ +>PROKKA_01451 +MGIIGWIVLGLIAGAIARAILPGRQGGGWLGALLTGIVGALLGGWIASLVFNINVNEKFF +SLGTWIFAIIGGVIVAAVWQAITRRTGTRA +>PROKKA_01183 +MFTIIAWIIIGLIAGAIARLILPGRQGSGWLGALITGLLGAVLGGWISTLLGGEGLGDAF +SWQTLIWSVIGGVIVAFIWQAITSRRGTRV +>PROKKA_01448 +MGFIAWIVLGLIAGAIARAILPGRQGTGWLGALITGVLGALLGGWIGHLMGFSTNDSFFD +LATWIFAIIGGVIVAFIWQAITGRRGTRV +>PROKKA_01352 +MGFLAWIILGLIAGAIARLILPGHQGSGWLGALITGVLGALLGGWLGRTLFGASTNDGFF +DLATWFWAIIGGVIVAFIWQAIAGRMGRGTRV +>PROKKA_01401 +MGIIGWIVLGLIAGAIARAILPGRQGGGWLGALLTGIVGALLGGWIASLLFDFDVNEKFF +DLGTWIFAIIGGVIVAAVWQAITRRTGTRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001199.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001199.fa new file mode 100644 index 0000000000000000000000000000000000000000..6021d8fc6e6c4c9a2b251b0ac1ff48bfc0da1c37 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001199.fa @@ -0,0 +1,33 @@ +>PROKKA_01452 +MTPHAEPMTHPRAERVRAVAALAGRSARRRTGTFLVEGPQACREALRAHLGEGPTAAAGQ +WRAGRVLTQVYVSGGLVDRDPALAELVARVRDRPTPGGERVLVREASDEVLTAMADAVTG +QDIVAVARMPEPQAVEAVLEEARLAAVLCRVQDPGNAGTVIRAADAAGADAVVLTPGSVD +PFNPKVVRSTAGSLFHLPVATAVPAEAAAAAARAAGLQVWAADGYASDRLDALAPGVVAA +PTAWLFGNEAQGLDDGELALADRRVAVPLYGAAESLNVGTAATVCLYSSAMAGARRAG +>PROKKA_01184 +MTPPAEPLTHPRAERVRAVAALAGRPARRRTGTFLVEGPQACREALRAHLGEGPAGAARQ +WPAGRVLTQVYVSAGLADRDSELAALVERVAADGPDGGERVFVREASDEVLTAMADAVTG +QGVVAVARVPDQPALEDAFDGAALAAVLCRVQDPGNAGTVLRAADAAGADAVVLTAGSVD +PFNPKVVRSTAGSLFHLPVLAGVQAEDVAVTARAAGLQVWAADGHGSDRLDALSPASLGA +RTAWLFGNEAQGLDEAELALAERRVAVPLYGAAESLNVGTAATVCLYASAMASPTTRD +>PROKKA_01447 +MARVKRAVNAHKKRRTMLELASGYRGQRSRLYRKAKEQMLHSFTYNYQHRHKRKGDFRRL +WITRINAAARANGMTYNRFMQGLKLAGVEVDRRMLAEIAVSDAATFAVLVKTAREALPAD +VNAPRRLPLVGPGTPGSPPRVRRGHRRRRGGPSDEEARPVGVCAPAPRRTRPGEPMTPPA +EPLTHPRAERVRAVAALAGRPARRRTGTFLVEGPQACREALRAHLGEGPAGAVRQWPAGH +VLTQVYVSAGLAERDPDLAALVERVADGGPGGERVLVREASDEVLTAMADAVTGQGIVAV +ARIPDQPPLADAFDGAALAAVLCRVQDPGNAGTVLRAADAAGADAVVLTAGSVDPFNPKV +VRSTAGSLFHLPVLTGAEAAAVADASRGAGLQVWAADGYGDDRLDALAPETTAAPTAWLF +GNEAQGLDEAELALADRRVAVPLYGAAESLNVGTAATVCLYASAMAAAVRRDG +>PROKKA_01351 +MSRAPQPDDELMQNPRAERVRAVAALAGRAARRRSGTFVVEGPQSCREALRAHLGEGPER +TRAQWRPGAVLTQLFVAPDLFARDPGLGDLVARLHDLTGPDRVLVREATDEVLTAMSDAV +TAQGIVAVARIPQPLTAEDAWSDARLAAVLCRVQDPGNAGTIVRAADAAGADLVAFTAGS +VDPFGPKAVRSTAGSLFHVPLVVGTEADAAADAARAAGMQVWAADGYGADRLDALEQDVL +GAPTAWLLGNEAQGLSAAELELADRRVAVPLYGAAESLNVATAATVCLYASAMAAPHA +>PROKKA_01402 +MTPHAEPMTHPRAERVRAVAALAGRSARRRTGTFLVEGPQACREALRAHLGEGPAAAAGQ +WRAGRVLTQVYMSVGLVDRDPALAELVARVRDRPTPGGECVLVRQASDEVLTAMADAVTG +QDIVAVARMPEPQAVEAVLGEARLAAVLCRVQDPGNAGTVIRAADAAGADAVVLTPGSVD +PFNPKVVRSTAGSLFHLPVVTAVPAEAAAAAAWAAGLQVWAADGYGSDRLDALAPGVVAA +PTAWLFGNEAQGLDGGELALADRRVAVPLYGAAESLNVGTAATVCLYSSAMAGARRAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001200.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001200.fa new file mode 100644 index 0000000000000000000000000000000000000000..e8d2a68109c44180bb0ad3efa30bdc7cc2ebecdd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001200.fa @@ -0,0 +1,15 @@ +>PROKKA_01454 +MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDQLVSKGSIKQIKR +MLGI +>PROKKA_01186 +MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDQLVSKGSIKQIKR +MLGI +>PROKKA_01446 +MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDKLVSKGSLKQIKR +MLGI +>PROKKA_01349 +MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLAGDKVVSKGSIKQIKR +MLGI +>PROKKA_01404 +MPKMKTHSGAKKRFRVTGSGKIMRQQANRRHYLEHKSSRLTRRLKGDQLVSKGSIKQIKR +MLGI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001201.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001201.fa new file mode 100644 index 0000000000000000000000000000000000000000..08dce4c8e5ab7fefd41ba7fbb865a5483bf73d52 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001201.fa @@ -0,0 +1,39 @@ +>PROKKA_01455 +MHGPGAAKWRPLSHPRQQDVRFAPGRVAGSPVGTAASWRAARTEGPVRRDRVEASVCVRA +GEAFLVSEGPSGGRGVTRRLTQRSTTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDAL +RLAAEADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKID +KHDYETKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPR +QDGRNMVMVVGPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDS +APVRNSVGDAFPEQLKAMAARTQENASAAPAETTQAPKTPAPAAPRPAAAAPAAKPASSA +TPASAPKPAATPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAP +KPGPRA +>PROKKA_01187 +MEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKIDKHDYETKTGH +AKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPRQDGRNMVMVV +GPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDSAPVRNSVGDA +FPEQLKAMAARTQENASAAPAETTQAPKTPAPAAPRPAAAAPAAKPASSATPASAPKPAA +TPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAPKSGPRA +>PROKKA_01445 +MNPSSQHRSSTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDALRLAAEADLDLVEVAP +TAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKIDKHDYETKTGHAKKFL +SQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPRQDGRNMVMVIGPLRT +KADARADQRKNSEDSHRERQGGGSRRDQAAREAKARAAEKAAANAAPVKNSVGDAFPEQL +KAMAARTQESAPAAPAASAEPKQAPKAPAKPAAQAAPKQAPKAPAKPAAAAKPAAKPAAA +PKPAAASKPASSGKPAAPASAPKPAAKPMPAPPKPAAPRGGAAKPGPRA +>PROKKA_01348 +MESSSHPRQQDVRHGRAELPGHRVSAAVAPGSDDPWRPGGTAKGPIRGRFEASRLHPQGR +PSAWRAPGVRSHQRPANRSGTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDALRLAAE +ADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKKQVNTVLKEVRFRLKIDQHDYE +TKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIRLLQKFAEDVAELGTVESQPRQDGRN +MVMVIGPLKAKAEAREEQRKSTEGTQRERKGGGSRRDQAAREAKAAAAEKAAANSAPVRN +SIGDAFPEQLRSFAAQQTEAPAEQAPVPAPKAAPAKATPAKAPAPKPAATPAPKPPASAP +KPPAAPKPAAAPKPAAKPMPAPPKPAAPKGAPKPGPRG +>PROKKA_01405 +MHGPGAAKWRPLSHPRQQDVRFAPGRVAGSPVGTAASWRAARTEGPVRRDRVEASVCVRA +GEAFLVSEGPSGGRGVTRRLTQRSTTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDAL +RLAAEADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKID +KHDYETKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPR +QDGRNMVMVVGPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDS +APVRNSVGDAFPEQLKAMAARTQENASAAPAETKQAPKTPAPAAPRPATKPASSATPASS +PKPAATPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAPKPGPR +A diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001202.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001202.fa new file mode 100644 index 0000000000000000000000000000000000000000..ec58557e77206754a24e8735043317a5b53f7644 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001202.fa @@ -0,0 +1,19 @@ +>PROKKA_01456 +MVYGKLTTMTDERQAQDATPMDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSP +DARELIDLDEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGK +GPGEKFTGPVN +>PROKKA_01188 +MDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSPDARELIDLDEARKLITALAG +LVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTGPVN +>PROKKA_01444 +MTDERQAHDANDQDSPAEVRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSPDARELVDL +DEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTG +PVN +>PROKKA_01347 +MTDQNQHQHAAGEDVPTEVREIHEVPAVEVITTTAVHLMTAAAVKVGLADSPDAREMTDL +DEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGKGPGEKFTG +PVN +>PROKKA_01406 +MVYGKLTTMTDERQAQDATPMDAPAEIRDIHEVPAVEVITTTAVHLMTAAAVKCGLADSP +DARELIDLDEARKLITALAGLVTAAAPEIGSQHAGPLRDGLRSLQLAFREASPFPDAPGK +GPGEKFTGPVN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001204.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001204.fa new file mode 100644 index 0000000000000000000000000000000000000000..f79bfa148f13c048b999742063df5cc6b61b6750 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001204.fa @@ -0,0 +1,15 @@ +>PROKKA_01458 +MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW +GGMSEDERRAMKRRAARARRAS +>PROKKA_01190 +MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW +GGMSEDERRAMKRRAARARRAS +>PROKKA_01442 +MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW +GGMSEDERRAMKRRAARARRAS +>PROKKA_01345 +MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRTCEVIDTCLKWAMESGQDSGVW +GGMSEDERRAMKRRAARARRAS +>PROKKA_01408 +MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW +GGMSEDERRAMKRRAARARRAS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001206.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001206.fa new file mode 100644 index 0000000000000000000000000000000000000000..39e320e755b9a198967d016388cab04fc682544c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001206.fa @@ -0,0 +1,51 @@ +>PROKKA_01460 +MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDLAELLAIARSGLVDAVLVAGDTESLT +AAFLEETARLPRPVGVAALSEVRTERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG +RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRGADEPDDAGPGAAPAA +ATPDGGPATADEGADPAPSPEEGEPAGPARESLVTVVWGPTGAPGRTTVAVNLAAEHAVA +GRNTLLIDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL +TVLTGLTRVDRWPELRPAAVSALIAAARERWDRVVVDVGFGLEQDEELSFDVPAPQRNGA +TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEVAPAARLRVVVNRLRPAAAGVAPRGQ +VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA +RRGRHRARPSQTIAAVSSDAARDATDTGRPARRRTLIPWSVRSRRTP +>PROKKA_01192 +MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLT +AAFLEETARLPRPVGVAALSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG +RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRDADEPDDAGPGAAPAA +ATPDDGPATAGEGADPAPSPEEGEPTAPARESLVTVVWGPTGAPGRTTVAVNLAAEHAMA +GRNTLLVDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL +TVLTGLTRVDRWPELRPAAVSALIAAAREHWDRVVVDVGFGLEQDEELSFDVPAPQRNGA +TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLRPAAAGVAPRGQ +VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA +RRGRHRARPSQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP +>PROKKA_01440 +MTVRIALATTVLPGLDHIGPLERHQTRITVVRRAEDLAELLAIARSGLVDAVLVAGATEA +VTGAFLEELARLPRPVGAAAISEVRAERRRLRALGVPCVRADAGPEPLAAAVVEAALAAA +DGRRARADAVAEDEGGEDPVDGLDGIELTYGVLDDDPRLGPPLLGGDPERSAVSAARPEA +GAGDEAVDDGRRGGRAGDDLVPADAAQGGVTRDGVAQDRAQDGFARDDAQDFAAWDADAA +GRSVPDVDRPDPRDPDGDAAEHAEDRPDVEASGTPGDARVIVVWGPTGAPGRTTVAVNLA +AEHAVAGRSTLLVDLDTYGPSVGAHLGLTEESAGVARAVRRADHGPLGPADLEAAGVRVR +VAGAELTVLTGLTRVDRWPELRPSALTSLLAAARGRWERVVVDVGFGLEQDEELSFDVPA +PQRNGATLAALAAADEVLAVGGPDAVSLPRLVRGTEELVEAAPEARLRVVVNRLRPAAAG +VSPRSQVEAVWSRYASAGIPLAAFLPWDPAAADRALLGGQVLAEAAPNSALRRALAELAD +VDPRGARRTGRRRRPTGQGPAGAARRHPQDEGAARPSRRRTLMPWSARSRRTP +>PROKKA_01343 +MRVALATTLMPGRDHVGPLEQAQAEVTVVRRAEDLAELLAAARSGLVDAVLVAGDLSALA +RGFVDEVREAPRPVAVVAMGEVRAERERVRTLGVPCLSADADPLALAAAVQSAVRARLTG +ARPELGSETPPADPPAPAPGTPDGGDPEAVRVAAVRDREGTPRLPEPNPVRVDALAASEV +DALFTEETSPVAAADEAGPASPDAAGPDAVTASPADTAPEDGPEGGPERGRTGRTVAVWG +PTGAPGRTTVAVNLAAESAVAGLRTLLVDLDTYGPSVGVHLGLTEETAGLARAVHRAERG +SVTREDLVDAAVRVRVAGGDLDVLTGLTRPDRWPEVRPGALREVLQAARDGWDRVVLDLG +FCVEEDEELSFDVPAPQRNGATLAGLAAADRVLVVGGADAVAMPRLLRAVEALPAGVEQD +RVRVVVNRVRPQASGVAPQAQVAGVWERYGPPIPLVAQLPWDPGAADRALLGGQVLAEAA +PGSALRAAVLELARLDPAVAARTQSAGRGRRPAVRGLRRRLAPWSAPSPRTP +>PROKKA_01410 +MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLT +AAFLEETARLPRPVGVAALSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEG +RRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPGLTDPWRDADEPDDAGPGAAPAA +ATPDDGPATAGEGADPAPSPEEGEPTAPARESLVTVVWGPTGAPGRTTVAVNLAAEHAMA +GRNTLLVDLDTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADL +TVLTGLTRVDRWPELRPAAVSALIAAAREHWDRVVVDVGFGLEQDEELSFDVPAPQRNGA +TLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLRPAAAGVAPRGQ +VEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPA +RRGRHRARPSQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001207.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001207.fa new file mode 100644 index 0000000000000000000000000000000000000000..a8d1c40e35107af35f5b4cb537935d46a4397b27 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001207.fa @@ -0,0 +1,25 @@ +>PROKKA_01461 +MSASAEGGRLRRPRWRDPRLLVGLVLVLASIAGVVALVASAQQTAAYWTAAEDLPPGTPI +ASGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV +ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVAAEQNGFGGSGTTRV +QLLAPEETLPRIVDAKVKDARVTLVPAHGVR +>PROKKA_01193 +MSASAEGGRLRRPRWRDPRLLVGLMLVLASIAGVVALVASSQRTAAYWTAAEDLPPGTPI +AAGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV +ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVTAEQSGFGGSGTTRV +QLLAPEETLPRIVDAKVKDARVTLVPAHGVR +>PROKKA_01439 +MSTSTSASAEGGRLRRPRWRDPRLLVGLVLVLASVAGVVALVASSQRTSAYWAAAVDLPP +GTPLEAGQLRAVEVNLADAEGKYVAAAPDSAPSGRMVASTVRAGELLPAAALVDADPEGR +RPVGVRLREPLAGGVGVGDRVDVWVAMPAEGGRGHADPERLAEALEIAEVATEQGSIGGS +GETRVQLLAPEATLPRVVDAQVKDARITLVPAHGVR +>PROKKA_01342 +MTTDPTAPAEGARLRRPRWRDPRLLVGLVLVLASLAGVTAIVAGAQRTQTYWAAARDLAP +GAPVPADAFVPVDANLADAAGHYLRADAPAPAGKVVGAVVRAGELVPADALADVDPQRRR +PVGVQLAEPLPAGTSAGDRVDVWVAARQDDGRDYEAPRRIAEGLEISELTEAEGGFGTGA +TTRLQLMAGEDVLAQLLDAKVSEARITVVPALGEG +>PROKKA_01411 +MSASAEGGRLRRPRWRDPRLLVGLVLVLASIAGVVALVASAQRTAAYWTAAEDLPPGTPI +ASGDLRPVEVNLSEAGERYLSADAPAPEGRMVSGTVRAGELLPAAALVDADPDGRRPVGV +ALDEPLPSGVGVGDRVDVWVAMPAEGGRGHADPARLAEALEISEVTAEQNGFGGSGTTRV +QLLAPEETLPRIVDAKVKDARVTLVPAHGVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001208.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001208.fa new file mode 100644 index 0000000000000000000000000000000000000000..2579cb141e8f25860ff3c47b78666dfa595ff025 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001208.fa @@ -0,0 +1,15 @@ +>PROKKA_01462 +MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR +ARVREWTEADAKAR +>PROKKA_01194 +MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR +ARVREWTETDAQAR +>PROKKA_01438 +MQRFLTLTDVAETLNISGQAARALIRSGELQAIQVGGRGQWRIEESWLQEYVDRQREATR +ARVQEWAEADAKSR +>PROKKA_01341 +MPQFLTLTDVAEVLNVSVGQARTLVRTGQLQAIQVGGRGQWRIEAGWLDEYVERQRELTR +SRVAERTREDAGHGA +>PROKKA_01412 +MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR +ARVREWTETDAKAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001209.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001209.fa new file mode 100644 index 0000000000000000000000000000000000000000..acdbd0f1ddb25f6c9ad7801d7af822dcdb5ea8ca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001209.fa @@ -0,0 +1,25 @@ +>PROKKA_01463 +MRWNGLFDDLEAHWADLGWQETVAEAAELTRAEWMALSLADRLRGARGRQVRLHLAWGEV +VDGVVHTVGQGWVGVHVDGSGSAIVAVDCVAAVEADLTRAVAAPELAAAGWGTVLRGIAR +TRQPVAVTGRLGAALAEGTVDRVGGDHLDIARHPRDEARRAAAVRGRLVIPFGALGTVRT +ALRPA +>PROKKA_01195 +MRWNGLFDDLEAHWVDLGWQETVAEAAELTRAEWMALSLVDRLRGARGRQVRLHLAWGEV +VDGVVHTVGQGWVGVHVDGSGSAIVAVDCVAAVEADLTRAALAPELAAAGWGTVLRGIAR +TRQPVAVTGRLGAALAEGTVDRVGGDHLDIARHPLDEARRAAAVRGRLVIPFGALGTVRT +ALRPA +>PROKKA_01437 +MRWDGLFDDLEARWADLGWRQSEAEAAELTRAEWMALTLADRLRGERGRPVRLHLAWGEA +LDGVLHAVGEDWAGLHLSGGRSAVVPLPGVAAVEAGLHRAVPAPTGPATGLGAVLRGIAR +ERVPVVVTGTRGVTLVEGTVDRVGRDHLDVSRHPRDEARRAAAVRGRLVVPFTALGVVRT +ASRLA +>PROKKA_01340 +MRWDGLFEDLEARWSALEWDATRAEAAELTRGEWAALTLEERLRGARGETVRLHLVWGEH +RDVRLGTVGDGWVSVNAAAADSLLVPLTSVVAWEGPLGAASTAPEGVRSRPGLPAALRQL +ARARAAVRVVAGNGVELGEGTIDRVGRDHVDLARHPRDEARRAGQVRGRLVVPLAALGLV +ATPGPLG +>PROKKA_01413 +MRWNGLFDDLEAHWADLGWQETVAEAAELTRAEWMALSLADRLRGARGRQVRLHLAWGEV +VDGVVHTVGQGWVGVHVDGSGSAIVAVDCVAAVEADLTRAALAPELAAAGWGTVLRGIAR +TRQPVAVTGRLGAALAEGTVDRVGGDHLDIARHPRDEARRAAAVRGRLVIPFGALGTVRT +ALRPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001211.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001211.fa new file mode 100644 index 0000000000000000000000000000000000000000..e1870acaf65359160844add8c7ebbc3fcfa7f695 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001211.fa @@ -0,0 +1,20 @@ +>PROKKA_01465 +MTTLATRPRAASDRRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI +AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPKSA +PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG +>PROKKA_01197 +MTALATRPRTASARRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI +AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPASA +PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG +>PROKKA_01435 +MIAVACVEVETGRRALRDLSAWLSPEVLDKMTRRMDLLGLAEQDRPRARSAAAGVSRAPA +AAPRPVGARVCEVAPGRVEASATVLCDGRARAFALRLERRISRWKVTSVEIG +>PROKKA_01338 +MTHSVRADRTMIRTSADRPAHRPAQEDPMTTLAPALAHGPTRPRPVSRTAPSRRDTESAL +LRGPARRMSAVPTGEDLVRRAEQEDDREELRRLRSLAAVVAVACVETEAGRRPVRDLAGW +LAPETYEKMCRRVDLLERTGTRPPSGSAPRPVGARVCAVRPGAVEASATVLVAGRARAVA +LRIERRLSRWKVTHLEIG +>PROKKA_01415 +MTTLATRPRAASDRRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI +AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPASA +PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001213.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001213.fa new file mode 100644 index 0000000000000000000000000000000000000000..785f531865cf4cbe86c62b36319ca79e97d08f1f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001213.fa @@ -0,0 +1,25 @@ +>PROKKA_01467 +MTMDVSYIARNLRLPESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL +TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRLRDRRKDRRHGKLGASRGAGEVGFV +PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN +AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED +>PROKKA_01199 +MTMDVSYIARNLRLPESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL +TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV +PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN +AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED +>PROKKA_01433 +MTMDVSYIARNLSLPESFRDHVAERTERLHTLAEGAETLEVRVTKSSHHKHSDETVRVEL +TARGPREVVRAEADADDKQVAFDMAVTRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV +PPLPPNGAQMAAEDAAREQDIPEEGTPVRIREKAFPATPMTVDEAVDAMELVGHDFFLFQ +NSETGVPSVVYRRRGWSYGVIRLDESLPADHVSATEGERAYQAREA +>PROKKA_01335 +MTLDVSYIARGITLSDRFREHVEERLEKIEPLAEGAETLEVKVSRSSHHRHSDEGMRVEL +TLRGAREVVRAEGDADDKAAAFDAALSRIAERLRRMRDRRKDRRHGKGSAASRGAGEIPF +VPPLPAVGQADAPADEAPESGTPVSIRAKRFPATPMSVDRAVDAMELVGHDFYLFQDETT +GVPSVVYRRRGWSYGVISLDESLPAHHVAPVEGERVYQASREADAE +>PROKKA_01417 +MTMDVSYIARNISLSESFRDHVVERTERLQPLAEGADTLEVRVTKSSHHKHSDETVRVEL +TVRGPRDVVRAEADADDKLVAFDQAATRLAERLRRMRDRRKDRRHGKLGASRGAGEVGFV +PPLPPSGAALAAEEAAEQDAPEVGTPVRIRQKAFPATPMSVDEAVDAMELVGHDFFLFQN +AETGVPSVVYRRRGWSYGVIRLDESLPQDHVSASEGERAYQARED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001214.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001214.fa new file mode 100644 index 0000000000000000000000000000000000000000..eec689a1d45b34ec42919453ff1d34f18b52172d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001214.fa @@ -0,0 +1,30 @@ +>PROKKA_01468 +MRSPPSSPSPPSVFGTLGRALADLVLPAECAVCAAPGHRLCPACAEGLTAVLSRPFRAEQ +DAPALPLGPGGAPLPVMAAGRYADPLAAAVLAFKDHHALHLRGVLGEALCRAVAAARLEP +DLPGARHALLVPVPGGAVGFRRRGYDPLAELTRALPAPWLVSDAVRARLLPRASTLRGGG +PSHAGAGAGQRRRRARDWRVAAGRLPAGAPVLLVDDVLTTGATLAALAEAVRRAGGHPVG +AVVLAAVAPPRDPAEPGPRPGPRVG +>PROKKA_01200 +MRSPPSSPSPAFGALGRALADLVLPAECAVCAAPGHRLCPACAEGLTAVLSRPFRAEQDA +PALPLGPGGAPLPVMAAGRYADPLAAAVLAFKDHHALHLRGVLGEALCRAVAAARLEPDL +PGARHALLVPVPGGAVGFRRRGYDPLAELTRALPAPWLVSDAVRARLLPRASTLRGGGPS +HAGAGAGQRRRRARDWRVAAGRLPAGAPVLLVDDVLTTGATLAALAEAVRRAGGHPVGAV +VLAAVAPPRDPAEPGPRPGPRVG +>PROKKA_01432 +MPHAPAPEPLLESDSGLPAARRAIAALAALGEAFVDLVLPAECAVCAAPGHRLCAPCRLE +LNAALARPFRAEHGAAALPLGPGGVPLPVVAAGRYADALAAAVLAFKDHHGLHLRAVLGE +ALCRSAAVARLAPDVPEAAHALLVPVPGGAAGFRRRGYDPLAELVRALPAPWVVSDAVRA +PRGPGRARRAGPSHAGAGSAQRRRRARRWRPVPGRLPAGAPVLLVDDVLTTGATLGALAE +AVRRAGGRPVGAVVLAAVAPPADDPGPVTGAGVG +>PROKKA_01334 +MHPLLESVVDLVLPADCAVCGAPGHRLCPDCRCLLGRELSAPHRAEEPALALPLGPDGAP +LPVWAAGDYRDGLAAALLAFKDHHGFGLRPILGDALARTVAAARLDPGLQEAAHALLVPV +PGSASGFRRRGYDPLAELVRSLPAPWVRDDVVRAAPAWSAWPPGGGPSHGGAGSRERRSR +RRGWRVREGALRPGTPVLLVDDVLTTGATLAALHRAVRRAGGRPVGGVVVAAVAPPTGDG +GAGVGGAGSTLAGAEPGE +>PROKKA_01418 +MRSPPSSPSPPSVFGTLGRALADLVLPAECAVCAAPGHRLCPACAEGLTAVLSRPFRAEQ +DAPALPLGPGGAPLPVMAAGRYADPLAAAVLAFKDHHALHLRGVLGEALCRAVAAARLEP +DLPGAPHALLVPVPGGAAGFRRRGYDPLAELTRALPAPWLVSDAVRARLLPRASTLRGGG +PSHAGAGAGQRRRRARDWRVVAGRLPAGAPVLLVDDVLTTGATLAALAEAVRRAGGHPVG +AVVLAAVAPPRDPAEPGPRPRPRVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001216.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001216.fa new file mode 100644 index 0000000000000000000000000000000000000000..2c9f4cda282a9d68af068279d4ed90777c5e7a4d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001216.fa @@ -0,0 +1,25 @@ +>PROKKA_01471 +MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI +DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE +GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV +WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG +>PROKKA_01203 +MGKAKILVVDDDEALAEMIGIVLRNDGFEPTFAADGTSALPAFHRERPDLVLLDLMLPGI +DGIEVCKLIRAESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE +GEAKPAEVLHIGDLEIDVAGHQVTRAGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV +WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG +>PROKKA_01429 +MSRAKILVVDDDEALAEMIGIVLRNDGFEAAFAADGTAALPAFHRERPDLVLLDLMLPGM +DGIEVCKLLRSESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE +GEAKPAEVLQIGDLEIDVAGHQVTRDGAAISLTPLEFDLLVALARRPRQVFTREMLLEEV +WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG +>PROKKA_01331 +MSKARILVVDDDEALAEMIGIVLRNDDFEPSFAVDGTSALPAFRSARPDLVLLDLMLPGI +DGIEVCKQIRAESDVPIIMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE +GEQRPAEALAIGDVRIDVAGHQVSRGGAPISLTPLEFDLLVALARKPRQVFTREMLLEEV +WGYRHQADTRLVNVHVQRLRAKVEPDPENPTVVLTVRGVGYKAGQV +>PROKKA_01421 +MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI +DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE +GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV +WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001218.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001218.fa new file mode 100644 index 0000000000000000000000000000000000000000..0417292b21e8fbe321c30e3f7d85f82f644cf1c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001218.fa @@ -0,0 +1,20 @@ +>PROKKA_01473 +MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD +LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP +GESPGDADD +>PROKKA_01205 +MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD +LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP +GESPGDADD +>PROKKA_01427 +MSPDYDPHASSLTGRTDPEVLAELYAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHE +LPPSDPGREAAQIERLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALASGAGPEAPAGD +PAADSLPDGTRTDAGDDPRRGGADA +>PROKKA_01329 +MSHDYDPHASSLAGTADQDILEELYEIRGSIDNIDASLVYLLAERFKFTQRVGRLKARHA +LPPSDPGREAAQIERLQDLARDADLEPEFAEKFLNFIIAEVIRHHRAIAEDEAPVARPAE +ASDAGSADA +>PROKKA_01423 +MSPDYDPHASSLPGTADPAVLDELFAIRGSIDNIDASLVYLLAERFKFTQRVGALKARHD +LPPSDPGREAAQIARLHRLALEADLEPAFAEKFLNFIIAEVIRHHRALAAEGRPDAEAEP +GAGSGDADD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001219.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001219.fa new file mode 100644 index 0000000000000000000000000000000000000000..7955a74e07244b084ceb3511e404c54514a9e9cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001219.fa @@ -0,0 +1,40 @@ +>PROKKA_01474 +MKVLAAMSGGVDSAVAAARAVDAGHDVVGVHLALSRMPGTLRTGSRGCCTIEDASDAWRA +CERLGIPFYTWDFSERFAEDVVDDFVAEYEAGRTPNPCMRCNERIKFAALLERALELGFD +AVCTGHYAAVRPGPDGSLELHRAADDAKDQSYVLGVLTADQLAHCLFPLADTPSKELVRA +EAAERGLSVAAKPDSHDICFIPDGDTRGWLAERIDLAPGPIVDPEGQELGTHAGAQAFTV +GQRKGLAIGRPAPDGKPRFVLEVRPKENTVVVGGRELLDVDRITGIRPSWAGAPVPEART +GAWFDCALQFRAHGEIVEARARQRADAAGHPGWEIEPGRPLRGVAPGQTAVLYRGTRVLG +QATIDTARNARLSAPADA +>PROKKA_01206 +MKVLAAMSGGVDSAVAAARAVDAGHDVVGVHLALSRMPGTLRTGSRGCCTIEDASDAWRA +CERLGIPFYTWDFSERFAEDVVDDFVAEYEAGRTPNPCMRCNERIKFAALLERALELGFD +AVCTGHYAAVRPGPDGSLELHRAADDAKDQSYVLGVLTADQLAHCLFPLADTPSKELVRA +EAAERGLSVAAKPDSHDICFIPDGDTRGWLAERIDLAPGPIVDPEGQELGTHAGAQAFTV +GQRKGLAIGRPAPDGKPRFVLEVRPKENTVVVGGRELLDVDRITGIRPSWAGAPVPEART +GAWFDCALQFRAHGEIVEARARQRADAAGHPGWEIEPARPLRGVAPGQTAVLYRGTRVLG +QATIDTARNARLSAPADA +>PROKKA_01426 +MKVLAAMSGGVDSAVAAARAVEAGHDVVGVHLALSRMPGTLRTGSRGCCTIEDASDAWRA +CERLGIPFYTWDFSERFAEDVVEDFVAEYAAGRTPNPCMRCNERIKFAALLERALELGFD +AVCTGHYAAVRPGPDGGLELHRAADDAKDQSYVLGVLTADQLAHCLFPLADSPSKELVRA +EAAERGLSVAAKPDSHDICFIPDGDTRGWLAERIDLTPGPIVDADGCAVGEHAGAQAFTV +GQRKGLAIGRPAPDGRPRFVLEVRPKENTVVVGGRELLDVDRITGIRPTWAGAALPEART +GEWFDCALQFRAHGEIVDARARQLEDEAGGPRWEIEPARALRGVAPGQTAVLYRGTRVLG +QATIDTARNARLAAGSDA +>PROKKA_01328 +MKVLAAMSGGVDSAVAAARAVEAGHDVVGVHLALSRMPGTLRTGSRGCCTIEDAQDAWRA +CEVLGIPFYTWDFSERFQADVVDDFVAEYAAGRTPNPCLRCNEKIKFEALLDRALELGFD +AVATGHYARVEWGEDGRVQLHRAAEDAKDQSYVLGVLREDQLEHCLFPLADTPTKELVRS +EAAERGLSVAAKPDSHDICFIPDGDTRGWLAERIDLAPGPIVGADGEVLGEHAGAQAYTV +GQRKGLAIGRPAPDGRPRFVLEVRPKDNTVVVGGRELLDVDRITAIRPSWAGAPLPEAAA +GGWFDCELQFRAHGEIVPARARQAADDDGRPRWEIRPERPLRGVAPGQSAVLYRGTRVLG +QATIDTARNAAVDAAERA +>PROKKA_01424 +MKVLAAMSGGVDSAVAAARAVDAGHDVVGVHLALSRMPGTLRTGSRGCCTIEDASDAWRA +CERLGIPFYTWDFSERFAEDVVDDFVAEYEAGRTPNPCMRCNERIKFAALLERALELGFD +AVCTGHYAAVRPGPDGSLELHRAADDAKDQSYVLGVLTADQLAHCLFPLADTPSKELVRA +EAAERGLSVAAKPDSHDICFIPDGDTRGWLAERIDLAPGPIVDPEGRELGTHAGAQAFTV +GQRKGLAIGRPAPDGKPRFVLEVRPKENTVVVGGRELLDVDRITGIRPSWAGAPVPEART +GAWFDCALQFRAHGEIVEARARQRADEAGNPGWEIEPARPLRGVAPGQTAVLYRGTRVLG +QATIDTARNARLSAPADA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001223.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001223.fa new file mode 100644 index 0000000000000000000000000000000000000000..e3dfbe95c157f8cbc5987dfbe1c4fe6a709403bb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001223.fa @@ -0,0 +1,35 @@ +>PROKKA_01480 +MSAAEEHRTAYEVLGVPRDATAEEVRRAYRRAARAAHPDVGGDPAAFRAVTRAWDLLGDA +EARRRYDLSLPGPDVGPRGPRATAGSGRARPSGRSGPGGRAARPVRYEPPPGEAEADPTV +LDLPRSSQRVHGAPRPRGILPDEHRVLRQARTLDVLLRHVADALPAARVLTGLRLGGRWG +RHLDVDHAVLCGHRLALIGSVMVPEGTYTWDGADLRSRGRPVAPPLLGPAMMAWQQALPQ +VTVGGFVHVMTDRDARHAPVIRHTRGADAPEAQADLLTAPPAPGIAFAREVALFLGTGTD +PDLVDRRALGALVGRLH +>PROKKA_01212 +MSAAEEHRTAYEVLGVPRDATAEEVRRAYRRAARAAHPDVGGDPAAFRAVTRAWDLLGDA +EARRRYDLSLPGPDVGPRGPRATAGSGRARPSGRSGPGGRAARPVRYEPPPGEAEADPTV +LDLPRSSQRVHGAPRPRGILPDERRVLRQARTLDVLLRHVADALPAARVLTGLRLGGRWG +RHLDVDHAVLCGHRLALIGSVMVPEGTYTWDGADLRSRGRPVAPPLLGPAMMAWQQALPQ +VTVGGFVHVMTDRDARHAPVIRHTRGADAPEAQADLLTAPPAPGIAFAREVALFLGTGTD +PDLVDRRALGALVDRLH +>PROKKA_01422 +MSAADEHCTAYEVLGVDRDADDAAVRRAYRAAARRTHPDAGGDPAEFRAVSRAWQVLGDA +DARRRYDLSLPAPGAGRAPASGGAARPGRAAASRPARGAAGRPARTVRYEPPPGEGESDA +AVLDLPRSSQRVHGAPRPRGILPDEHRVLRQARTLDVLLRHVADALPAARVLTGLRLAGR +WGRPLDVDHAVLCGHRLALVGSVMVPEGAYTWDGSDLRSRGRPVAPPLLGPAMMAWQQVL +PQVTVGGFVHVMTDRDALHGPVVRHARGADDPGARADLLTVPPAPGREFVRDLLLFLGTG +EDPDLVDRRVLGTLVERLH +>PROKKA_01322 +MSGTGDRRTAYEVLGVPRDADAERIRRAWRAAARRTHPDAGGDARDFRAVTRAWEQLGDP +EARRRYDLSLPPEPAGTTGRTASAGRSAAQAWPPAGVRERDRPAPGSVVYDPPPGQGEHD +SSVLDLVRSSQRLHGAPRPRGILPDEHRVVRQARTLDLLARTLPPVLPAVRILTGLHLGG +RFGRGLDVDHAVLCGRRLALVGSVQVPDGTYTWDGADLRAGARGRPVAPPLLGPAMQAWQ +HALPQVTVGGFVLVMTDRDAVHSPVIRQARGADRPEAQADLLTAAPAAGRDLLRELQLFL +GSGPDPDVVDRRALAVLVRHLH +>PROKKA_01430 +MSAAEEHRTAYEVLGVPRDATAEEVRRAYRRAARAAHPDVGGDPAAFRAVTRAWDLLGDA +EARRRYDLSLPGPDVGPRGPRATAGSGRARPSGRSGPGGRAARPVRYEPPPGEAEADPTV +LDLPRSSQRVHGAPRPRGILPDEHRVLRQARTLDVLLRHVADALPAARVLTGLRLGGRWG +RHLDVDHAVLCGHRLALIGSVMVPEGTYTWDGADLRSRSRPVAPPLLGPAMMAWQQALPQ +VTVGGFVHVMTDRDARHAPVIRHTRGADAPEAQADLLTAPPAPGIAFAREVALFLGTGTD +PDLVDRRALGALVDRLH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001224.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001224.fa new file mode 100644 index 0000000000000000000000000000000000000000..b409189e6bb336dad5aa5bdb79cf8949e6d6a127 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001224.fa @@ -0,0 +1,24 @@ +>PROKKA_01481 +MPDSPTPPRPNPHEGADRAPAPGTPGFRILLLTPEIPGNTGNAIRLAALTGAELHLVEPL +GFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGSVRHDRVAYRPGD +VLLFGRESTGLPEEVLTDPRVTETVCLPMQPARRSLNLANAVSIAVYEAWRQHDFAGSAA +RPDSLD +>PROKKA_01213 +MPDSPAPPRPNPHEGADRAPAPGTPGFRILLLTPEIPGNTGNAIRLAALTGAELHLVEPL +GFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGSVRHDRVAYRPGD +VLLFGRESTGLPEEVLADPRVTETVCLPMQPARRSLNLANAVSIAVYEAWRQHDFAGSAV +RPDSLD +>PROKKA_01421 +MEPLGFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGRVRHDRVDY +RPGDVLLFGRESTGLPEEVVADPRVAETVALPMQPSRRSLNLANAVSIAVYEAWRQHGFA +GAASETDSLD +>PROKKA_01321 +MPQTPPDPSPAAPPPAARNPHLDAERAPAPGTPGFRILFHTPEIPGNTGNAIRLAAITGA +ELHLVEPLGFDFSDAHLRRAGLDYHDLAVMTVHPDLDTALAALAPARVFAFSARGRVRHD +RVAYEAGDVLLFGRESTGLPEDVLSDPRVTDTVSLPMQPSRRSLNLANAASIAVYEAWRQ +HGFAGAGSPAADSLH +>PROKKA_01431 +MPDSPTPPRPNPHEGADRAPAPGTPGFRILLLTPEIPGNTGNAIRLAALTGAELHLVEPL +GFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGSVRHDRVAYRPGD +VLLFGRESTGLPEEVLTDPRVTETVCLPMQPARRSLNLANAVSIAVYEAWRQHDFAGSAA +RPDSLD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001227.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001227.fa new file mode 100644 index 0000000000000000000000000000000000000000..c51d63c93d2797c89ca40b9f7759468b5a1d2033 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001227.fa @@ -0,0 +1,45 @@ +>PROKKA_01484 +MDQTAAPTQPPVPTARTVARPRPQSRARAGAGLLAAAVLMVGLSGCAVAEDGGEAASEAA +SSSSSQATDTSAEAGGQPVADTAVGDAARTALPSVVTISATSSSASGSGSGSILDTEGHI +LTNTHVVTLGGQANDAELTVRTSDGEVYAATVVGTDPLSDLAVIKIDAPDLTPIQIGRSG +DLKVGDEAVAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPEPQGESSGSSSGSDQYRFQ +LPGTPQGTRGEVYINVLQTDAAINPGNSGGALVDAEGRLVGVNVAIASAGQDPSEAGNIG +VGFAIPVDYAQRVAQDLIDHGKATHAMLGVSVTPEPAEVQGGGENAQTVFSDGARVQQVV +GGSAADAAGLKEGDVITAVGDRAVIDSESLTAVVREYRVGDSVDVTYLRDGAEQKTEVTF +TEDTQS +>PROKKA_01216 +MDQTAAPTQPPVPTARTVARPRPQSRARAGAGLLAAAVLMVGLSGCAVAEDGGEAASEAA +SSSSSQATDTSAEAGGQPVADTAVGNAARTALPSVVTISATSSSASGSGSGSILDTEGHI +LTNTHVVTLGGQANDAELTVRTSDGEVYAATVVGTDPLSDLAVIKIDAPDLTPIQIGRSG +DLKVGDEAVAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPEPQGESSGSSSGTDQYRFQ +LPGTPQGTRGEVYINVLQTDAAINPGNSGGALVDAEGRLVGVNVAIASAGQDPSEAGNIG +VGFAIPVDYAQRVAQDLIDHGKATHAMLGVSVTPEPAEVQGGSENARTVFSDGARVQQVV +GESAADAAGLKEGDVITAVGDRAVIDSESLTAVVREHRVGDSVDVTYLRDGAEQTTEVTF +TEDTRS +>PROKKA_01418 +MRSEDTVAHTPADQTPTDQTPTDQTPAPARPAAEARHPGRRAPRARAGLGLLAAAVLVTG +LAGCGVAAEPGADASGSAPDSSTSSGSASADPGQDVADTAVGTAAKTALPSVVTISATSG +QGSGSGSGTILDEEGHILTNTHVVTLGGQASDAELTVRTADGTVYAATVVGTDPLSDLAV +IKIDAPDLTPIQMGRSADLKVGDDAIAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPRQ +QESEQGQGPGQGSSSGPERFRFELPGAQQGPQGEVYINVLQTDAAINPGNSGGPLVDGQG +RLVGVNVAIASAGQGQGEAGNIGVGFAIPVDYAQRVAQDLIEHGEATHAVLGVSVTPEPA +EVQGGDAQARTVFSDGARVREVVADSPAAQAGLREGDVITAVGERAVIDTESLTAVVREH +RVGDSAEITYLRDGAEQKAQVEFQEDTSQ +>PROKKA_01318 +MGRAAHRPDCTDGGADQKPAQTRSEATVEHPAPDTVTPEAAPVASSPRPASPRGRRRALG +GALAATVLAGSLAACGVAGPGAGASASASASGSSSAAAAPAVGSTDQPVADNPVGAAAAK +ALPSVVTISATSGSSAGSGSGSILDAEGHILTNTHVVTLGGTASDASITVRTSDGKVYAA +KVVGTDPVSDLAVIKIDAQGLTPITIGSSKDVKVGDDAIAIGAPLGLSNTVTDGIISTLN +RTIAIQSSAAPEGQTGSSGTERFRFQLPGEQGQSQQQDIYINVLQTDAAINPGNSGGALV +NGAGELVGVNVAIASAGGSSASGAESGNIGVGFAIPVDYAKRVADDLIADGTASHGLLGV +TVQPQPAQVQGAAGGSKSTEFSAGALVHTVSSGSPAEKAGLKEGDVITQVGERTVTDTES +LTAAVREYRDGETTPVRFTRDGREQTADVTLTAMEASR +>PROKKA_01434 +MDQTAAPTQPPVPTARTVARPRPQSRARAGAGLLAAAVLMVGLSGCAVAEDGGEAASEAA +SSSSSQATDTSAEAGGQPVADTAVGNAARTALPSVVTISATSSSASGSGSGSILDTEGHI +LTNTHVVTLGGQANDAELTVRTSDGEVYAATVVGTDPLSDLAVIKIDAPDLTPIQIGRSG +DLKVGDEAVAIGAPLGLPNTVTDGIISTLDRTIAVASSEAPEPQGESSGSSSGAEQYRFQ +LPGTPQGTRGEVYINVLQTDAAINPGNSGGALVDAEGRLVGVNVAIASAGQDPSEAGNIG +VGFAIPVDYAQRVAQDLIDHGKATHAMLGVSVTPEPAEVQGGSENARTMFSDGARVQQVV +GESAADAAGLKEGDVITAVGDRAVIDSESLTAVVREHRVGDSVDVTYLRDGAEQTTEVTF +TEDTRS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001228.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001228.fa new file mode 100644 index 0000000000000000000000000000000000000000..576e2920449b12703a6d4b65847163a7b9d71cb3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001228.fa @@ -0,0 +1,66 @@ +>PROKKA_01485 +MTVLTRPADVGRLARAVTAAGLGGLGLLVAAPTAQAVAVPPGVYVVDEAGVLSTSDEQRL +TQEIQDLRRDTGQGLYVVYVDEFSTDAQTLAQDVARQRGLGTNDSVLAIAVEERAYGLDS +GGDANLQNQVTRTYVGPQLSKIGTDPGSAEWLAVGIAAVQGLDDAADGTLDGTGASGAEY +DPAGALPAGTTGGGSTAQGASDGGGALTAVLGAGAVAAAVGGGVLVARSRRRTQGGAVER +GRTEEARRDPLDELSVEQLRTQAGSKLVAADDAIRSSEQELGFAEASYGEKSVATFRQDI +DQAKEHMRASFQLQHQLDDEIPDTEAEQRAWLKEIIQRSEAVGASLAAHKKEFDSLRDLE +NQVPEALERLEARLPEARSRVQDSESAITALHGQYAESALAEVADNAAQARERLEFVETA +LAKSRSAWEAQDRSTAALAVRAAEEALSQVDTLTEAVGKAEGSLRAMLGNLQTGLAQSEQ +DVAEAEALVANGSHPELAGPVAGMKTAVNAVRQALAAGRPDPLELLHQLEAAHRQLNTPL +AGVRDAREQARQASQVLTSTIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRSA +ISLGRTDPVAALQQAQRASQLAERASELARADVEGFGYGPGMGSRYGTRPRAGVGGSFGG +GLGGALLGGILMNSILNSGHGDSWGGGGFGGFDGGGLGGGDFGDISGGGF +>PROKKA_01217 +MTVPTRPADVGRLARAVTAAGLGGLGLLVAAPASHAVTVPPGVYVVDEAGVLSTSDEQRL +TQEIQDLRRDTGQGLYVVYVDEFSTDAQTLAQDVARQRGLGTNDSVLAIAVEDRAYGLDS +GGDADLQNQVTRTYVGPELSKIGTDPGSAEWLAAGTAAVQGLDDAADGTLDGTGASGAEY +DPAGALPAGTAGDGSTAQGASGGGALTAVLGAGAVAAAVGGGVLVARSRKRTQGGAVEGG +RTEEVRRDPLDELSVEQLRTQAGSKLVAADDAIRSSEQELGFAEASYGEKSVATFREDID +RAKEHMRASFQLQHQLDDEIPDTEAEQRAWLKEIIQRSEAVGAALAAHKKEFDSLRDLEN +QVPEALERVDARLPEARSRVQESESAIAALHGQYAESALAEVADNATQARERLEFVETAV +AKARSAWDAQDRSTAALAVRAAEEALSQVDTLTEAVGKAEGSLRAMLGNLQTGLAQSEQD +VAEAEALVANGSNPELAGPVAGMKNAVNAVRRALAAGRPDPLELLHQLEAAHRQLNTPLA +GVRDAREQARQASQVLTSTIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRSAI +SLGRTDPVAALQQAQRASQLAERASELARADVEGFGYGPGMVGGMYGARPRAGVGGSFGG +GLGGALLGGILMNSILNSGSWGGGGFGGFDGGGLGGGDFGGFGDISGGGF +>PROKKA_01417 +MTAAGLGGVGLVLAAPGAGAGIAPPGVYVVDEAGVLSSADEQRLTQEITDLRRDTGQGLY +VVFVDSFETNAQGLADDVARQRGLGTNDSVLAIAVEDRSYGLGSGGDASLQNQITRTYVG +PQLSRIGTDPGSAEWLAAGTAAVQGLDDAADGTLDGTGASGAEYDPEGALPAGSGAGAGT +GAGSSQGSDEGSGVLTAVLGAGAVAAAVGGGVLVARNRRKKDGGAVERSGRDARPVERDP +LDEMSLEDLRTRAGSKLVAADDAIRSSEQELGFAMASYGEDAVRTFREDIDQAKEHMRAS +FQLQHQLDDHIPDTEEDQRSWLKEIIQRSDAVGAALASHQKDFDSLRDLENNVPEALERI +DARLPEARARVQQAESSISALHGQYAESALAEVADNAAQARERLDFVETAEAKARQAWET +QDRSTAALAVRAAEESLSQVDTLTEAVGKAEGSLRTIVGNLQTGLAQSEQDLAEAEALVA +NGSHPELAGPVAGMKTTLAAVRRSLSGGRPDPLDLLHQLEAAHRQLNTPLSGVRDAREQA +RQASQMLNSAIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRAAIDLSRTDPVT +ALQQAQRASQLAERASELARQDVEGFGYGGSMYGPGMGGMYGGRQRSGAGASFGGGLGGA +LLGGILMNSMFNSGGGSWGGGGFGGFDGGGLGGGDFGGFGDISGGGF +>PROKKA_01317 +MAESVVRPSAPRLSRAAVLGGLGAITTTALLAPGAHAAVDVPPGTFVVDQAEVLSSAQES +ELTQDITQLQSKAGQNLYVVYVDKFDSTPQATIDSVVQQRGLGNSDSVLAIAVENRNYGF +DTGMSSTMQSDIRSAYILPALRKAAAGGDWEAPAVAAVQGLDDAANGTLDGRGRSGETYQ +PDGTLPQAAEQDSSAQTSTSDSGNGASGALVGAGALAAVAGGAYVVSRRRRKSDGGAEPG +AVATGPQASRDPLDELSVDELRKRAGATLVAADDAIRSSEQEVGFAMASYGEGAVGTFRQ +DIEKAKEHMRASFQLQHQLDDEIPDTEADQRSWLKEIIARSEQVGATLAAHKKEFDSLRD +LENSVPEAISALESRVPQAEGAVQAAERELVDLHGRYAESALTEVNDNATQARERLEFVK +TAEAKARASLEAGDRSTAAVAVRAAEESLSQVGTLTEAVSKAGAALSTHVANLQMGISQS +EQDLAEAQALLSAGRNPELAGPVGGMQQTLAAVRAELQSGRPDPLALLQRLESAHRQLNT +PLSGVRDAREQARQAEQMLSAAISQAQAQIDGTADFIGARRGAVGSEARTRLAEADRSLQ +TAMSLRSTDPVAALDHAQRASQLADRASERAQQDVADFGYGGMGGYGGLGGGYAGAGYRG +GYGMPRSGAGGGFAGGLGGALLGGILMNSMFGGHHHDSGFGGGDWGGGGFGGFGGGGLDG +GDFGGFGDADFGGF +>PROKKA_01435 +MTVPTRPADVGRLARAVTAAGLGGLGLLVAAPASHAVTVPPGVYVVDEAGVLSTSDEQRL +TQEIQDLRRDTGQGLYVVYVDEFSTDAQTLAQDVARQRGLGTNDSVLAIAVEDRAYGLDS +GGDADLQNQVTRTYVGPELSKIGTDPGSAEWLAAGTAAVQGLDDAADGTLDGTGASGAEY +DPAGALPAGTAGDGSTAQGASGGGALTAVLGAGAVAAAVGGGVLVARSRKRTQGGAVEGG +RTEEVRRDPLDELSVEQLRTQAGSKLVAADDAIRSSEQELGFAEASYGEKSVATFRQDID +QAKEHMRASFQLQHQLDDEIPDTEAEQRAWLKEIIQRSEAVGASLAAHKKEFDSLRDLEN +QVPEALERLEARLPEARSRVQDSESAITALHGQYAESALAEVADNAAQARERLEFVETAL +AKSRSAWEAQDRSTAALAVRAAEEALSQVDTLTEAVGKAEGSLRAMLGNLQTGLAQSEQD +VAEAEALVANGSHPELAGPVAGMKTAVNAVRQALAAGRPDPLELLHQLEAAHRQLNTPLA +GVRDAREQARQASQVLTSTIAQAQAQIDGTADFIGARRGAVGSEARTRLAEADHTLRSAI +SLGRTDPVAALQQAQRASQLAERASELARADVEGFGYGPGMVGGMYGARPRAGVGGSFGG +GLGGALLGGILMNSILNSGSWGGGGFGGFDGGGLGGGDFGGFGDISGGGF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001231.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001231.fa new file mode 100644 index 0000000000000000000000000000000000000000..28e2b5244336b6b7a39c42578347f63ec6c80253 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001231.fa @@ -0,0 +1,94 @@ +>PROKKA_01512 +MSFGQGGGGPFGGPPRDGGGTAGGQSGPFGAFGPFGGAPRGPGDDGDRGPGGPFGGGGSS +AARGRGRPGRPSALVLTIIAVAVLVGLFVVFTNVYTDVLWFSQLGFTEVFWTEVLAKAAL +FLIAGLGMALAVWLAIRTAWRHRPADASAAARDSLSQAQRQLEPIRRLVFLGVPLVLGVF +AGSTAMNGWNTVLLFLNQVPYGQADPEFGLDLMFFMATLPFLTLMVGYLISVVLVSGITG +LLVHYLYGAVRVEEGGSVRITPAARAHIGITLAVFLLLQGVNFWLNRYRTTQSQTGNWAG +ALYTDVNAVIPTSAILAVTAVIVAGLFVWTVVSGRWRLSLIGTAVLVITALVVGTAYPFI +VQEYQVKPSERTLESQYIERNIAMTREAYGLDDVEVTNYEGATDPEAGALAGEEANTANV +RLMDPNLISQTFGQLQQFRPYYSFPTTLHVDRYEVDGQTRDTILAARDVNVDDMQSWVNR +HTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDQDYEPRIYFGLNSPSYSVVG +APEGAPAVERDRPQTADSQEDTAYTFSGDGGPSVGNLFNRLAYAVKFGSPELVLSSDVNE +ASQILYDRDPAERVRKVAPYLTVDTAPYPAIVDGRVQWIVDAYTTSDQFPYSTAQQLGEV +TVDSLSQGQNPALQGRVNYIRNSVKATVDAYDGSVSLYAWDDQDPLLQAWQNVYPSSLRP +YSEMSAGLLDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPTREEDVKQPP +YYMTLQMPGQDEPAFSLTSSYIPQITDGAQQRNVLYGFLSAAGDAGTGEDGVKAEGYGQL +RLLELPRSTTVPGPGQAQANFDSNADVSRELNLLRQGASEVLNGNMITLPVAGGILYVQP +VYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEKQAEAPAPGE +EPTAPGTVEEELSAALEEAQDALTQGQERLAEGDWAGYGEQQKRLNEALKRATAADDALG +GDAPAQEQAPAEASPAPSSSPSPTPSG +>PROKKA_01221 +MSFGQGGGGPFGGPPRDGGGTAGGQSGPFGAFGPFGGAPRGPGDDGDRGPGGPFGGGGSS +AARGRGRPGRPSALVLTIIAVAVLVGLFVVFTNVYTDVLWFSQLGFTEVFWTEVVAKAAL +FLIAGLGMALAVWLAIRTAWRHRPADASAAARDSLSQAQRQLEPIRRLVFLGVPLVLGVF +AGSTAMNGWNTVLLFLNQVPYGQADPEFGLDLMFFMATLPFLTLVVGYLISVVLVSGITG +LLVHYLYGAVRVEEGGGVRITPAARAHIGITLAVFLLLQGVNFWLNRYRTTQSQTGNWAG +ALYTDVNAVIPTSAILAVTAVIVAGLFVWTVVSGRWRLSLIGTAVLVITALVVGTAYPFI +VQEYQVKPSERTLESQYIERNIAMTREAYGLDDVEVTNYEGATDTEAGALAGEEANTANV +RLMDPNLISQTFGQLQQFRPYYAFPTTLHVDRYEVDGQTRDTILAARDVNVDDSQSWVNR +HTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDQDYEPRIYFGLNSPSYSVVG +APEGAPAVERDRPQTADSQEDTAYTFSGDGGPSVGNLFNRLAYAVKFGSPELVLSSDVNE +ASQILYDRDPAERVRKVAPYLTVDTAPYPAIVDGRVQWIVDAYTTSDQFPYSTAQQLGEV +TVDSLSQGQNPALQGRVNYIRNSVKATVDAYDGSVSLYAWDDQDPLLQAWQNVYPSSLRP +YSEMSAGLLDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPTREEDVKQPP +YYMTLQMPGQDEPAFSLTSSYIPQITDGAQQRNVLYGFLSAAGDAGTGEDGVKAEGYGQL +RLLELPRSTTVPGPGQAQANFDSNADVSRELNLLRQGASEVLNGNMITLPVAGGILYVQP +VYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEKQAEAPAPGE +EPTAPGTVEEELSAALEEAQDALTQGQERLAEGDWAGYGEQQKRLNEALKRATAADDALG +GDAPAQEQAPAEASPAPSSSPSPTPSG +>PROKKA_01413 +MSFGQGGGGPFGGPPRDGGGSAGGSSGPFGAFGPFGGAPQGPGGDGRDGGQGGGPFGPFG +GGAGGSSAADRPRSGRPGRPSALVLTVIAVAILVGLFVLFTNVYTEVLWFSQLGFTEVFW +TEVLAKAALFLLGALGMALAVWLAIRTAWRHRPSDASAAGRDSLSQAQRQLEPIRRLVFL +GVPVVLGLFAGSAAMNGWDTVLLFLNQVPYGQADPEFGLDMMFFMATLPFLSLVAGYLTS +VVLVAGIAGVLVHYLYGSVRVEEGGGIRVAPAARVHVGVVLALFLLLQAVNFWLNRYRTA +QSQSGSWAGALYTDVNAVIPTSAILAVTAVIVAGLFVWTVFSGKWRLSLIGTAVLVITAL +VVGTAYPFVVQEYQVKPSERTLEAEYISRNIELTREAYGLDAVEVTNYEGVTETEAGALA +GEEANTANVRLMDPNLISQTFGQLQQFRPYYAFPDTLHVDRYEVDGQTRDTILAARDVNV +DDTQSWVNRHTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDEDYEPRIYFGQ +NSPSYSVVGAPEGAPAVERDRPQTADSQDDTAYTFSGDGGPSVGGLFNRLAYAVKFGSPE +LVLSSDVNEASQILYDRDPADRVSKVAPYLTVDTSPYPAIVDGRVQWIVDAYTTSDQFPY +STAQQLGEVTVDSLSQGPNAALQGRVNYIRNSVKATVDAYDGSVTLYAWDDQDPLLQAWQ +KVYPSSLRPYSEMSAALMDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPT +RDGDVKQPPYYMTLQMPGQEEPAFSLTSNYIPQITQGSQQRNVLYGFLSAAGDAGTGEDG +VKAEDYGTLRLLELPRSTTVPGPGQAQANFDSNATVSRELNLLRQGASEVLNGNMITLPV +AGGVLYVQPVYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEG +QAGDPPQGEDGAAPAPGSVQEELSSALAEAQDALTRGQERLAEGDWAGYGEQQDRLNEAL +RRATAADDALDGDAPADGEAPAEGQPPAEGSEAPSPAPEG +>PROKKA_01312 +MSFGQEGAGPFGGPPHHDGDGGAHAARRVRAGGGRPSALLLTVIAVAALVALYMLFTQVY +TEVLWFDQLGFSEVFWTEVLTKAALFVVAGAVMALAVWLSLRTAWRHRPGTAGADGRDSL +SRARRQLEPMRRLVWAALPAVLGLFAGSAAMNGWKTVQLFLHQVPYGKADPEFGLDLMFY +LATLPFLTMAVGYLISVVLVAGLAGLAVHYLYGALGVGDDGRVHVSVPARVHLGVLAGLF +LLLQAATFWLNRYRTLQSQAGNWAGAMYTDVNAAIPTSAILAVTAALVAALFVWAAFTGR +FRLPLVGAAVLVITALVVGTAYPYVVQQYQVKPSERTLESPYIARNIEMTREAYGLDQVQ +VANYEGTTDAQAGDLKGEEANTANVRLMDPNLISQTFGQLQQFRPYYAFPGTLHVDRYEV +DGQTRDTILAARDVNVDPEQSWVNRHTIYTHGYGVVAADASAVGAGGRPQWMLSEIPSRG +VLGDDSTYEPRIYFGLNSPAYSVVGAPEGAPAVERDRPQTADSTDDTAYTFQGDGGPSVG +GLFNRLAYAVKFGSPELVLSSDVNEASQILYDRDPVDRVAKVAPYLTVDTAPYPAIVGGR +VKWIVDAYTTSDQFPYSTAQQLGEATQDSLSEGQAAALQGRVNYIRNSVKATVDAYDGSV +ELYAWDAEDPLLKSWQGVYPASLKPYSEMSAALLDHVRYPEDMFKVQRELLGRYHVTNPG +DFYENNDAWSVPSDPTTDKDVKQPPYYMSLRLPGQEETAFSLTSTYIPQITDNGQQRNVL +YGFLSADGDAGTGRDGERAPGYGTLRLLELPRSTTVPGPGQAQANFDSNAQVSQELNLLR +QGASEVLNGNMITLPVAGGILYVQPVYVRSSGGTTYPTLRKVLVSFGDKVGFADTLDEAL +NQVFGGDSGATTPDAGEPAQEPRGTAEEELSSALAEAQDALAEGQERLAQGDWAGYGEQQ +TRLNEALKRATAADDAAKGAQESADPAPEG +>PROKKA_01439 +MSFGQGGGGPFGGPPRDGGGTAGGQSGPFGAFGPFGGAPRGPGDDGDRGPGGPFGGGGSS +AARGRGRPGRPSALVLTIIAVAVLVGLFVVFTNVYTDVLWFSQLGFTEVFWTEVVAKAAL +FLIAGLGMALAVWLAIRTAWRHRPADASAAARDSLSQAQRQLEPIRRLVFLGVPLVLGVF +AGSTAMNGWNTVLLFLNQVPYGQADPEFGLDLMFFMATLPFLTLVVGYLISVVLVSGITG +LLVHYLYGAVRVEEGGGVRITPAARAHIGITLAVFLLLQGVNFWLNRYRTTQSQTGNWAG +ALYTDVNAVIPTSAILAVTAVIVAGLFVWTVVSGRWRLSLIGTAVLVITALVVGTAYPFI +VQEYQVKPSERTLESQYIERNIAMTREAYGLDDVEVTNYEGATDTEAGALAGEEANTANV +RLMDPNLISQTFGQLQQFRPYYAFPTTLHVDRYEVDGQTRDTILAARDVNVDDSQSWVNR +HTIYTHGYGMVVADASEVAAGGRPQWLLSEIPTRGPLASDQDYEPRIYFGHNSPSYSVVG +APEGAPAVERDRPQTADSQEDTAYTFSGDGGPSVGNLFNRLAYAVKFGSPELVLSSDVNE +ASQILYDRDPAERVRKVAPYLTVDTAPYPAIVDGRVQWIVDAYTTSDQFPYSTAQQLGEV +TVDSLSQGQNPALQGRVNYIRNSVKATVDAYDGSVSLYAWDDQDPLLQAWQNVYPSSLRP +YSEMSAGLLDHVRYPEDMFKVQRELLGRYHVTDADDFYENNDAWSVPSDPTREEDVKQPP +YYMTLQMPGQDEPAFSLTSSYIPQITDGAQQRNVLYGFLSAAGDAGTGEDGVKAEGYGQL +RLLELPRSTTVPGPGQAQANFDSNADVSRELNLLRQGASEVLNGNMITLPVAGGILYVQP +VYVRSSGGTTYPTLRKVLVSFGDKVGFADTLQEALDQVFDGDSGAVTPEEKQAEVPAPGE +KPTAPGTVEEELSAALEEAQDALTQGQERLAEGDWAGYGEQQKRLNEALKRATAADDALG +GDAPAQDQAPAEASPAPSSSPSPTPSG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001232.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001232.fa new file mode 100644 index 0000000000000000000000000000000000000000..2ffec731e52db2c127daf37ce06137cfa1e8b2ca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001232.fa @@ -0,0 +1,35 @@ +>PROKKA_01513 +MRAVPSRTTRAARVPFSGWLALGSAGLALLAPTPYILEGPGPAVDLLGEREGRPVLRVEG +GEADPGEGTLHMTTVMVGGPPIGTTSLLDLGRGLTDPAVDVAPRELMYPTGVTSDEVGEA +NSAAMSDSQQTATAAALHELGREVPQRLVVQQLVPGGPAEGVLRAGDEVIAAEGRPVADL +EAVRAAVGAAGPDPVTLTVRRDGVEQDLEVPVAAAPEGAPQPWQMGALIETAYDVPVDVE +LTVPDIGGPSAGLMFALTVIERLTPGAMTGGASIAGTGTITGDGVVGPIGGIPQKVRGAA +EAGATTFLAPTANCEELAGRVPEGLTVYPVDTLGQARDIVEAVARGESPAAARTCG +>PROKKA_01222 +MRAVPSRTTRAARVPFSGWLALGSAGLALLAPTPYILEGPGPAVDLLGEREGRPVLRVEG +GEADPGEGTLHMTTVMVGGPPIGTTSLLDLGRGLTDPAVDVAPRELMYPTGVTSDEVGEA +NSAAMSDSQQTATAAALHELGREVPQRLVVQQLVPGGPAEGVLRAGDEVIAAEGRPVADL +EAVRAAVGAAGPDPVTLTVRRDGVEQDLEVPVAAAPEGAPQPWQMGALIETAYDVPVDVE +LTVPDIGGPSAGLMFALTVIERLTPGAMTGGAPIAGTGTITGDGVVGPIGGIPQKVRGAA +EAGATTFLAPTANCEELAGRVPEGLTVYPVDTLGQARDIVEAVARGETPAAARTCG +>PROKKA_01412 +MRAVPPRTTRAYRLPASGWLALGSAGLALLLPTPYILESPGPAVDLLGERDGAEVLRVEG +GTPDEGEGTLDMTTVMVGGPPISTTSVIDLARSLVDPAVDVVPRELMYPTGMSSEEVGAA +NTAAMSDSQDTAAAAALHALGRPVPSTLVVHELVPGGPSEGVLRPGDEVIAAAGEPAEDL +EDLRAAVGAAGPDPVTLTVRRDGAVTELRVPVAAAPEGAPQPWQMGALIETVVDVPLDVE +LTVPDIGGPSAGLMFALTVLERLTPGAMTGGAPIAGTGTITPDGVVGPIGGIPQKVRGAA +QAGATTFLAPTANCGELDGRVPEGLQVYAVDTLAQAREIVEAVGRGEPPESARTCG +>PROKKA_01311 +MPYILEGPGPAIDVLGEQDGTPVLTVEGGTADPGEGRLDMTTVLVSGPPGGTTGLGDLVT +ALADGTVDAQPRELVHPSGVSADTVAQSNAAAMTDSQDVATAAALRALGRDVPAHLAVHA +TVPGAPAEGILREGDVILAAAGRSVTDMAGIRAAVDAAGPGDLALTLRRDGTERQVSVPV +TAADPATGRSWQLGVLLEQRFDLPVQVEFALEDIGGPSAGMMFALAVIERLTPGDMTGGA +RIAGTGTITADGVVGPIGGIPQKMQGAARDGADVFLAPRENCADLAGRVPAGMTVYAVDT +LATARAVVEAVGRGERPDDVPTCS +>PROKKA_01440 +MRAVPSRTTRAARVPFSGWLALGSAGLALLAPTPYILEGPGPAVDLLGEREGRPVLRVEG +GEADPGEGTLHMTTVMVGGPPIGTTSLLDLGRGLTDPAVDVAPRELMYPTGVTSDEVGEA +NSAAMSDSQQTATAAALHELGREVPQRLVVQQLVPGGPAEGVLRAGDEVIAAEGRPVADL +EAVRAAVGAAGPDPVTLTVRRDGVEQDLEVPVAAAPEGAPQPWQMGALIESAYDVPVDVE +LTVPDIGGPSAGLMFALTVIERLTPGAMTGGAPIAGTGTISGDGVVGPIGGIPQKVRGAA +EAGATTFLAPTANCEELAGRVPEGLTVYPVDTLGQARDIVEAVARGESPAAARTCG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001233.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001233.fa new file mode 100644 index 0000000000000000000000000000000000000000..3277c33c33b167982017a6c03bc48971b905930a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001233.fa @@ -0,0 +1,26 @@ +>PROKKA_01515 +MRLVRSTARTRTVSAAWRDGRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPD +GRPADARSDDALLAWAGRLSAAHLGGRARPVAVTWSARQRRRWGSCTPARGTIRLSTQLR +GMPDWVVAAVLVHELAHLLESGHGPAFRRLVDRYPRYAEAMAFLEGVTFAEGRGRTAPDR +WAEDEDAG +>PROKKA_01224 +MRLVRSTARTRTVSAAWRDGRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPD +GRPADARSDDALLAWAGRLSAAHLGGRARPVAVTWSARQRRRWGSCTPARGTIRLSTQLR +GMPDWVVAAVLVHELAHLLESGHGPAFRRLVDRYPRYAEAMAFLEGVTFAEGRGRTAPDR +WAEDEDAG +>PROKKA_01410 +MADNGRMPPADAAVPVPAEHERGEPVPAAAAVSALARRPVRRGAVRQSTDLDWEGTPVRL +VRSTARTRTVSAAWREGRLQVNVPARLTPAHEREWIARMVEQVARRAGAGASPGRPGAGS +QPGSGPGAGSGGDEALMAWAQRLSAAHLGGRARPASVAWSARQRRRWGSCTPSRGTIRLS +DRLRGMPDWVVAAVLVHELAHLLESGHGPAFRRLVAAYPRYAEAMAFLDGVAFAESRGRT +AQDTWVDDEDAMDADAPDDGPTEDERA +>PROKKA_01309 +MSPSRTVTDLDWHGTPVRLVRSARRTRTVAAVWREGRLQVSVPARLSRAEERRWIERMVD +RAGPAPAAHPAPSASAPSTGLGSAPDPRGDADLLARADALASAHLDGAAPGGRAPRPASV +TWSSRQRQRWGSCTPARGTIRLSAQLRGMPDWVVDAVLVHELAHLSERGHGPRFQALVGR +LPRYTEAMAFLAGVTYATSRGLPGAYPADADVADHARGWPGGDDDVVEG +>PROKKA_01442 +MPDNGRMRPVPPAPGRPPRAVPAAHRGPARESTDLDWEGTPVRLVRSTARTRTVSAAWRD +GRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPDGRPADARSDDALLAWAGRL +SAAHLGGRARPVSVTWSARQRRRWGSCTPGRGTIRLSTQLRGMPDWVVAAVLVHELAHLL +ESGHGPAFRRLVDRYPRYAEAMAFLDGVTFAEGRGRTAPDRWAEDEDAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001235.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001235.fa new file mode 100644 index 0000000000000000000000000000000000000000..d9349924641347c6076a28fde5b09cb6565c40be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001235.fa @@ -0,0 +1,65 @@ +>PROKKA_01517 +MSTPDEILRGLDPEQRRAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA +LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT +EVAQRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAAKEREMPAGWTATTVARLYTGY +EEAKTARNMIDFEDVLLILVGILSTEPQIAATIRDQYRVFVVDEYQDVSPLQHRLLDLWL +GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERYPAATVVRLVRDYRSSPQIVEAANRLL +ADRTKAGERDRTMPRWPDPLELVSQRPAGPDLVFAECTDDEAEAGWVADRIAALIDDGVP +ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT +GDDVTDRVRDVLSSLGYSAEPPSATGAARERWESLHALVNLADQLATTRGAEFTLTELVA +ELDERAQHQHAPTVQGITLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL +LYVGITRARQHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAAGPTAP +RRRGAKVAVCRTCGKPLETGAERKVGRCLDCPATYDEAVLEELRDWRTRTAAEMRMPAFV +VFTDATLVAIAEAMPRTPAELLKVPGLGKAKLEKHGPELLELLHGTPTA +>PROKKA_01226 +MSTPDEILRGLDPEQRRAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA +LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT +EVAQRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAAKEREMPAGWTATTVARLYTGY +EEAKTARNMIDFEDVLLILVGILSTEPQIAATIRDQYRVFVVDEYQDVSPLQHRLLDLWL +GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERYPAATVVRLVRDYRSSPQIVEAANRLL +ADRTKAGERDRTMPRWPDPLELVSQRPAGPDLVFAECTDDEAEAGWVADRIAALIDDGVP +ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT +GDDVTDRVRDVLSSLGYSAEPPSATGAARERWESLHALVNLADQLATTRGAEFTLTELVA +ELDERAQHQHAPTVQGITLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL +LYVGITRARQHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAAGPTAP +RRRGAKVAVCRTCGKPLETGAERKVGRCLDCPATYDEAVLEELRDWRTRTAAEMRMPAFV +VFTDATLVAIAEAMPRTPAELLKVPGLGKAKLEKHGPELLELLHGTPTA +>PROKKA_01408 +MSTPDEILRGLDPEQRRAATALQGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA +LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT +EVAQGMRMSVDRAGLRDLAGEIEWAKVSLHAPEGYAEAARGREMPAGWDATTVARLYTGY +EEAKTARNMIDFEDVLLILVGILSTEPRIAATIRDQYRVFLVDEYQDVSPLQHRLLDLWL +GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERHPDATVVELVRDYRSSPQVVEAANRLL +ADRTKAGQRDRTMPRWPDPLELVSQRPNGPDPVFAECTDDEAEAGWVADRIRALIDDGVA +ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT +GDDVPDRVRDVLASLGYSAQPPAATGAARERWESLHALVNLAEQLAGSRGAEFTLTELVA +ELDERAQHQHAPTVQGVTLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL +LYVGITRAREHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAPGAAKP +RRRGATVATCRTCGKPLETGAERKVGRCLDCPATYDEAVLEQLRDWRSRTAAEMKMPAFV +VFTDATLVAIAEAMPASPKELLAVPGLGRTKLEKHGEALLELLHGTPTA +>PROKKA_01307 +MSTPDEILRGLDPEQRKAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA +LTFTARAAAEMRTRLRDLGVDGVQARTFHSAALRQLQYFWPQAVGGQMPTLVENKVRLLT +EVAHRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAARDREMPAGWTATTVARLYTGY +EEAKTARNMIDFEDVLLILVGILSTEPKIAATVREQYRVFVVDEYQDVSPLQHRLLDLWL +GDRQDLCVVGDSSQTIYSFTGATSRFLTGFRERYPEATMVKLVRDYRSSPQIVGAANTLL +AERTQAGLRDRSLPFWPEPLALSSQRPSGPDVVFAECQDDEAEAGWVAQRIQGLLDDGVP +AAEIAVLFRTNGQSEAFETALSAAGIGYQLRGGERFFSRREVREGVLQLRAAAREAQDLV +GADVVQRVKDVLSSLGYSDTPPSASGAARERWESLHALVNLADQLAGTREDFTLVQLVAE +LDERAQAQHAPTVQGVTLASLHSAKGLEWDAVFLVGLSEGLMPISFADTPAEVDEERRLL +YVGITRARQHLHLTWTLARSGGGRANRRPSRFLRAIDPTLGGTREHAPAAAMPARRPRRG +ATVAVCRTCGRPLETGAERKTGRCVDCPALYDEGVLDTLKDWRSRVAKTDKVPAFVVFTD +ATLEAIAETMPATPAELIKVKGVGKSKLDRFGQDVLDLLHGTSAA +>PROKKA_01444 +MSTPDEILRGLDPEQRRAATALHGPVCILAGAGTGKTRAITHRIAYGVASGVFDPHRTLA +LTFTARAAAEMRTRLRDLGVAGVQARTFHSAALRQLQYFWPQAVGGPMPSLIENKVRLLT +EVAQRMRMTVDRAGLRDLAGEIEWAKVSLHAPEGYAEAAKEREMPAGWTATTVARLYTGY +EEAKTARNMIDFEDVLLILVGILSTEPQIAATIRDQYRVFVVDEYQDVSPLQHRLLDLWL +GDRGDLCVVGDASQTIYSFTGATSRFLTDFRERYPAATVVRLVRDYRSSPQIVEAANRLL +ADRTKAGERDRTMPRWPDPLELVSQRPAGPDLVFAECTDDEAEAGWVADRIAALIDDGVP +ASEIAVLFRTNGQSQAFETALSSAGIGYQLRGGERFFSRREVRDGILQLRAAARAAQDLT +GDDVTDRVRDVLSSLGYSAEPPSATGAARERWESLHALVNLADQLATTRGAEFTLTELVA +ELDERAQHQHAPTVQGITLASLHSAKGLEWDAVFLVGLSEGLMPISFAETQAEVDEERRL +LYVGITRARQHLSLTWTLSRGTGGRSTRRPSRFLWAIDPTLGGTREHAPARGSAAGPTAP +RRRGAKVAVCRTCGKPLETGAERKVGSCLDCPATYDEAVLEELRDWRTRTAAEMRMPAFV +VFTDATLVAIAEAMPRTPAELLKVPGLGKTKLEKHGPELLELLHGTPTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001237.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001237.fa new file mode 100644 index 0000000000000000000000000000000000000000..f1c04e803c2afaf8da25e2ffe26a18660ea0bcec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001237.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001238.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001238.fa new file mode 100644 index 0000000000000000000000000000000000000000..46e91307eb2cbe6f7efac5f2390bdaa6229da4a6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001238.fa @@ -0,0 +1,105 @@ +>PROKKA_01520 +MAPLTGDPAAPTDRPRVEDAVHSPEDIAARLRLPPPTEEQAEVVTAPLTPRLVLAGAGSG +KTSTMADRVVWLVANGLVRPDEVLGVTFTRKAAGELAERINGRVDALLRSGLEIPGFDGE +PEDLGRASVSTYHSYAGALVRDHGLRIGVEPEARLLGGADAHRLMGAVVRSHPVVADTLG +VAPSRLITQALRLAGDMAEHLVTADEVRGFLARLAEQGSALPLPPRAKTPSKEIQEFLTG +LADRALMADLVARYDEVKREQDVMDFGDLLRHAARIAVEVPAAGEQERARFPVVLLDEFQ +DTSHAQMRIFAGLFGPRGPEDDAPGLGHCVTAVGDPHQSIYGFRGASAGQLFAFPHAFPR +LETGPGGAPRRVNADVSHLTIAWRNEESILAVANAVAAPLNAHAAAAGGAPVEVRTLRPR +PGAGEGVVRVDRFVTAEEEAADVVARLGALTGSGPGGTTPSRAVLCRTRAQFGPVLDALD +AAGLPYEVLGLSGLLALPEVAEVLAVLHVLADPTRSDQLVRLLTGPRWRIGVADLEVLQE +RARFVSRLRAQRAAGGREDPAGAAPDAAPDRDVSPEEDADAAALLEALDSLPGEGTDWVG +SRGRGFSPEGLARLRAVNAELRRLSTRTGEDPADLIAEVIRETGLDVEVALRPGVSAAAA +RRHLNAFQDAARDFGAGTTATDLTAFLAWTESVLEHEDGLGVENAEPTPGLVQVLTAHAS +KGLEWDVVAVPGLQEGTFPSTRADRWTSPGAGALPWPLRGDRASLPQWDGSWAQDQRDWV +QSAGTKYSSKAAQEGNPDPYAVAVAAHAEREERRLAYVAYTRARSALWLSTSLFKGVNKE +PLPASAFLEEVAGLAGEVPGVALGPAPAEDDLPEANPAAARTLVARWPFDPLDGPEAFVA +DPEDPEDEERWQPLPHRSRARRHGVEAAAAAVHAADPAALGDDPELARQVDWVLLRRRDV +AGTGGETALPEHVSVSLYGELAADPQAVAEQLRRPLPRPPAHAARRGTAFHAWLEERFGA +TGMLDIGSAEDAADLWVDEALDLGPMQEWFRSSRWAERTPAFVEAPVETTVGGITLRGRV +DAIYRSGGDPRLPFDPEADWELVDWKTGAVPRGRDLELKSLQLAVYRLAWSRLHGIPLER +IGASFVYVAHGQERSFPDLPGEEELERHITDALARR +>PROKKA_01229 +MAPLTGDPAAQTDRPRVEDAVHSPEDIAARLRLPPPTQEQAEVVTAPLTPRLVLAGAGSG +KTATMADRVVWLVANGLVRPDEVLGVTFTRKAAGELAERINGRVDALLRSGLEIPGFDGE +PEDLGRASVSTYHSYAGALVRDHGLRIGVEPEARLLGGADAHRLMGAVVRSHPVVADTLG +VAPSRLITQALRLAGDMAEHLVTADEVRGFLARLAEQGSALPLPPRAKTPSKEIQEFLTG +LADRALMADLVARYDEVKREQDVMDFGDLLRHAARIAVEVPAAGEQERARFPVVLLDEFQ +DTSHAQMRIFAGLFGPRGPEDDAPGLGHCVTAVGDPHQSIYGFRGASAGQLFAFPHAFPR +LETGPGGAPRRVNADVSHLTIAWRNEESILAVANTVAAPLNAHAAATGGAPVEVRTLRPR +PGAGEGVVRVDRFVTAEEEAADVVARLGALTGSGPGGTTPSRAVLCRTRAQFGPVLDALD +AAGLPYEVLGLSGLLALPEVAEVLAVLHVLADPTRSDQLVRLLTGPRWRIGVADLEVLQE +RARFVSRLRARRAGGGREDPAGDAPDPARDVSPEEDADAAALLEALDSLPGEGTDWVGSR +GRGFSPEGLARLRAVNAELRRLSTRTGEDPADLIAEVIRETGLDVEVALRPGVSAAAARR +HLNAFQDAARDFGAGTTATDLTAFLAWTESVLEHEDGLGVENAEPTPGLVQVLTAHASKG +LEWDVVAVPGLQEGTFPSTRADRWTSPRAGALPWPLRGDRASLPQWDGSWAQDQRDWVQS +AGTGYSSKAAQEGNPDPYAVAVAAHAEREERRLAYVAYTRARSALWLSTSLFKGVNKEPL +PASAFLEEVAGLAGEVPGVALGPAPAEDDLPEANPAAGRTLVARWPFDPLDGPEAFVADP +EDPEDEERWQPLPRRSRARRHGVEAAAAAVHAADPAALGDDPELARQVDWVLVRRRDVAG +TGGETALPEHVSVSLYGELAADPQAVAEQLRRPLPRPPAHAARRGTAFHAWLEERFGATG +MLDIDSAEDAADLWVDEALDLGPMQEWFRSSRWAERTPAFVEAPVETTVGGITLRGRVDA +IYRSGGDPRLPFDPEADWELVDWKTGAVPRGRDLELKSLQLAVYRLAWSRLHGIPLERIG +ASFVYVAHGQERSFPDLPGEEELERHITDALARR +>PROKKA_01405 +MAPLTGGPAAPDADRPAGPDAVPADRPGTADAVHAPQDIAARLGLPAPTEEQAEVVTAPL +APRLVLAGAGSGKTATMADRVVWLVANGVVRPDEVLGVTFTRKAAAELAERINGRVDALL +RSGLRIPGFDGEPEDLGRASVSTYHSYAGALVRDHGLRIGVEPEARLMGGADAHRLMGSV +VRSHPVVADTLGVAPSRLVSQALHLAGDMAEHLVTPEEVRTHLARVAQQGRDLPLPPRTK +APTKEIAAFFTGLADRALMADLVARYDEVKREQDVMDFGDLLRHAARIASEVTAAGEQER +ARFPVVLLDEFQDTSHAQMRIFAGLFGPRGPEDDAAGLGHCVTAVGDPHQSIYGFRGASA +GQLFAFPHAFPRLETGPDGGRRRVNADVSHLTVAWRNEESILAVANTVAAPLNAHAAASG +GAPVEVRTLRPRPGAGDGVVRVDRFLTPEEEAHDVVRRLAALAEADGAAPSRAVLCRTRA +QFGPVLEALEAAGVPYEVLGLSGLLALPEVAEVLAVLHVLADPVRGDQLVRLLTGPRWRI +GPADLEVLHERARFVARMRARRAAGEDAQDPEGTGGADPEATAAEDVSPEEEADSAALLE +ALDSLPGEGTEWTGSRGRGFSAEGLARLRAAHAELRRLSARAGEDPADLIAEVVRETGLD +VEVALRPGLSAAAARRHLNAFQDAARDFGAGTAGADLAAFLAWTESVMEHEDGLGVENAE +PTPGLVQVLTAHASKGLEWDAVAVPGLQEGTFPSTRADRWTTPGSGALPWPLRGDRGSLP +QWDGTWAQDQRDWVQSAGTKYSSKAAQEDNPDPYAAAVEAHAEREERRLAYVAVTRARRE +LWLSTSAYKGTNKDPLPPSAFLEEAAGLAGRVPGVVAGHAPDEDGMPEANPAAGRTLVAW +WPFDPLDGPEAFLADPEDPEDEGQWRPLPRRARARRDAVEAAAAAVRAAEPSALAAEPEL +ARQVDWVLLRRRDVAGSGGDVALPDHVSVSLYGELAADPQAVAEQLRRPLPRPPAHAARR +GTAFHAWLEERFGATGMLDIDSAEDAEDLWVDEALDLEPMQAWFRSSRWAERTPAFVEAP +VETTVGGITLRGRVDAIYRSGGDPRNPVDPEADWELVDWKTGAVPRGRDLELKSLQLAVY +RLAWSRLHGIPLERIGASFVYVAHGQERSFPDLPGEAELERRLAEALRRR +>PROKKA_01304 +MASLSSPVPLRPAPVDAGPRVDVSRAVHSPQDIAARLGVFPPTDEQVEVIAAPLTPRLVV +AGAGSGKTATMSDRVVWLVANGFVRPDQVLGVTFTRKAAGELAHRINAKVDALLRSGLPI +PGFEGEPEDLGRASVSTYHSYAGALVRDYGLRIGVEPEARPLGEADAHRLMSAVAASHPI +VADGLRVSASTLVAAALRLSGDLAEHLVEPAQVRAHLRERIAVGEALELPPRMKEPSDEI +VEFFAGLETRVLMADLVERYTQAKAERGVMDFGDLLRHAARVAREIPAAGRAERERFPVV +LLDEFQDTSHAQMEIFRGLFGPESTDLDAPGLGHCVTAVGDPHQSIYGFRGASAGQLFTF +PSAFPRLGELPGGAPGRVNADVSHLTVAWRNDEAILAAANAVVAELNAHAADAGTPLELK +PLRPRPGAGTGEVRVDRHVSAQDEAEALVARLAALGEDPATADLSRAVLCRARTQFGPVL +DALEAAGVPYEVLGLSGLLSLPEIAEVLSVLHVLADPGRSDHLVRVLAGPRYRIGPADLE +LLHERARFVSRLRRRAAAHEPLDPATAVEAPDVSADEDADAPALLEALDSLPGESTVWTG +SHGRPFSAEGLRRLRAANAELRRLSAWAGADPADLIGEVVREIGLDVELALRPGPSAASA +RRHLDAFQDAARGFAAGDGAPADLPAFLAWTEAVEEHEKGLGIASADPAPGVVQVLTAHA +SKGLEWDVVAVPGLQTGTFPTARPDRWTSGGTGMLPWALRGDAASLPQWDGSWAENRRDW +VQSAGTGYSSKTAAATNPAPYGDAVADHAAREERRLAYVAFTRARSALWLSTSHWKGTAK +KPVDPSPFLVEAAALAGEVPGVVLGEEPAPEELGEANPTAERTLVAWWPADPLEGPEAFE +ADGEDLDDEAAWTPLPRRTRPRRARVENAARQVAAADPAALAEDTDLARALDWVLLRRRR +VGAAADGVALPEHLSVSLYGELAADPQAVADQLRRPMPRPPAHAARRGTAFHAWLEQRFD +ATGMLDIDESDDAADAWVEDALDLAPMQEWFLASRWADRVPAFVETAVETTLAGITLRGR +IDAVFRTGARPGMPFDPEADWELVDWKTGRVPGGAELRRKALQLAVYRLAWSRLHGIPLE +RIRASFVYVAAGQERVFDDLPGEEELEAIVTAAVAGPGATSSGEVSPPDAAR +>PROKKA_01447 +MAPLTGDPAAQTDRPRVEDAVHSPEDIAARLRLPPPTEEQAEVVTAPLTPRLVLAGAGSG +KTATMADRVVWLVANGLVRPDEVLGVTFTRKASGELAERINGRVDALLRSGLEIPGFDGE +PEDLGRASVSTYHSYAGALVRDHGLRIGVEPEARLLGGADAHRLMGAVVRSHPVVADTLG +VAPSRLITQALRLAGDMAEHLVSADEVREFLARLAEQGSALPLPPRAKTPSKEIQEFLTS +LADRALMADLVARYDEVKREQDVMDFGDLLRHAARIAVEVPAAGEQERARFPVVLLDEFQ +DTSHAQMRIFAGLFGPRGPEDDAPGLGHCVTAVGDPHQSIYGFRGASAGQLFAFPHAFPR +LETGPGGAPRRVNADVSHLTIAWRNEESILAVANAVAAPLNAHAAATGGAPVEVRTLRPR +PGAGEGVVRVDRFVTAEEEAADVVARLGALTGSGPGGATPSRAVLCRTRAQFGPVLDALD +AAGLPYEVLGLSGLLALPEVAEVLAVLHVLADPTRSDQLVRLLTGPRWRIGVADLEVLQE +RARFVSRLRARRAGGGREDPAGDAPDPARDVSPEEDADAAALLEALDSLPGEGTDWVGSR +GRGFSPEGLARLRAVNAELRRLSTRTGEDPADLIAEVIRETGLDVEVALRPGVSAAAARR +HLNAFQDAARDFGAGTTATDLTAFLAWTESVLEHEDGLGVENAEPTPGLVQVLTAHASKG +LEWDVVAVPGLQEGTFPSTRADRWTSPRAGALPWPLRGDRASLPQWDGSWAQDQRDWVQS +AGTGYSSKAAQEGNPDPYAVAVAAHAEREERRLAYVAYTRARSALWLSTSLFKGVNKEPL +PASAFLEEVAGLAGEVPGVALGPAPAEDDLPEANPAAGRTLVARWPFDPLDGPEAFVADP +EDPEDEERWQPLPRRSRARRHGVEAAAAAVHAADPAALGDDPELARQVDWVLLRRRDVAG +TGGETALPEHVSVSLYGELAADPQAVAEQLRRPLPRPPAHAARRGTAFHAWLEERFGATG +MLDIDSAEDAADLWVDEALDLGPMQEWFRSSRWAERTPAFVEAPVETTVGGITLRGRVDA +IYRSGGDPRLPFDPEADWELVDWKTGAVPRGRDLELKSLQLAVYRLAWSRLHGIPLERIG +ASFVYVAHGQERSFPDLPGEEELERHITDALARR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001239.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001239.fa new file mode 100644 index 0000000000000000000000000000000000000000..842aa7aafa4711d60681f7aae3400a8b2c7339c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001239.fa @@ -0,0 +1,104 @@ +>PROKKA_01521 +MTREHGVDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHNAVLVLGAPG +TGRTTVAVEYAARRIEAGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT +WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPADVAP +AVEARGFRREVRELVDRMSELGLEPGRLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE +AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAAERDRLAVLVVEDLHEATPAVHDLLT +VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPGVLDPDPVPGAAPPASPDGRVRVLTRG +HRMRAEVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV +LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLV +DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD +ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER +WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP +VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT +LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVVTAVRSPDEGPSDFLDLVDPPE +RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAVL +AADGVGVADPRRWWGLLPLSTEAALVDPEREVVALSPSRVETALRNPLDWVLYHVGANAG +GTLAQSVGTLVHSVAEHHPEGVPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI +GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP +TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLERPTTPAGAALVQLGAG +TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ +VTEWPR +>PROKKA_01230 +MTREHGVDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHNAVLVLGAPG +TGRTTVAVEYAARRIEAGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT +WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPDDVAP +AVEARGFRREVRELVDRMSELGLEPGCLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE +AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAEERDRLAVLVVEDLHEATPAVHDLLS +VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPEVLDPDPVPGAAPPASPDGRVRVLTRG +HRMRAAVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV +LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLL +DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD +ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER +WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP +VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT +LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVATAVRSPDEGPSDFLDLVDPPE +RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAAL +AEDGVTVADPRRWWGLLPLSTEAALVDPEREVVALSPSRVETALRNPLDWVLYHVGANAG +GTLAQSVGTLVHSVAEHHPEGVPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI +GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP +TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLEHPTTPAGAALVQLGAG +TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ +VTEWPR +>PROKKA_01404 +MTWQADEDLLLDDDAAAPERAARLVSPAAAPAERVALTLEQEAVAAMGPGHGAVLVLGAP +GTGRTTVAVEYAARRLESGTDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVR +TWTSYAFDLLRRARVTGPLSHLPVAPRLLTGAEQDTVIAELLEGYAAGHAEAPRWPQDVA +AAVETRGFRREVRELVDRMSEFGVEPGRLQELGAAHARPVWEAAAVLLQDYRDRIDLGLA +EAFDAAGLISAAVRVLTERHPEDPERDAAALAFAAAERERLRTLVVEDLQEATPAVHDLL +AVLGRGRDVLLTAGPDTAVEGFRGARPDLVSRYPQALDPDPVPGAPEAPSSGERTRVLTQ +GHRMAPEVQDAFLRVARRVRQRTAAVEHTRTQTAPADGPGTVRGHVVPTRAHEDQLVLER +VLRVHHEDEVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTL +LAAAGVLADDPEAGVEDVLDPDEVVALLTGRYGMAGALHVRRLRQDLLAAERGRGGRRSS +DALLAAALLDPALAGPEHERHRALRRVHWMLRAGIEAARAPSASPEAVLWALWSASGRAE +RWRSTALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGAAPEAFAVYMESQDL +PVDTLARRAEAGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLADLL +TLPEGGAWPTDHRTRLREVRQDELRMLAAAVSRARRQVVVTAVRSAEDAPSDFLDLVDPP +ERLPAPARDEAGVRRLTAVPDPITAPALAGTLRRRLEEDPGQGPAAAGLAALARDGVGVA +DPRRWWGLLPLSTDAGLADPAQDVVALSPSRVETALHNPLNWLLYHVGATAGGTLAQSVG +TLVHSVAEHHPEGVPEQVRAELERRLPELGLPEGWITEIEHERARALVDAYIGYWSIARD +AGRRPVAQEVRLLAELTWGGTTVRITGVVDRLEADAEGRPFIADLKTGRSAPTGPEMARQ +PQLAAYQVAVLAGGLAQIRDDPDADPALRAALADLARPAAPAGAALVQLGAGTQKTKVQE +QPALGPEDDWALEQVFTAARRTVGPRFLAIHEAGGRRCALPSVCPLCSEGRQVTEWPR +>PROKKA_01303 +MSTTPHPSEPRTEPTPQAADADPADLAALLAEPDEEPPHAAPVPARLVRGVGQDRAGVVL +TVEQEAVAGLGEGHGAHLVLGAPGTGRSTVAVEYAARRLEAGLDPESLLVLAPSREAAAR +LRDALTERLAAAGHGTRAVTPVRTWASYAFDLIRRARVTGPLRGLSRPPRLLSGAEQDTV +IAELLDTYAAGLAPAPEWPRDVAQAVDTRGFRREVRELVDRMSEFGVEPGVLQELGRRHG +RPVWEAAAELVQDYRDRLDLGMAEAFDAAGLISTAVRLLTERFPDDPERDAAALAFAEAE +QARLRAIVVDDLQEAGPAVHDLLVHLGRGRDVLLTASPDTTVQGFRGARPDLVSRYPAAL +DPDAVPGASSPDPDARTHVLTAGHRMSAGVQEGWLRAARRIRQRTVGVELTRTRTVPAGE +GGAVEGHAVPSRAHEDQLVLERVLRVHHEDGVPLDGLAVIARSGARAAALGRHLEAAGVP +VRREAAGEVLKDEPAVAPLLTLLRAVSDQAEDPEAGVALEADEAVALLRGPYGRATALNI +RRLRQDLLAAERARGGRRTSDELLVAAFGDPALAGEETDRHRALRRLAWMHRDGLAAARE +PGATAETVLWAVWAASGRADRWRAAALGRAEGAEGRREARRADADLDAVVALFRIAERFV +DQFPGAAPADFSRYMESQDLPMDTLARRAETGDAVHVLTPAGAAGREWDTVIVVGLQEGA +WPNTALRGQLLGATDLTDLLTAAAVDGAWPTDHRTRLAEVRQDELRMLAAAVSRARRRVV +ATAVRNEDETPSDFLDLLDPVADVAAGRPLTEVPLPLTAAALVAAARRRLEAPDLPEALV +GLEDPAAAAVLAALAEDGVAAAAPDRWWGLAPLSTDAPLTDITAEPVRLSPSRAQTALEN +PLNWLLYHVGAQAGGTLAQSIGVLVHSVAEHHPDGEPGAVRAELERRLPELGLPEGWTTD +LQHARARRLVEAYIRYWSQMRAEGRRPVAQEVALHVPLAWGDERVEISGVIDRLEVDATG +RPYVVDLKTGSSKPDTAELERLPQLAAYQVAVRARGLELLAEDPATDPALRRALSAIEAP +AEPGGAALVQLGAATKTKATVQPQPAVTADDDWALDQVFTAARRTVGPRFLAVHRPGVRC +ALPSVCPLCTEGRQATEWHR +>PROKKA_01448 +MTREHGEDPFDDDAAAPERAARLVRTAAAPEDRITLTDEQEAIASLAPGHGAVLVLGAPG +TGRTTVAVEYAARRIEEGLDPESLLLLAPSRDAAARLRDALTRRLAAAGRGTRAVTPVRT +WSSYAFDLLRRARVTGPLRHLEVAPRLLTGAEQDTVIAELLEGYAAGLAAAPDWPADVAP +AVEARGFRREVRELVDRMSELGLEPGRLQELGTAHGRPEWEAAAVLLQDYRDRIDLGMAE +AFDAAGLLSAAVRVLTERHPEDPERDAAAQAFVAAERDRLAVLVVEDLHEATPAVHDLLT +VLGRGRDVLLTASPDTTVEGFRGARPDLLARYPGVLDPDPVPGAAPPASPDGRVRVLTRG +HRMRAEVQDAYLRVARRVRQRTAGVERTRTETVPADGDGAVRAHVVPTRAHEDQLVLERV +LRVHHEDGVPLDRILVVARSGSRVAALARHLEAEGVPVLRDAAGLVLKEEPAVAPLLTLV +DAAGALAEDPEARVEDVLDPDEVVGLLTGRYGMASALHVRRLRQDLLAAERGRGGRRTSD +ALLAAALLDPSLAGPEHERHRALRRVHWMLRDGLEAARAPSASPETVLWALWSASGRAER +WRSLALRPAEHANDRRESRRADADLDAVVALFKVAERFVDQFPGASPESFAVYMESQDLP +VDTLARRAESGDAVHVRTPAAAAGQEWDTVIVVGLQEGVWPNTRLRGQLLGATDLVDLVT +LPADAPWPTDHRTRLREVRQDELRMLAAAVSRARRQVVATAVRSPDEGPSDFLDLVDPPE +RLPAEARDAAGVRRLTAVPDPITAPALVGRLRRVLEAGDEADAADGATPRAAAAAGLAAL +AEDGVTVADPRRWWGLLPLSTEAALVDPKHEVVALSPSRVETALRNPLDWVLYHVGANAG +GTLAQSVGTLVHSVAEHHPEGMPEDVRAELERRLPELGLPEGWITEIEHDRARGLVDAYI +GYWSIARAAGRRPVAQEVRLLADLTWGGTTVRITGVVDRLEADAQGRPFIADLKTGRSAP +TGAEMARQPQLAAYQVAVRAGGLEQVRDDPATDPALRAALAGLERPTTPAGAALVQLGAG +TQKTKVQDQPALEDEDTWALEQVFTAARRTTGPRFLALHEAGARRCALPSVCPLCSEGRQ +VTEWPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001242.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001242.fa new file mode 100644 index 0000000000000000000000000000000000000000..84939b12248ac962eb3702c0f3a4c0a04af7197e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001242.fa @@ -0,0 +1,45 @@ +>PROKKA_01524 +MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL +VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT +EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET +LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW +DEVLTGFRATATGGWGLSGQPEGWTPDVWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV +YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGLDHSIQRAGT +LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSLLASGVYLPPSVFEAWFVSAAHDDAAV +TRVLDALPAAAKAAAAATPQG +>PROKKA_01233 +MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL +VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT +EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET +LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW +DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV +YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGVDHSIQRAGT +LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSMLASGVYLPPSVFEAWFVSAAHDDAAV +TRVLDALPAAAKAAAAATPQG +>PROKKA_01401 +MTTSTRTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGREYVDL +VCSWGPMLLGHGHPEVTDAVHAAVDRGLGFGTSTLEETALAELIAAKVPVERVRFVSTGT +EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET +LVVDYNDRDALEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITARHGALLIW +DEVLTGFRATATGGWGLSGQVDGWTPDIWCFGKVIGGGMPAAALAGSAEIMNHLAPLGPV +YQAGTLSGNPVAMAAGHATLSRADDAVYAAVQRASDAVREGLVAALDAEGVDHSIQRAGT +LFSVAFGTSGTGVRDYRDAQAQEAFRYAPFFQSMLESGVYLPPSVFEAWFVSAAHDDAAV +QRVLDALPAAAKAAAAATPQG +>PROKKA_01300 +MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGTEYVDL +VCSWGPMLLGHRHPEVLEAVHAAVDRGLGFGTSTLEETALAELIASRVPVERVRFVSTGT +EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET +LVVDYNDRAALEAVFAEHGERIAAVITEAVPCNMGVVEPAEGYNAFLREITAQHGALLIW +DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALAGSAEIMNHLAPLGPV +YQAGTLSGNPVAMAAGHATLSRADDAVYAAVQRASDAVREGLAAALTAEGVDHSIQRAGT +LFSVAFGTSEHGVRDYRDAQGQDVFRYAPFFQTMLESGVYLPPSVFEAWFVSAAHDDAAV +ERVLAALPTAAKAAAAATPQG +>PROKKA_01451 +MTASQPTTNAAAFAAAQAVIPGGVDSPVRAFGSVGGTPRFMAGARGPYLTDVEGNEYVDL +VCSWGPMLLGHQHPEVVEAVHAAVDRGLGFGTSTLEETALAELIASKVPVERVRFVSTGT +EATMTALRLARGVTGRNLIVKFAGCYHGHSDGLLAAAGSGVATAALPGSAGVTEAAASET +LVVDYNDRAAVEAVFAEHGERIAALITEAVPCNMGVVEPAEGFNAFLREITRRHGALLIW +DEVLTGFRATATGGWGLSGQPEGWTPDIWCFGKVIGGGMPAAALGGSAEIMDHLAPLGPV +YQAGTLSGNPVAMAAGHATLSRADEAVYAAVTRASDAVREGLVAALDAEGVDHSIQRAGT +LFSLAFGTSGTGVRDYRDAQGQEVFRYAPFFQSMLASGVYLPPSVFEAWFVSAAHDDAAV +TRVLDALPAAAKAAAAATPQG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001244.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001244.fa new file mode 100644 index 0000000000000000000000000000000000000000..107082c770a1d0d410a6034b14dec1b9b5867183 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001244.fa @@ -0,0 +1,45 @@ +>PROKKA_01526 +MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI +VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG +LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALMAAAVVAPMSTGALPSP +TPAYADGALVRGLLDGYNTMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA +AMAVVYASLAYVGATSHGAFAQAANGGDVLARSASHFFGAAGVYLIAAIVVVACLKTCIG +LIVACTEMFAEMFPGSYRLWASLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL +GLAWAWVRDHPAVARWVVACTGLAAFFDLLGALPEALATTPPVTALTGLAGRVLPGYAVG +FGWVVPALVGLVVGTVAAASRPRPRRGEREAIPVTAGHGRTAAD +>PROKKA_01235 +MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI +VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG +LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVAPMSTGALPSP +TPAYADGALVRGLLDGYATMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA +AMTVVYASLAYVGATSHGAFAQATNGGDVLARSASHFFGTAGAYLIAAIVFVACLKTCIG +LIVACAEMFAEMFPGSYRLWAGLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL +GLAWAWVRDRPAVARWVVACTGLAAFFDLLGALPEALVTTPPVTALTGLAGRVLPGYAVG +FGWVVPALVGLVVGTLAAASRPRSRRGEREAIPVTAGHGRTAAD +>PROKKA_01399 +MPPHLRPGQTLLLASLVFGLFFGAGNLIFPASLGRDAGAAVTPATLGFLVTAVGLPVLGI +VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGS +LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVTPMSTGALPSP +APAYADGALVRGLLDGYTTMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA +AMAVVYASLAYIGATSHGAFAQAANGGDVLARTASHFFGTAGAYLIAAIVFVACLKTCIG +LIVACAEMFAEMFPGSYRLWAGLFLVVSFALANLGLEAIIAWSVPVLMLLYPIAVVVILL +GLAWAWVRDRPAVARWVVACTGLAAVFDLLGALPEALGTTALVTALTGLAGRVLPGYAVG +FGWVVPALVGLVVGAVAAASRPRPRRGEREATPIAAGHGRTAAD +>PROKKA_00047 +MSARLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGSAVVPATLGFLLTAVGLPVLGI +IASALTRSRSVREMTAPISPWFATAFTCLLYLAIGPLFAIPRTATVSYEIGVAPLAGDGP +WLPVFTLVFFGVAAVAAFRPGRLLDWVGRFLTPVFLLLLGALAVAAVVAPMSSGDLPAPA +GPYADGALTAGILDGYNTMDALASLAFAVLIVEAAGRLGVDSPRRLAVELGKAGIVGGLG +MAVVYGALAYIGATSHGALPGAASGGAVLAGTASHYFGPAGTWLIAAIVLAACLKTSIGL +IVACGEMFAEMFPGSYRVWASVFLLVSLVIANLGLEAIIAWSIPVLMFLYPLAIVIIALG +LGWGWVRHHLTVARAVVAFTAVAAVFDLLAALPETLAATGPVTALTDLAGRILPWYENGF +GWVVPALVGLVVGLVLEAARGRGRSAAVADA +>PROKKA_01453 +MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI +VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG +LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVAPMSTGALPSP +TPAYADGALVRGLLDGYATMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA +AMAVVYASLAYVGATSHGAFAQAANGGDVLARTASHFFGTAGAYLIAAIVFVACLKTCIG +LIVACAEMFAEMFPGSYRLWASLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL +GLAWAWVRGRPAVARWVVACTGLAASFDLLGALPEALATTPPVTALTGLAGRVLPGYAVG +FGWVVPALVGLVVGTVAAASRPRPRRGEREAIPVTAGHGRTAAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001245.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001245.fa new file mode 100644 index 0000000000000000000000000000000000000000..7f433575ccdad77692046748d3914458f4e3bca5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001245.fa @@ -0,0 +1,38 @@ +>PROKKA_01527 +MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN +HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK +RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS +GSRRGGRGRGRGAKTTDATDTPEATDADAEAPIADEAPAADEAPAADEAPAGDAAAGKDG +KAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNAT +STDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRR +SRRAEG +>PROKKA_01237 +MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN +HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK +RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS +GSRRGGRGRGRGAKTTDATDTPEATDADAEAPAVDEAPAADEAPAADAAPAGDAAPAGDA +AAGKDGKAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALT +KAVNATSTDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEV +SLVRRRSRRAEG +>PROKKA_01398 +MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN +HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK +RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDALAKEENAKASEGSGRS +GSRRGGRGRGRGSKTTDATDTPDADVADAEAPAADAAPAGDAATGRDGKGTEAKSGAGRR +GRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNATSTDDGWATLSLI +GQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRRSRRAEG +>PROKKA_01289 +MSEPTPASLRIAVLLDCDNVSPKYAGLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN +ELAIQPVQQFAYTIGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLRESGK +RVIGLGARKTPASLRNAVDQFIYLELLGTHTEGVDDDEPAPSLQAEPSPKDEREAKEGPA +TGNRRGSRGRGAKAKPAADVASEQPAEAEPAPVVEPAPDVTPAPESDEAAPQRAVRGRGR +GAGRGSVLVDVDSAEVITAEDPTPPDVRADADDDAEPASRINLQSALVKAVNATSGDDGW +ASLSLIGQHMSRTHVDFDPRDFGHAKLSTLVADQPYLETRTEGRSMEVTLKQRRRRAQG +>PROKKA_01454 +MPEPTPASLRIAVLMDSDNVSPKFAPLILEELATYGTPTIKRAYGDWTTTNLNGWKKALN +HHAIQPVQQFAYTVGKNSSDSALIIDAMDLLWMGNVDAFALVSSDSDFTRLATRLREGGK +RVIGLGARKTPASLRNAVDQFIYLELLGTATDHDVDDDETGEDAPAKEENAKASEGSGRS +GSRRGGRGRGRGAKTTDATDTPEATDADAEAPIADEAPAADEAPAADEAPAGDAAAGKDG +KAAEAKSGAGRRGRRASSSDVTEDPTPPEVPVEAEPEHDEADAAPRIDLQAALTKAVNAT +STDDGWATLSLIGQHLSRTHVDFDPRDFGHSKLSTLVEDQPYLRTRTEGRTMEVSLVRRR +SRRAEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001246.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001246.fa new file mode 100644 index 0000000000000000000000000000000000000000..ae3831f4b60d1e6590b30d82103e11988abc05a4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001246.fa @@ -0,0 +1,15 @@ +>PROKKA_01528 +MGNTLDFLRGVDRLHAFYTENVRMLAHAYDLTDEEASELLANTGFTNVSVAILRGPRVDI +MAAATGVPQDERHDAGPAPTEDDAPDPDGGRPD +>PROKKA_01238 +MGNTLDFLRGVDRLHAFYTENVRMLAHAYDLTDEEASELLANTGFTNVSVAILRGPRVDI +MAAATGVPQDERHDAGPAPTEDDAPDPDGGRPD +>PROKKA_01397 +MGNTLDFLRGVDRLHAFYTENVRMLAHAYDLTDEEASQLLSNTGFNNVAVAILREPRVDL +MASATGVPQDEKHDAGPAPTEDDATDPDGDRPD +>PROKKA_01288 +MPDSVRMANTLEFLRGVDRLHAFYTENVRMLAHAYDLSDEEASRLLAHTGFANVSVAILR +EPRVDLLAGLGASVEDEVHTHPVVDDASAPAEEPPASGGADDPEEPPAGSAPADPDDGAR +>PROKKA_01455 +MGNTLGFLRGVDRLHAFYTENVRMLAHAYDLTDEEASELLANTGFTNVSVAILRGPRVDI +MAAATGVPQDERHDAGPAPSEDDAPDPDGDRPD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001247.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001247.fa new file mode 100644 index 0000000000000000000000000000000000000000..f4808a3a6a631f6e58554c9626a97891cdf7deed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001247.fa @@ -0,0 +1,30 @@ +>PROKKA_01529 +MRVLLTRQPAQAGDLEAGLAGTEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG +DAAGPVRSDGSRWLVVTSPNTVRALRAVGWDGHVPAGARIAVTGPGTARVLTEAGCDAAP +WLPPEDRSAEGLIAGLAALHPRGARAWLPQSDRARSRLADGLRAAGWDVRTGLAYRTVPY +PAQAGRRLLDGAADEGRGDVVTPARLAAVAAGTAVVLTSSSAAEEFVAAGLTPLVGERVR +LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRAAA +>PROKKA_01239 +MRVLLTRQPAQAGDLEAGLAGTEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG +DAAGPVRSDGSRWLVVTSPNTVRALRAVGWDGHVPAGARIAVTGPGTARVLTEAGCDAAP +WLPPEDRSAEGLIAGLAALHPRGARAWLPQSDRARSRLADGLRAAGWDVRTGLAYRTVPY +PAQAGRRLLDGAADEGRGDVVTPARLAEVAAGTAVVLTSSSAAEEFVAAGLTPLVGERVR +LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRAAA +>PROKKA_01396 +MRVLLTRQPAQAGDLEAGLAGAEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG +DAAGPGRSDGSRWLVLTSPNTVRALRAVGWDGHVPAGARIAVTGPGTARVLTEAGCDAAP +WLPPEDRSAEGLIAGLAALHPRGGRAWLPQSDRARPRLADGLRAAGWDVRTGLAYRTVPY +PAQAGRRLLDAAADEGRGDVVTPARLAAVAAGTAVVLTSSSAAEEFLAAGLTPLVGERVR +LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRAAA +>PROKKA_01287 +MDGRPLVLTRQPAQAGTLEADLAAAGRRVAFCPLTDFELPPTPGGLRAVVEAVVGGRCAW +LLVTSPNAVRALQAAGWTGAVGAGVRVAVTGAGTARVLADAGCAVEPWMPESASAAGILA +EFPAAPAETGDGARRVLLPQSALATAELEEALTRRGWAVDRVEAYRTVPYPADAARRLLT +EEPGDAGTVVPVAELAGADVVLTSPSAARALAVHPALDDPELRRTWRLVALGAPTAREAR +RLGLRLTGQAATPDATGILAALARPVG +>PROKKA_01456 +MRVLLTRQPAQAGDLEAGLAGAEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAGADG +DAVGPVRSDGPRWLVVTSPNTVRALRAVGWGGHVPAGARIAVTGPGTARVLTEAGCDAAP +WLPPEDRSAEGLIAGLAALHPRGARAWLPQSDRARPRLADGLRAAGWDVRTGLAYRTVPY +PAQAGRRLLDGAADEGRGDVVTPARLAAVAAGTAVVLTSSSAAEEFVAAGLTPLVGKRVR +LVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVLRGAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001248.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001248.fa new file mode 100644 index 0000000000000000000000000000000000000000..76111f0a762c18e2b2e5ddd085466d98aed00443 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001248.fa @@ -0,0 +1,40 @@ +>PROKKA_01530 +MTPLRIGTRGSALATTQTSHVAETLTERSGLAHELVVIRTEGDVTTGSLASLGGTGVFAS +ALRAAVLDGVVDAAVHSLKDLPAAQPETLEIAAVPARADLRDALCARDGLTLATLPEGAR +VGTGSPRRVAQLKALRPDLELVDIRGNVQTRLARVPGLEQHDDHAPAAAGSPRGDLDAVI +LACAGLNRLGLDHVITERIDPEVMVPAPGQGALAVEIRAEDESFLGRALLDPEAPVGRLH +AALELVDDRDTHVAVTAERALLRRLEAGCAAPIGAVARVTDGEAGAPRIEMTAMVAALDG +SRVLRRTSSVQLDPVPTDVAGDPAAGDEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT +VRGVDRGDGAPRPDDPA +>PROKKA_01240 +MTPLRIGTRGSALATTQTTHVAETLTERSGLAHELVVIRTEGDVTTGSLASLGGTGVFAS +ALRAAVLDGVVDAAVHSLKDLPAVQPETLEIAAVPARADLRDALCARDGLTLATLPEGAR +VGTGSPRRVAQLKALRPDLELVDIRGNVQTRLARVPGLEQHDDHAPAAAGSPRGDLDAVI +LACAGLDRLGLDHVITERIDPEVMVPAPGQGALAVEIRAEDESFLGRALLDPEAPVGRLH +AALELVDDRDTHVAVTAERALLRRLEAGCAAPIGAVARVTDGEAGAPRIEMTAMVAALDG +SRVLRRTSSVQLDPVPTDVAGDPAAGDEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT +VRGVDRGDGAPRPDDPA +>PROKKA_01395 +MSTLRIGTRGSALATTQTTHVAQALAERAGLEHELVVIRTEGDVTTGSLASLGGTGVFAS +ALRAAILDGAVDLAVHSLKDLPAAQPDTLEIAAVPERADLRDALCARDGLTLATLPEGAR +VGTGSPRRVAQLKALRPDLVLVDIRGNVQTRLARVPGLEQHDDGAPAAAGSPRGDLDAVI +LACAGLDRLGLDHVITERIDPDVMVPAPGQGALAVEVRAEDESFLGAALLEPDAPVGRLR +AGLELVDDRATHVAVTAERALLRRLEAGCAAPIGAVARVVDGEAGAPRIEMTAMVAAVDG +SRVLRRTSSVQLDPVPEDLAADPAAADEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT +VRGVDRGDGAPQPDDPA +>PROKKA_01286 +MSGPGAPAGDGLRVGTRGSALATTQTTHVAEALTDRSGMPHELVVIRTEGDVTTGSLASL +GGTGVFASALRSAVLDGRVDLAVHSLKDLPAAQPAGLEIAAVPPRADLRDALCARDGLTL +ATLPEGARVGTGSPRRVAQLRALRPDLELVDIRGNVQTRLARVAGHEVHDDDAPAAAGAP +RGDLDAVVLACAGLDRLGLQHVITERIDPEVMLPAPGQGALAVEIREEDGPLLGPSAVDP +DSHAGRLRAALELVDDRDTHVAVTAERALLLRLEAGCAAPIGAVARVEEGTAVDGSPAPR +IVMSAMVAAVDGSQVLRRTSSVQLDAVPEDVAGDPAEADEWIEDTLFMAAGALGVHLAEL +FVAEGADLLPGTVRGVAKPDPEA +>PROKKA_01457 +MTPLRIGTRGSALATTQTSHVAETLTERSGLAHELVVIRTEGDVTTGSLASLGGTGVFAS +ALRAAVLDGVVDAAVHSLKDLPAAQPETLEIAAVPARADLRDALCARDGLTLATLPEGAR +VGTGSPRRVAQLKALRPDLELVDIRGNVQTRLARVPGLEQHDDHAPAAAGSPRGDLDAVI +LACAGLDRLGLDHVITERIDPEVMVPAPGQGALAVEIRAEDESFLGRALLDPEAPVGRMH +AALELVDDRDTHVAVTAERALLRRLEAGCAAPIGAVARVSDGEAGAPRIEMTAMVAALDG +SRVLRRTSSVQLDPVPADVAGDPAAADEWLEDTLFVAAEALGVHVAEQFVAEGADLLPGT +VRGVDRGDGAPRPDDPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001250.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001250.fa new file mode 100644 index 0000000000000000000000000000000000000000..5bd810e97f8c30322c7f761a2a445366b9055547 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001250.fa @@ -0,0 +1,25 @@ +>PROKKA_01532 +MTKDSTTTPAEAGKDWFTTYTVFARPQGEPGWLGLEGRDAKKAAKEFDEAVARVAQTGVT +VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRELRRTRLLEGTTMVLSAMGADRMAEFN +KDHVPAFAMGRKALKWLCFYPFVRSYDWYLLDPKERARMLREHGQLGQDFPQVWANTTSA +FGLNDWEWLLGLEADELTDLVDMMRHLRNNETRLHVRSEVPFYTGRRLETAEIAEVLA +>PROKKA_01242 +MTKDSTTTPAEAGKDWFTTYTVFARPQGEPGWLGLEGRDAKKAAKEFDEAVARVAQTGVT +VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRELRRTRLLEGTTMVLSAMGADRMAEFN +KDHVPAFAMGRKALKWLCFYPFVRSYDWYLLDPKERARMLREHGQLGQDFPQVWANTTSA +FGLNDWEWLLGLEADELTDLVDMMRHLRNNETRLHVRSEVPFYTGRRLETAEIAEVLA +>PROKKA_01393 +MTKDTATTPAEAGKDWFTTYTVFARPQGQPGWLGLEGRDAKKAVQEFDALVADLAKAGVT +VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRRLRRTRLLERTTMVLSAMGADRLAEFN +KDHIPAFAMGRKALPWLCFYPFVRSYDWYLMEPKERARMLREHGQLGQEFPQVWANTTSA +FGLNDWEWLLGLEAPELKDLVDMMRHLRNNETRLYVRAEVPFYTGRRVETADLLEVLA +>PROKKA_01284 +MSNTAAQPGQDWFTTYTVFARPQGEPGWLGLDGREAKKAVKEFDGVVKSLATRGVTVRGV +YDVSGMRAEGDVMVWMYAHAPEDLQAAIRDLRRTRLLDGTNMVLSAMGADRMAEFNKDHI +PAFAMGRKPLDWLCFYPFVRSYDWYTLDPKERARMLREHGKLGQDFPQVWANTTSAFALN +DWEWLLGLEAPKLNDLVDMMRHLRDNETRHYVREEVPFYTGRRLETSELPEVLA +>PROKKA_01459 +MTKDSTTTPAEAGKDWFTTYTVFARPQGEPGWLGLEGRDAKKAAKEFDEAVARVAQTGVT +VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRELRRTRLLEGTTMVLSAMGADRMAEFN +KDHVPAFAMGRKALKWLCFYPFVRSYDWYLLDPKERARMLREHGQLGQDFPQVWANTTSA +FGLNDWEWLLGLEADELTDLVDMMRHLRNNETRLHVRSEVPFYTGRRLETAEIAEVLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001251.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001251.fa new file mode 100644 index 0000000000000000000000000000000000000000..32768c6026459282290da1635b392cae7a84441c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001251.fa @@ -0,0 +1,50 @@ +>PROKKA_01533 +MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ +TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG +DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA +PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL +TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV +TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL +THVTAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV +DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG +TGLAAVVAGVDRTLGADAPPAG +>PROKKA_01243 +MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ +TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG +DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA +PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL +TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV +TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL +THATAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV +DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG +TGLAAVVAGVDRTLGADAPPAG +>PROKKA_01392 +MTGTALVVGGGIAGLVAAHRLCAAGWEVTLAEATSVLGGAVSARFLDVPSHGETGAPESQ +TLELDAGAESFAVRGTAVRALLEELGLGGKVVAPEPLGSWLHGPAGPVPAPRLGLVSIPG +DLEAEDLAAALSGPGLARAREDAVAPMDRWADALAAGEPVTVAAIVADRLGEEVLKRLVA +PVVAGVHSADPAVVELERVAPGLLASAVEHGGLAAGVAALRGSSTPGSLVAGVDGGMSRV +TGRLVDALREAGATVLRGVRVAALSRVPAMGGWWAQISDRDDEVVRGLDVDRVVLAVDGA +TAWDLLAPLSGGDLDPDAGPALGDGVALTTLVVEAPGLDAAPRGTGMLVGAGTDVAAKAL +THATAKWAWLREVVARPDHDGVARHPHRHVVRLSYGRSGAEPGGLGHRSTDEELLARAVV +DAAALTGVPLSEQDVVARAVVRWRPSIPPQAGPDREAADALIAWSRGQAGLDLVGSWVHG +TGLAAVVASVDRAFDAPPPAG +>PROKKA_01283 +MSGSALVVGGGIAGLLAARRLNQQGWEVTLAEATSVLGGTLSARFLDVPSVSDSGAVERQ +TLELDGGAESFAVRGAAVRALVDELGLGDDVVSPEPLGSWLHGPAGAVPAPRVGLVGIPG +DLDAPDVAAALSPAGLERARRDLTEPMDRWAAARAAGEPVTVAALVADRLGDDVLERLVV +PVVGGVHSADPAVVDVERVAPGLLAAAVEQGSLARGVAALRGGQTPGAAVAGVDGGMAKV +TGRLVQTLREDGVTVLRGVRVAALSRLGADGRWWAQISDRDEEVVRGLEADRVVLAVDGV +AAWELLAPVSGDAVDPDAGPALGEGVALATLVVEAPGMDAAPRGTGLLVAPGTDVRAKAL +THSTAKWAWLRSVVDRPDESGAPRHPHRHVLRLSYGRHGGAAGDLGFRSADEDLLAAAVA +DAEALTGVELSADDVLASTVTRWRRPIPPQHGPDREAMDRLIAWAQDVPGLDLVGSWVHG +TGLAAVVAGVERTVAPAAA +>PROKKA_01460 +MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ +TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG +DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA +PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL +TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV +TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL +THATAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV +DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG +TGLAAVVAGVDRTLGADAPPAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001254.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001254.fa new file mode 100644 index 0000000000000000000000000000000000000000..4d187c4ea1950d354cecd23f8d445f6e658a4f35 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001254.fa @@ -0,0 +1,24 @@ +>PROKKA_01536 +MTDHPAATAPDEPGRGRRLPRQERRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL +YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRDNRERVRATVAAVFEYMASPERTHRL +IFDSGIDGDPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW +ADRLDADARPAAAEMARTVDALVWRGLASLPSADDAPR +>PROKKA_01246 +MTAHPAATAPDEPGRGRRLPRHERRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL +YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRDNRERVRATVAAVFEYMASPERTHRL +IFDSGIDADPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW +ADRLDADARPAAAEMARTVDALVWRGLASLPSADDAPR +>PROKKA_01389 +MFAAEGYAGASMDQIAERAEVSKPVLYQHFPGKHELFLELLDAEVADLQERLGAAMDTRR +GRDNRERVRATVAAFFEYMGAPERTHRLVFDSGADQDPEVRSRSEAVHRLLSSEITRTIS +ADTSVGEAEAEVLSRGLVGLLLGAARHWADRLDVQARPPAAEMARTVDALVWRGLATLPT +DDDAL +>PROKKA_01280 +MAAPARLPRAERRGQLLEVARVVFAAQGYVGTSMDEITERADVSKPVVYQHFGGKQELFL +ELLDAEVERLRALIVEGTASTQDNRTRARSAVHAVFRYMDSPTSAHRREGGRGRGERAVA +GPGRDRGPRRRRVLSRAALRPGVNARRPPGARPRLP +>PROKKA_01463 +MTAHPAATAPDEPGRGRRLPRHKRRRQLLDCARAVFAAERYAGASMEQIAERAEVSKPVL +YQHFPSKHELFLELLDAEVASLRALLEAAMDTRRGNRARVRATVAAVFEYMASPERTHRL +IFDSGIDGDPEVRTRSEAVHRLLSSEVARTIRADTTVAEAEAEVLSRGLVGYLLGAARHW +ADRLDADARPAAAEMARTVDDLIWRGLTSLPSADDAPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001260.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001260.fa new file mode 100644 index 0000000000000000000000000000000000000000..6b88c057941a162e2eea08c7c008254c495fe0b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001260.fa @@ -0,0 +1,30 @@ +>PROKKA_01543 +MSIMMPNPQPGAEQGLPRGELLATYATYAQAREQVDRLAATDFPVSAVSIVGKDLRVVER +VRGRLNYAQVALSAGVRGVFFGGLIGVFLYLLAPEAGPGQILTSMLLGLAVWLIFGVIGF +AMRRGQHGFASSQAVVPTAFDLVVAFDHAARARQELGLGGAAAPTPPAASQPAPAPAAEA +EDGSVQATPAPAPSSGGSHAAPAPGGPEAPARPAPEADPAPTGLDRSYGVTLPPEEVAKL +IEARGGHPPRPQDEPRG +>PROKKA_01253 +MSFMMSNPQPGAEQGLPRGELLATYATYAQAREQVDRLAATDFPVSAVSIVGKDLRVVER +VRGRLNYAQVALSAGVRGVFFGGLIGVFLYLLAPEAGPGQILTSMLLGLAVWLIFGVIGF +AMRRGQHGFASSQAVVPTAFDLVVAFDHAARARQELGLGGAAAPTPQPAPQPAPAPAAEE +AGGGSVQATPAAAPSSGGSHAAPAPGGPEASARPTPEADTAPTGLDRSYGVTLPPEEVAK +LIEARGGHPPRPQDEPRG +>PROKKA_01382 +MSFMMSSPPPGADRGLPRGELLATYASYADAREQVDRLAATDFPVSAVSIVGKDLRVVER +VRGRLNYAQVALSAGVRGVFFGGLIGVFLFLLTPEGGAGQILTSMLLGLAVWLIFGVIGF +GMRKGRHGFASSQAVVPTGYDLVVAFEHAARARTELGLGGAAATAAAAVSTSPATPAPAA +PQAGPNQNGAGQVDAPRPDAPQADAQHAPQAGAPSSGGSHAAPDADAQPAGAEAAPAAGA +VPTGLDRSYGVTLPPEEVAKLIQARGGQASRPQEDPRD +>PROKKA_01273 +MMMSGPAAGGLPQGELLATYSTYEQAREQVDRLAEADFPVTALSIVGKDLRVVERVRGRL +NYGRVALGAAVQGALFGAMIGAFLLLLDSSAGGMQIVTSALLGVAVWVIFGVVGFASRKG +RHGFASTQALVPGGYDLVVAFEHAGRARQELGLGARGAATPAPAPMPVQESAPAPAPAPA +PSGSAVSGPSGSHAAPASSAEPAPAHVDGPAQDPAAPAGLDRSYGVTLPPEEVARLIEAR +GGRPRQDPQAPQGQPHPWDRPQS +>PROKKA_01470 +MSIMMPNPQPGAEQGLPRGELLATYATYAQARDQVDRLAATDFPVSAVSIVGKDLRVVER +VRGRLNYAQVALSAGVRGVFFGGLIGVFLYLLAPEAGPGQILTSMLLGLAVWLIFGVIGF +AMRRGQHGFASSQAVVPTAFDLVVAFDHAARARQELGLGGAAAPTPPAASQPAPAPAAEA +EDGSVQATPAPAPSSGGSHAAPAPGGPEAPARPAPEADPAPTGLDRSYGVTLPPEEVAKL +IEARGGHPPRPQDEPRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001261.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001261.fa new file mode 100644 index 0000000000000000000000000000000000000000..5942c2cbd2b04cd3fc4db2b6d3e083045543ec10 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001261.fa @@ -0,0 +1,45 @@ +>PROKKA_01544 +MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM +TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR +NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA +DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD +DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA +MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV +SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP +AT +>PROKKA_01254 +MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM +TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR +NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA +DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD +DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA +MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV +SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP +AT +>PROKKA_01381 +MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAVPPFATGLVIEVPGKKRVFVPM +TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAADLFDRRVRLTDGSGEAFLEDIGLEQQR +NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLDWDEARWTGQAEPQAATSFLAAHEDLKPA +DLADMLHEMPEKRRVEVARELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD +DAADLLHELPDSQQELLLERMEPEEAEDVRRLLEYEEGTAGSVMTPVPVILPPEATVAEA +MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAVGNIMDKDLEPV +SDLAPIAHVTRELATYNLTSIPVVNEHHRVVGAVSVDDVLDHILPDDWRAMDHDDHDPRP +AA +>PROKKA_01272 +MNSPRIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGRGARSAATGLVIEVPGKKRVFVPM +TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAGDLFDRRVHLTDGSGRAVVEDLGIEQQR +NGDWLVTDYYVRRDDGRTAFGRPRGEHLLVSWDEVAWGAAAEPQGASSFVAAHDDLKPAD +LADMLHEMTDKRRVEVANELQDERLADVLQELPDDDQVQILSHLDIERAADVLEEMDPDD +AADLLNELPDSQQELLLELMEPEDAEDVRRLLEYEEDTVGSIMTPVPVVLPPEATVAEAM +ATIRQQEISPALASLVIVARPPLETPTGRYLGVVHFQRLLRYPPPEAIGNIMDKDLEPVS +DMDSVAHVTRELATYNLTSIPVVNAQHRVVGAVSVDDVLDHILPEDWRAMDPEDHPETEG +QD +>PROKKA_01471 +MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM +TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR +NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA +DLADMLHDMSEKRRVEVARELQNERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD +DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA +MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEAV +SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDAETRP +AT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001262.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001262.fa new file mode 100644 index 0000000000000000000000000000000000000000..be9e572c7487c753ba1777764e47b787c101eca1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001262.fa @@ -0,0 +1,30 @@ +>PROKKA_01545 +MTQTARDLRPGRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF +CAAWLGWNTFGPMEWRFDSAELGFTALTLMLSLQASYAAPLLLLAQNRQDDRDRVALRED +RDRAERNLADTEFLTREIAGLRLAVQEVATRDFVRGELRGVQDDLRDDLREALRAELREE +IREEIREELRAGLPGAEAQPRKNKKTKGRGRDARRGDAGAEPTTTTLATLAAQEAREAGG +SGPAAGPADGAGPVDGGGR +>PROKKA_01255 +MTQTARDLRPGRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF +CAAWLGWNTFGPMEWRFDSAELGFTALTLMLSLQASYAAPLLLLAQNRQDDRDRVALRED +RDRAERNLADTEFLTREIAGLRLAVQEVATRDFVRGELRGVQDDLRDDLREALRAELREE +IREEIREELRAGLPGAEAQPRKNKKTKGRGRDARRGDAGAEPTTTTLATLAAQEAREAGG +SGPAAGPADGAGPVDGGGR +>PROKKA_01380 +MSQTSRDARPSRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF +CAAWLGWNTFGPEDLRFDSAALGFTALTLMLSLQASYAAPLLLLAQNRQDDRDKVALRED +RDRAERNLADTEFLTREISGLRLAVQEVATRDFVRGELRGVQEDLRDELREALRAELREE +IRAELRAELAEGRRERTDPGAEPRPRKQKKHKGRDRGRDERRAGDDGVDPSTTTLAVIAA +REAAQAAQSAQAGQDAGPEAGRAVDGRDDADGAAR +>PROKKA_01271 +MPQSPRDPRDTRATGLDTPMRARERVMPRLTPNPDAFGEWTEGIARFMGTPQFLLWMTLF +CLVWVGWNSYAPEPWRFDSAALGFTALTLMLSLQASYAAPLLLLAQNRQDDRDKVALRED +RDRAERNLADTEFLTREISGLRIALQDMATRDYVRGELRAMNEDLVAALREVVREEVREE +LRAEEAGPAVAPKPKEKSKKKSSRREPGRPDGTEAHTTTLAIIAAQEAADQGGAAPDAAH +AADDAGQDAP +>PROKKA_01472 +MTQTARYLRPGRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF +CAAWLGWNTFGPMAWRFDSAELGFTALTLMLSLQASYAAPLLLLAQNRQDDRDKVALRED +RDRAERNLADTEFLTREIAGLRLAVQEVATRDFVRGELRGVQDDLRDDLREALRAELREE +IREEIREELRAGLPGAEAQPRKNKKTKGRGRDARRGDAGAEPTTTTLATLAAQEAQEARE +AGGSGPVTGPAGGAGPVDGGGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001263.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001263.fa new file mode 100644 index 0000000000000000000000000000000000000000..1514a251f134d76bb71d5ee4ed131d4fcb30b994 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001263.fa @@ -0,0 +1,40 @@ +>PROKKA_01546 +MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI +AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT +RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM +ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD +IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL +DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ +IAQRVAVRPRGLAGRRLPVTPR +>PROKKA_01256 +MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI +AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT +RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM +ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD +IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL +DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ +IAQRVAVRPRGLAGRRLPVTPR +>PROKKA_01379 +MSDLGLHVPEVRTDLERRVLDRLATVQDPEIRRPVTELGMVESVVETAPGTVEVTVLLTI +EACPMRGTIQGDVAAAVADVPGCDAVDVRTGVMSPERRLALQDALRAARPANPFGEGSLT +RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTASPTKLDRM +ILPPVVRDVKVISIGMFLDEDRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD +IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQAVAGVIENMGPMTLPDGTVL +DVFGAGGGQEVAERLERVLGSAVPLLGSVPLDPALRRGGDAGDPVVLSAPDSPAGRALAG +VAERLAVRPRGLVGRRLPLSPR +>PROKKA_01270 +MSAPALPRPEVRTPLEAAVLAALDGVVDPEIRRPITELGMVRSVAETGGGHVAVEVLLTI +AGCPLKGTIQADVAAAVADVPGCAGVDVRLGVMTPTERAALQEALRGARPANPFAEDSLT +RVLAVASGKGGVGKSTVTANLAVALAGRGLSVGLIDADVHGYSIPGLLGVQASPTRVGEL +ILPPVSRGVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD +IAISTAQLLPASELVVVTTPQHAAAQVAARAGQLAAQTGQRVAGVVENMGPMALPDGTVL +DVFGAGGGQEVADRLSGALGTSVPLLGTVPLDPALRRGGDAGEPVVVSAPESPAAAALQE +VAARLAVRPGSLRGRGLPVSPR +>PROKKA_01473 +MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI +AACPLRGTIQTDVAAAVADVPGCGSVDVRVGVMEPERRLALQDALRAARPTNPFGKDTLT +RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM +ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD +IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL +DVFGTGGGAEVAERLSGVLGTQVPLLGTVPLDPALRAGGDAGDPVVVSAPESPAGRALAE +IAQRLAVRPRGLAGRPLPFTPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001264.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001264.fa new file mode 100644 index 0000000000000000000000000000000000000000..c7298922e9b02dd3120d9642978ac25b4ce11cb2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001264.fa @@ -0,0 +1,23 @@ +>PROKKA_01547 +MFGINGSEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE +VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGISAEDVHGGLTRQDLTDMDP +RTLFRRPAGAGSTAAAESGAAAAQTRSTEPAAGAAAVGGAAAALMASGRAEALTEERPAA +VETEPDPLELLGLAPAPFDVDAT +>PROKKA_01257 +MFGINGSEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE +VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGISAEDVHGGLTRQDLTDMDP +RTLFRRPAGAGSTAAAESGAAAQTRSTEPAAGAAAVGGAAAALMASGRAEALTEERPAAV +ETEPDPLELLGLAPAPFDVDAT +>PROKKA_01378 +MHGGLTRQDLVDMDPRSLFRRPAGAGSSAAPAASSGSAAPAAGASLATGAAVGGAAAALM +ASGRAEEAVAEERPAVEPDPLELLGLAPAPYDVDAT +>PROKKA_01269 +MFGINGSELIVLIVLAFVVLGPEKLPEYTRALAQGIRKTRDMAEGAKTQFKEETGTDFDS +VDWRRYDPRQYDPRRIIRDALREPADGSTAAARAQELTGVAAEDLQGGLSAQDLRDMDPR +SLFRRPSGDGSTAAPAGGGASAPSDAPTPEDVPSAAVPVAAASPSPAGAAAAGVAAALLA +SGRAEEVLTDPAPLQHLGTDPDPLDLLGKAPAPFDVDAT +>PROKKA_01474 +MFGINGGEFIILAVLAIVILGPEKLPEYTRAFTDWLRVMRDKAEGAKAQFKEETGTDFDE +VDWRKYDPRQYDPRRIIRDALREPAGGSSTPASRAAQATGVSAEDVHGGLTRQDLADMDP +RTLFRRPAGAGSTAAAESGAAAQTRSTAPAAGAAAVGGAAAALMASGRAEALAEERPAAV +ETAPDPLELLGLAPAPFDVDAT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001265.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001265.fa new file mode 100644 index 0000000000000000000000000000000000000000..74f9393d34b912f2b41da2ce83515761df8feba8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001265.fa @@ -0,0 +1,30 @@ +>PROKKA_01548 +MGRRHTQRHMDAYLEGSLPAASRARIARHLDRCPECRATVQARARVLDAARTVHQRPAGA +VVAPVLRARGVSGRLVVGLLTFVVLLGGLFTAVWVAGAPRTAAVRTAPTPTDTVALPAAG +TASTDRRGTVAELRGQGWTVPSLVGAGLEPLTVDTAQTAEDVEVVVGWGRDEPTVTVREC +RPRIVGATPKGCASTAPLSTGVQERRLAGGGVYRIVPAGEQDGWTAELTTPQAAYRVEAS +LPDERADAVLTHLLVSERARVLELGGGDAVEERLERGLERIADAVPRPRG +>PROKKA_01258 +MGRRHTQRHMDAYLEGSLPAASRARIARHLDRCPECRATVQARARVLDAARTVHQRPAGA +VVAPVLRARGVSGRLVVGLLTFVVLLGGLFTAVWVAGAPRTAAVRTAPTPTDTVALPAAG +TASTDRRGTVAELRGQGWTVPSLVGAGLEPLTVDTAQTAEDVEVVVGWGRDEPTVTVREC +RPRIVGATPKGCASTAPLSTGVQERRLAGGGVYRIVPAGEQDGWTAELTTPQASYRVEAS +LPDERADAVLTHLLVSERARVLELGGGDAVEERLERGLERIADAVPRPRG +>PROKKA_01377 +MGRGHTLRHLDAYLEDALPSASRRRIARHLDGCPDCRAAVRARARVLDAARTVHQRPAGV +VASPVLRSRGISGRVVVGLLAFVVLVGGLLAAVWMAGAPRAGVARLAPSPTDAVGLVSGG +SADGRAAVAQLRGHGWTVPSLLGAGLEPLTVDAAQTPRDVEVVVGWGLQEPTVTVRECRP +RIAGAAPEGCASAAPLPEDAQERTLTGGDVYRIQPAEADGAWTAELTTAQAAYRVEARLP +DERADAVLTHLLVSERSRVRELGGPDAVEERLERGIERIVESVPRVRD +>PROKKA_01268 +MGVLARGHCLPVLDSYLEGVLAPRASRRVEAHLSRCPDCRAVAGQRARVLDAARSVDARP +AAGAVMRPRGVSGRAVVCGLLVLVVLAGLVAAVWMLGGPASTAAPADVDPVRAVSAPVSA +SADEDDVATRVDELRGQGWALPSLSASGMRPLSVHADRVGEAAEVSVAWGRTSPVVTVRE +CRGADADERTRCARQGGVGVSGASEARLPVGMDYRIADHADGGWEAWLSTSDAVYRVDAS +VPRSQAEALLSQLVVVERSGLAPPRRDEDPRDRLERGLDRLLDGRVGGAAVRNPAAGAR +>PROKKA_01475 +MGRRHTQRHMDAYLEGSLPAASRARIARHLDRCPECRATVQARARVLDAARTVHQRPAGA +VVAPVLRARGVSGRLVVGLLTFVVLLGGLFTAVWVAGAPRTAALRTAPTPTDTVALPAAG +TASTDRRGTVAELRGQGWTVPSLVGAGLEPLTVDTAQTAEDVEVVVGWGRDEPTVTVREC +RPRIVGAAPEGCASTAPLSTGAQERRLAGGGVYRIVPAGEQDGWTAELTTPQAAYRVEAS +LPDERADAVLTHLLVSERARVLELGGGDAVEERLERGLERIADAVPRPRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001274.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001274.fa new file mode 100644 index 0000000000000000000000000000000000000000..f639468934462b9a852fd7d5e82a9c1a588701a1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001274.fa @@ -0,0 +1,35 @@ +>PROKKA_01558 +MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA +DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG +PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV +MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL +GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAAHTVKAVDLSGVPNLLFRRNSTTG +GVEALPRAGRTVELNAALHAN +>PROKKA_01268 +MTQTAAQQPSPRLVSGHGLATTAADGAVLDVWFPTPVAGPLSAADASLRDTLRALAADDA +DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLARPNELNLDGVFGLLTNVVWTNHG +PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV +MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL +GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG +GVEALPRAGRTVELNAALHAN +>PROKKA_01367 +MTETAAQHPSARLVSGHGLATTAADGTVLDVWFPAPVAGPLADADATLAETLRSLAADDA +DRGTTQSVVELEADLDAAPATAEDAWLRLHALSHRLVRPNELNLDGVFGLLANVVWTNFG +PCAVEGFELTRARLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTV +MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLL +GANSGVGISIGDDCVVEAGLYVTAGALVTVVRPGEEPRTVKAVELSGVPNLLFRRNSATG +VVEVLPRAGRTVELNAALHAN +>PROKKA_01258 +MTDTSQTSSARLVSGHGLATRAADGAVLDVWFPAPVTGPLASADASLAGTLEGLAAADAD +RGTTQDIVALEADLDVAPASAEDAWLRLHALSHRLVRPNELNLDGVFGLLTNVVWTNFGP +CAVEGFEATRAKLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTVM +HEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLLG +ANSGVGISIGDDSVVEAGLYVTAGTVVTVVEPGRKPRTVKAVELSGVTNLLFRRNSVTGG +VEVLPRDGRTVALNAELHAN +>PROKKA_01485 +MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA +DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG +PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV +MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL +GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG +GVEALPRAGRTVELNAALHAN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001278.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001278.fa new file mode 100644 index 0000000000000000000000000000000000000000..bcfe72031b54fa5a6a58ab11668817ade5bf688f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001278.fa @@ -0,0 +1,60 @@ +>PROKKA_01564 +MTSTETRRSDLRNVAIVAHVDHGKTTLVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI +TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL +PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS +VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN +LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLERVPAEEAGPG +EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ +VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR +TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG +FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGSATPFAMINLQERGTFF +VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF +AREDECVEITPEDIRIRKVVLDANERLKAARARARA +>PROKKA_01274 +MTSTETRRSDLRNVAIVAHVDHGKTTMVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI +TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL +PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS +VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN +LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLGRVPAEEAGPG +EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ +VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR +TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG +FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGSATPFAMINLQERGTFF +VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF +AREDECVEITPEDIRIRKVVLDANERLKAARARARA +>PROKKA_01362 +MTSTDTRRSDLRNVAIVAHVDHGKTTLVDAMLRQGGAFAAHGEVAERVMDSGDLEREKGI +TILAKNTTVFYSGPSAPEGQTVTFNVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL +PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLADEVEDLDLDS +VLNLPVVFASGKAGRASLNQPEDGSLPDSEDLEPLFATMMEHIPAPAYTKGEVLQAHVTN +LDASPFLGRLALLRIFNGTLKKGQQVAWARQDGTLKTVKITELLGTKGLSREPIEEAGPG +EIVAVAGIEDIMIGETLTDVENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ +VKDRLDAELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTK +TVDGKVHEPMELMTIDTPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFSVPARGLIG +FRTQFLTDTRGAGIASSIANGYEPWAGTIEYRNNGSLVADRAGTATPFAMINLQERGSFF +IQPGSEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSDSFEGLTPPRQLTLEESLEF +AREDECVEITPEDIRIRKVVLDANERLKAARARARA +>PROKKA_01253 +MTSTDTRRSDLRNVAIVAHVDHGKTTLVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI +TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDASEGPL +PQTRFVLRKALAAKLPVVLVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPELDLDS +VLDVPVVYASGKAGRASREQPGDGALPDSEDLEPLFNVIMEHIPAPVYDESEVLQAHVTN +LDASPFLGRLALVRIVNGTLKKGQTVAWARQDGQLKSVKITELLATKGLERVPADEAGAG +EIVAVAGIEDIMIGETLTDLEDPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ +VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTK +QIDGKLHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG +FRTRFLTDTRGAGIASSEAAGYEPWTGDIEYRTNGSLVADRAGTATPFAMINLQERGTFF +IQPGAEVYEGMIVGENARADDMDVNITKEKKLTNMRAASSESFEGLTPPRTLTLEESLEF +AREDECVEITPEDIRIRKVVLDANERLKAARARARA +>PROKKA_01491 +MTSTETRRSDLRNVAIVAHVDHGKTTMVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI +TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL +PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS +VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN +LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLERVPAEEAGPG +EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ +VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR +TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG +FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGTATPFAMINLQERGTFF +VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF +AREDECVEITPEDIRIRKVVLDANERLKAARARARA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001279.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001279.fa new file mode 100644 index 0000000000000000000000000000000000000000..402f40c6e89649df52673240d393a85cbc25161f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001279.fa @@ -0,0 +1,60 @@ +>PROKKA_01565 +MSANDKKGRSMFGKKKENDVTDGGQGSHAASSADLEARGAAVPGSSGAGGVPPGPATSAM +GVVARHDDLGGEPVLAFRDVDVKFATEFGEVHAVKGVTFDVKPGEVVALVGESGSGKSVT +SATAMGLLPGNADVTGSVKLAGREVLTMTPGQLRGIRGDEVAMVFQEPMTALNPVLTVGD +QLTEALELHGIAYGTEADKRAVELLTMVGIPDAATRLKQYPHQFSGGQRQRIVIAMAISC +SPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMADRVCVMLHG +ELVEQGSVHQVLQHARHPYTQKLLSAVPRLGEPLEVAEPEPVTATQTQARYAIEAENLHL +EYDHRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEGSLRIQGHDL +ATMPKAEQRALRKNIGVVFQDPAASLDPRFPIGDIITEPMVVHKVGDRRSRLARAEELLD +AVRLPRSVVNRYPHELSGGQRQRISIARALTLDPQVLIADEPTSALDVSVQAAVLDMFAE +LQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTEEVLHRPKEEYTRRLLAAAP +VPDPDQQAERRQERREFLASLGEGVY +>PROKKA_01275 +MSANDKKGRSMFGKKNQNDVTAGGQGSHAASSADLEARGAAVPGSSGAGGVPPGPATSAM +GVVARHDDLGGEPVLAFRDVDVKFATEFGEVHAVKGVTFDVKPGEVVALVGESGSGKSVT +SATAMGLLPGNADITGSVQLAGREVLTMTPGQLRDIRGDEVAMVFQEPMTALNPVLTVGD +QLTEALELHGIAYGTEADKRAVELLTMVGIPDAATRLKQYPHQFSGGQRQRIVIAMAISC +SPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMADRVCVMLHG +ELVEQGSVHQVLQHARHPYTQKLLSAVPRLGEPLEVAEPEPVTATQTQARYAIEAENLHL +EYDHRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEGSLRIQGHDL +ATMPKAEQRALRKNIGVVFQDPAASLDPRFPIGDIITEPMVVHKVGDRRSRLARAEELLD +AVRLPRSVVNRYPHELSGGQRQRISIARALTLDPQVLIADEPTSALDVSVQAAVLDMFAE +LQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTEEVLHRPKEEYTRRLLAAAP +VPDPDQQAERRQERREFLASLGEGVY +>PROKKA_01361 +MTAHGNDKEGRPMSGKKNQHDAAGTEATAVGTGAGEHGSHSADLDARGAAVPGSSGTGGP +TPGPATSSMGVVARHDDLDGKPVLAFRDVDVKFGTEFGEVHAVKGVTFDVKPGEVVALVG +ESGSGKSVTSATAMGLLPSNADITGSVQLAGREVLDMTPGQLRGIRGDEVAMVFQEPMTA +LNPVLTVGDQLTEALELHGIAYGTEADKRAVELLTMVGIPDAAERLKQYPHQFSGGQRQR +IVIAMAISCSPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMA +DRVCVMLHGELVEQGTVHQVLQHAQHPYTQKLLSSVPRLGATYEVAEPEPVTATQTTAKY +AIEAEDLHLEYDYRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEG +SLRIQGHDLAAMPKSEQRKLRKNIGVVFQDPAASLDPRFPIGDVITEPMVVHKVGDRRSR +LARAEELLDAVRLPRSVVNRYPHELSGGQRQRVSIARALTLDPQVLIADEPTSALDVSVQ +AAVLDMFAELQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTKEVLHNPREEY +TRRLLAAAPVPDPDQQAERRQERRDFLASLGEGVY +>PROKKA_01252 +MSSKAFDPKDSGTTETSAEDLRARAETLPGSSGEAPQGVVTTATGSLKVPGPATTTMGVV +EHHDDLGGEPVLAFQDVAVRFATEFGSVHAVKGVTFDVKPGEVVALVGESGSGKSVTSST +AMGLLPPSADITGSVKLGGREVLTMTDSQLRSIRGQDVAMVFQEPMTALNPVLTVGDQLT +EALQLHGLAFGTEATKRAVELLTMVGIPDAADRLKQYPHQFSGGQRQRIVIAMAISCSPR +VIIADEPTTALDVTVQAEILELLRSLKDKMNTGILLITHNMGVVADMADRVCVMLHGELV +ESGTVQQVLQRPQHPYTQRLLAAVPRLGEALETAEPEPVTSTQTAVKYAIEAEDLCIEYD +HRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKAVLGLLPVASGALRLQGEDLATM +KAAEQRALRRKIGVVFQDPAASLDPRFPIGDVITEPMVIHGVGDRRSRLARAEELLDAVR +LPRDVVNRYPHELSGGQRQRVSIARALTLDPEVLIADEPTSALDVSVQAAVLEMFAELQT +RYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTGRVLHHPQAEYTQRLLAAAPVPD +PDQQAERRRERRRLLASFGESAY +>PROKKA_01492 +MSANDKKGRSMFGKKNENDVTADGQGSHAASSADLEARGAAVPGSSGAGGVPPGPATSAM +GVVARHDDLGGEPVLAFRDVDVKFATEFGEVHAVKGVTFDVKPGEVVALVGESGSGKSVT +SATAMGLLPGNADVTGSVQLAGRDVLTMTPGQLRDIRGDEVAMVFQEPMTALNPVLTVGD +QLTEALELHGIAYGTEADKRAVELLTMVGIPDAATRLKQYPHQFSGGQRQRIVIAMAISC +SPKVIIADEPTTALDVTVQAEILELLRSLKNKMNTGILLITHNMGVVADMADRVCVMLHG +ELVEQGSVHQVLQHARHPYTQKLLSAVPRLGEPLEVAEPEPVTATQTQARYAIEAENLHL +EYDHRGKKNRVVHDVSFQVAPGEILGLVGESGSGKSTIAKSVLGLLTIAEGSLRIQGHDL +ATMPKAEQRALRKNIGVVFQDPAASLDPRFPIGDIITEPMVVHKVGDRRSRLARAEELLD +AVRLPRSVVNRYPHELSGGQRQRISIARALTLDPQVLIADEPTSALDVSVQAAVLDMFAE +LQQRYEFACLFVSHDLAVVDMLAHKVLVLKDGRQVEQGPTEEVLHRPKEEYTRRLLAAAP +VPDPDQQAERRQERREFLASLGEGVY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001281.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001281.fa new file mode 100644 index 0000000000000000000000000000000000000000..0dc3a7e34eb54c3ebcf2eb8485fce7a33118fe42 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001281.fa @@ -0,0 +1,50 @@ +>PROKKA_01567 +MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTAFMGLDQ +PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVADLLSNAAASTLRLVVLATVLAIIIGIA +IGIVTAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG +VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA +AAVGATAVISGLRNRSVLKAALVTVAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI +LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD +AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLPERQVI +LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL +VTGTAAVLMNLVADVLYAVLDPRIRV +>PROKKA_01277 +MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTAFMGLDQ +PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVADLLSNAAASTLRLVVLATVLAIIIGIA +IGIVTAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG +VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA +AAVGATAVISGLRNRSVLKAALVTVAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI +LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD +AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLPERQVI +LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL +VTGTAAVLMNLVADVLYAVLDPRIRV +>PROKKA_01359 +MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTEFMGLDQ +PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVGDLLSSAAASTLRLVVLATVLAIIIGIA +IGIVTAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG +VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA +AAVGATAVISGLRNRSVLKAALVTVAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI +LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD +AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLSERQVI +LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL +VTGTAAVLMNLVADVLYAVLDPRIRV +>PROKKA_01250 +MLKFILRRLGSSALVLFGASILLYVLTVNSGDPLKDLRESQASNREQLMQARIDYMGLDD +PWYERYWNWLTGVVKYLIGAGTLGTDRSGVQVESLLGNAAASTLRLVVLATVLAIVIGVA +IGIITAIRQYSGLDYAVTFLIFLFFSLPVFWAAVLLKEYLAIGFNNWIARPTMDWPLVIG +LAVVLGLALQAAMGGRLVRRLLTFAATVAVIVLGGYLLFALDMWRNPRMGPLVQLLIGLA +VAVGGTALVAGLKNRSVLKAALATVAVGVVAYYATYGVLMQSPSGWLIAGLGVIAVLVGV +LAGRLLGGFSKGSAVSVSVVTALVMGLSILAEHMMNYWPQLLKAKPRPIATIGAETPNLT +GHFWVLFLDKGTQLLLPTVLLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLGERQVI +LKHAFRNSLIPITTIMAFDFAGLIGGAVITESVFGWKGMGELFRTGLDQVDPAPVMAFFL +VTGTAAVLMNLVADILYAVLDPRIRV +>PROKKA_01494 +MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTEFMGLDQ +PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVGDLLSNAAASTLRLVVLATVLAIIIGIA +IGIITAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG +VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA +AAVGATAVISGLRNRSVLKAALVTAAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI +LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD +AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLPERQVI +LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL +VTGTAAVLMNLVADVLYAVLDPRIRV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001283.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001283.fa new file mode 100644 index 0000000000000000000000000000000000000000..98f0c3325a5dc5cec755715e2593f7c811e7145c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001283.fa @@ -0,0 +1,30 @@ +>PROKKA_01570 +MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLAAGVMLAVSFLEMLPAAV +EGLGGAVGPAATAVAVAALILGAGSYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT +VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRRKA +FAWAAFTGIAEPLGALIGWLLLAPFLTPALLAAVFAAVAGVMVTVSLDALLPAARAAGGR +AAALGGVLLGVAAMALSLDLLS +>PROKKA_01280 +MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLSAGVMLAVSFLEMLPAAV +EGLGGAVGPAATAVAVAALALGAGAYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT +VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRCKA +FAWAAFTGIAEPLGALIGWLLLAPFLTPALVAAVFAAVAGVMVTVSLDALLPAARAAGGR +GAALGGVLLGVAAMALSLDLLA +>PROKKA_01354 +MDPLWIALALTAFAGLATVLGGVLAVVGKEPSGRGLGAALGLAAGVMIAVSFLEMLPVAV +EGLAGAVGGAATALAVGALAVGTAGYVLLERAVPVPAAGVPDDVDGPDGLSRLRLMRLGM +VTALAIGLHNVPEGFVTFAGALQDPSVGVALAVAMAVHNVPEGIAVAVPVRRATGSRRKA +FAWTAFTGLAEPVGALVGWLLLAPFLTPALVAVVFAAVTGVMITVSLDALLPAARAAGGR +AATLAGVLLGVAAMAISLDLLG +>PROKKA_01247 +MEPFWTAVALTSLAGAATIVGGALGALGRPVSDRALAAALGLAAGVMLTVGAVEMGPAAA +RGLATAVGDGPGVLAAGAAVGGGALAYLLIDRLLPEAATPSGSSASAAREARVGRLGVAT +ALAIGAHNLPEGFVTFAGALEDSAVGLALAVAMAVHNVPEGIAVSVPVRRATGSARTGFL +WAATAGILEPAGALLGYWLLRPLLTDAVLGGVYGAVTGVMAALSLAALLPGAVRCGGVPT +ALAGAAAGAAAMLGSLSLLA +>PROKKA_01497 +MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLAAGVMLAVSFLEMLPASV +EGLGGAVGPAATAVAVAALTLGAGSYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT +VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRRKA +FAWAAFTGIAEPLGALIGWLLLAPFLTPALLAAVFAAVAGVMVTVSLDALLPAARAAGGR +AAALGGVLLGVAAMALSLDLLS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001287.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001287.fa new file mode 100644 index 0000000000000000000000000000000000000000..fc1df212a5de958caf172190839eaa5050db0bb5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001287.fa @@ -0,0 +1,21 @@ +>PROKKA_01574 +MSETRRARPGVDPASTPPSDVPRGPGGRDALVRRRVFRTPLLRRVVYAVVFELLAILFTT +VILAALGNGGGPSLAVAVVSSTVALLWNIVFNSVFETLERRLGITGRPWWVRVAHAVGFE +GGLIVFLVPAVALILGVGLGEAFLIEAGLLVFFLVYAAVYAYAFDSVFGLPDSAARAEA +>PROKKA_01284 +MSETRRARPGVDPASTPPSDVPRGPGGRDALVRRRVFRTPLLRRVVYAVVFELLAILFTT +VILAALGNGGGPSLAVAVVSSTVALLWNIVFNSVFETLERRLGITGRPWWVRVAHAVGFE +GGLIVFLVPAVALILGIGLGEAFLIEAGLLVFFLVYAAVYAYAFDSVFGLPDSAARAEA +>PROKKA_01350 +MPRLSAVSEPLTIAPRSDDAPSVPSSSSDAPRGPGGRRALVRRRVFRSPLQRRIVYAVVF +ELLAILFTTGILAAFGNSGGSSLAVAVVSSTVALLWNIAFNSMFEAVERRAGITGRPWWL +RALHAVAFEGGLILFLVPAVALILGVGLWQAFLIEAGLLVFFLVYAAVYAYAFDSVFGLP +DSAAGATR +>PROKKA_01243 +MTPPHDDAPRGPGGRRALVGRRVFRSPLRRRIVFAVVFELLAILFTTLILRAVGNEGAAS +FAVAVVSSTVALIWNVVYNSLFERLERALGVHGRPWWARVGHTVGFEGGLVLFLVPAVAL +LLGVTLWEAFLIELGLIVFFLVYNAVYTYLFDAVFGLPDSAGVTAPGTP +>PROKKA_01501 +MSETRRARPGVDPASTPPFDVPRGPGGRDALVRRRVFRTPLLRRVVYAVVFELLAILFTT +VILAALGNGGGPSLAVAVVSSTVALLWNIVFNSVFETLERRLGITGRPWWVRVAHAVGFE +GGLIVFLVPAVALILGVGLGEAFLIEAGLLVFFLVYAAVYAYAFDSVFGLPDSAARAEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001293.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001293.fa new file mode 100644 index 0000000000000000000000000000000000000000..fac86c5c96a7dd98dbe1c8e7e952d35b1296cd97 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001293.fa @@ -0,0 +1,35 @@ +>PROKKA_01580 +MTPADRAPATPAPQPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREPGVLSG +TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI +ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH +LAALGFGSAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS +PAELRAGVERVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE +EVSPRR +>PROKKA_01290 +MTPADRAPTTPAPRPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG +TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI +ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH +LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS +PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE +EGSPRR +>PROKKA_01343 +MSAGTRGAWGPTPAPIADVERIVAAALAEDAPWGDVSSEAFVPADARITARVVAREAGVL +SGTAALEAAFRLVDPATEVTLHLPDGTALAPGAVVAAVAGPARSVLRAERVALNLAQRMS +GIATATAAHVAAVRAGGGHTRVADTRKTTPGLRVLERQAVRDGGGHNHRHGLSDAVMLKD +NHLAALGFGGEDAPGEELTRALRAGKARLPHTVHVEVEVDRLDQLPAVLAAGVGTVMLDN +FSLADLRAGVELVAGRAVVEASGGVSLETIGEIAATGVDVVSVGALTHSVRALDLGLDAV +VDAADAPAPGRR +>PROKKA_01236 +MTPADRAPATPAPQPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG +TNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI +ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRSSLSDAVMLKDNH +LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVGTIMLDNFS +PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVRSLDLGLDAVVE +EVSPRR +>PROKKA_01507 +MTPADRAPTTPAPRPDVERIVAAALAEDAPWGDVSSEAFVPEQARITARVVAREAGVLSG +PNALEAAFRLVDPAVSVTLHLADGADLSPGAVVAEVAGPARSVLRAERVALNLVQRLSGI +ATTTAAHVAAVRAGGGHARVVDTRKTTPGLRVLERQAVRDGGGHNHRFSLSDAVMLKDNH +LAALGFGGAGDPGEALTAALRAGMARLPHTTHVEVEVDRLEQIPAVLAAGVDTIMLDNFS +PAELRAGVELVAGRAVVEASGGVSLETIGAIAATGVDVISVGALTHTVQSLDLGLDAVVE +EGSPRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001295.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001295.fa new file mode 100644 index 0000000000000000000000000000000000000000..1a3e2ee69900d47323e25fc787b94a9e1dca1bca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001295.fa @@ -0,0 +1,55 @@ +>PROKKA_01589 +MFVVLGPAPASVGSPGAWWALDGEGDGASPLGSCAAGSVAGLVAGLPARLGVDPSTVRWV +LADVGTEYAAWLVAGVRVDRCWDLALVQRILRHAATAPGSGVRYTPVAQLEVADPTEPVR +PARVPAGQESFFDLPDEAGPAPDVTVLAAELAAQRAAVEGSAHPHRLRLLAAAESQGALV +AAEIRAAGLPWDRGVHEALLAEQLGPRPAPGERPARLQTLAERIADVLGSPGLSPDSQPS +LLRALQTAGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWHWLD +QWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQVPAGVRDAVRADPGWTLTVADASQVEPR +ILAAMAADEALARAGTTPDLYREVAEQGRAAGTALADRGRAKIALLGAMYGSTTGDSAAL +MPHLRRLYPRAIGLLERAASVGEGGGQVSTWLGRWSPAPGRKWQESVSDVGTQAAESAAR +RRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRLRSAGMRTELVFFVHDEVVLHGPATEV +EAVRTVVAESASAAGRLLFGPAPVDFPLTVSSVGSYADAK +>PROKKA_01300 +MRAMFVVLGPAPASVGSPGTWWALDGEGDDAVPLGSCAAGSVAGLVAGLPARLGVDPSTV +RWVLADVGTEYAAWLAAGVRVDRCWDLALVQRILRHAATAPGSGVRYTPVAQLEVADPTE +PERPARVPAGQESFFDLPDEADPAPDVTVLAAELAAQRAAVEGSAHPQRLRLLAAAESQG +ALVAAEIRAAGLPWDRGVHEALLAEQLGPRPAPGERPARLQALAERIADVLGSPGLSPDS +QPSLLRALQTAGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWH +WLDQWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQIPAGVRDAVRADSGWTLTVADASQV +EPRILAAMAADQALARAGTTPDLYREVAEQGRAAGTALADRGRAKIALLGAMYGSTTGDS +AALMPHLRRLYPRAIGLLERAASVGEGGGQVSTWLGRWSPAPGPTWQESVSDVGTQAAES +AARRRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRMRSAGMRTELVFFVHDEVVLHGPA +TEAEAVRTVVAESASAAGRLLFGPAPVDFPLTVSSVGSYADAK +>PROKKA_01333 +MRDMFVVLGPAPASVGSPGAWWAVDGDDATPLGSCPAGSVAGLVAGLPARLGVDPSTVRW +VLADVGTEYAAWLAAGVRVDRCWDVALVQRILRHAATAPGSGVRYTPVAQLEVADPTEPE +RPARVPAGQESFFDLPDGTGSAPDVTVLAAELAAQRAAVEGSAHPHRLRLLAAAESQGAL +VAAEIRAAGLPWDRGVHEALLTEQLGPRPAQGERPARLQALAERIADVLGSPGLSPDSQP +SLLRALQTAGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWHWL +DQWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQIPAGVRDAVRADPGWALTVADASQVEP +RILAAMAADEALARAGTTPDLYREVAEQGRAAGTALADRGRAKVALLGAMYGSTTGDSAA +LMPHLRRLYPRAIGLLERAASVGEAGGQVATWLGRWSPAPEQAWLDSVADVGTQAAESAA +RRRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRLRAAGLGTELVFFVHDEVVLHGPAPE +AEAVRGVVAEAASAAGRLLFGAAPVDFPLTVASLDSYADAK +>PROKKA_01231 +MVIVLGPDPAPGTPPGRWCALVLPDDAAPSPADASPGQGDGGPVARFARDELADVVRALP +GRLGVDPAVVRWTVADAAEVYPALLAAGVRWDRCRDLSLGQRILRGAAAAGLAYAPTVDL +PVHEPEAEDPATARRAPGQGAMFELAGPEPAPDAAALARELAAQQAAVAASAHPHRLRLL +LAAESQGALVAAEMHHAGLPWRADVHEALLAEQLGPRPPEGARPARLQALGERVAAALGS +PGLNPDSPPALLRALQTAGVTVDSTRKWELTAWADQGGAQRQAREALIAPLLEYKALYRL +WTAHGWHWLDTWARDGRFRPTYLVGGVVTGRWAAHGGGAMQVPSGVRDAVRADPGHVLTV +ADASQVEPRILAAMSRDAALAAAGATPDLYREVAEQGRSAGTALDDRSRAKVALLGAMYG +ATTGDSAALLPHLRRLYPAALAMLEAAAADGEAGRPVHTWLGRTSPAPAERWLERVADRS +TREAEARARSLRRSAGRFTRNFVVQGTAAEWALCWMGQIRGGLHRAGLSTALVFFVHDEV +VLHGPAEEAGAVARIVTEAASQAGRLLFGAAPVDFPLTVAQVESYAQAK +>PROKKA_01516 +MFVVLGPAPASVGSPGAWWALDGEGDGASPLGSCAAGSVAGLVAGLPARLGVDPSTVRWV +LADVGTEYAAWLVAGVRVDRCWDLALVQRILRHAATAPGSGVRYTPVAQLEVADPTEPVR +PARVPAGQESFFDLPDEAGPAPDVTVLAAELAAQRAAVEGSAHPHRLRLLAAAESQGALV +AAEIRAAGLPWDRGVHEALLAEQLGPRPAPGERPARLQTLAERIADVLGSPGLSPDSQPS +LLRALQTTGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWHWLD +QWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQVPAGVRDAVRADPGWTLTVADASQVEPR +ILAAMAADEALARAGTTPDLYREVAEQGRAAGTALADRGRAKIALLGAMYGSTTGDSAAL +MPHLRRLYPRAIGLLERAASVGEGGGQVSTWLGRWSPAPGRKWQESVSDVGTQAAESAAR +RRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRLRSAGMRTELVFFVHDEVVLHGPATEA +EAVRTVVAESASAAGRLLFGPAPVDFPLTVSSVGSYADAK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001297.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001297.fa new file mode 100644 index 0000000000000000000000000000000000000000..cc6fa009b760361fbf6ac5e11ec148a333af2426 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001297.fa @@ -0,0 +1,55 @@ +>PROKKA_01594 +MALHLQRYREIAHVMARNGLMATAVQAGLSRWLPLEEGEPHLGIDAEARPELFVRTFEEL +GVTFVKLGQLISARPDVFPEAYCAAFARLTDSTSAVPFEAVARTVEEDLGADVDTLFAWF +DRAPLATASIGQAHRARLHDGRAVVVKVRKPGVVEQVQADLEILRTLAATWSRASRTFAD +LDVPAMVDEFDRSLRAELDYVVEARACEEIAAGFRDTPGVRFPWIEWDLTTSRVLTMQEL +SGLRVDDLAGLDAAGIDREELAYRAADVLLAMVFEHGVFHADPHPGNLFIEPDGTVGFID +FGSVGRISPSLRRRFAGLAMALARQDTDGLVRALLDIAPPRGPVDRRRLRLEVARIVGRL +EGRELEDIRVAQLISEIFALVRRHRLSLPPELVQLLRMLIIVDGIGRRLHPGFDYTRVLD +PFALRLVGEHLDPRRVAGRIGRATIAAAELGIDLPEYARKVMERIDDGGIDVTVRASELE +PLVTRLERTGDRVVAAMVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLA +WISRPRRRPR +>PROKKA_01306 +MALHLQRYREIAHVMARNGLRATAVQAGLSRWLPLEEGEPHLGIDAEARPELFVRTFEEL +GVTFVKLGQLISARPDLFPEAYCAAFARLTDSTTAVPFEAVARTVEEDLGADVDTLFAWF +DRAPLATASIGQAHRARLHDGRAVVVKVRKPGVVEQAQADLEILRTLAATWSRASRTFAD +LDVPAMVDEFDRSLRAELDYVVEARACEEIAAGFRDTPGVRFPWIEWDLTTSRVLTMQEL +SGLRVDDLAGLDAAGIDREELAYRAADVLLAMVFEHGVFHADPHPGNLFIEPDGTVGFID +FGSVGRISPSLRRRFAGLAMALARQDTDGLVRALLDIAPPRGPVDRRRLRLEVARIVGRL +EGRELEDIRVAQLVSEIFALVRRHRLSLPPELVQLLRMLIIVDGIGRRLHPGFDYTRVLD +PFALRLVGEHLDPRRVAGRIGRATIAAAELGIDLPEYARKVMERIDDGGIDVTVRASELE +PLVTRLERTGDRVVAAMVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLA +WISRPRRRPR +>PROKKA_01327 +MPSRLHRSREIALILGRNGLQATALAAGLGRWLPAADARTARDAVLRPDMLVDVFEQLGT +TFVKLGQLISARPDMFPESICTAFARLTDDTTPVPFEAMAATVLEDFGASVDELYAWFDP +VPLATASIGQAHRARLHDGRDVVVKIRKPGVVEQVRTDLEILRTVASRLSRASRALQDMD +VVSLVDEFDRALRAELDYLVEARACEQIAENLRDVPGVRVPWVDWATTSSRVLTMEEITG +FRVDDLASLDAAGIDRADLAYRAAEVLMGMVFEDGLFHADPHPGNVFIEADGGIGFIDFG +SVGRISSGMRRRFARMAMALVRQDPDGLVRALVAIAPPRGDLDRRALRLEVSRITGRLEG +RDLADIRVDQLVGQIFGIVRRHRLALPPELVQLFRMLIIVDGLGKRLHPGFDYTRVLNPF +AVRVAGEELDPRRVAGRIGQAGLAAAELGLDLPEYARKVIDHLEDGGLDVTLRTGELEPL +VARMERTGDRVVAALVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLAWT +GRPRRMRRRPRG +>PROKKA_01215 +MALHLQRYREIAHVMARNGLDATARLAGLGRWLAPQDPTARRPLDAEARPELLVRTFEEL +GTTFVKLGQLISTRPDLFPESYCTAFARLTDRATPVPYAAIARTVEEDFGAPVDELFAEF +DRTPLATASVGQVHGAVLHDGRDVVVKVRKPGVVEAVTADLEILRTLTGRLVRASRTLAD +MDVAGMVDQFDRSLRAELDFVVEARACEEIAAGFTGTPGVRFPWIAWELTSARVLTMERM +AGMRVDDLPALEAAGIDREELAYRAADVLMRMVFQHGVFHADPHAGNVFIEPDGTIGFID +FGSVGRIGPGVRERISGLAMALARQDVDGLVRALLEIAPPRGPVDRRRLRSEVGRIVARV +DGRDLQDIKVPQLVSEVFAIVRRHRLSLPPELVQVFRMVLIVDGLGRRLDPGFDYTRVLD +PFVRRMVMDQLDPRRLARRLRRATITTADIGLELPQYLRTLMERIEDGGIDVNVRTSELE +PLVARVERTGDRVVAALVVAAMITGGTNVLVAYKDRLGPFAGPLVAAGGAALTSGSAYLA +WISRPRRAPRR +>PROKKA_01521 +MALHLQRYREIAHVMARNGLMATAVQAGLSRWLPLEEGEPHLGIDAEARPELFVRTFEEL +GVTFVKLGQLISARPDVFPEAYCAAFARLTDSTSAVPFEAVARTVEEDLGADVDTLFAWF +DRAPLATASIGQAHRARLHDGRAVVVKVRKPGVVEQVQADLEILRTLAATWSRASRTFAD +LDVPAMVDEFDRSLRAELDYVVEARACEEIAAGFRDTPGVRFPWIEWDLTTSRVLTMQEL +SGLRVDDLAGLDAAGIDREELAYRAADVLLAMVFEHGVFHADPHPGNLFIEPDGTVGFID +FGSVGRISPSLRRRFAGLAMALARQDTDGLVRALLDIAPPRGPVDRRRLRLEVARIVGRL +EGRELEDIRVAQLISEIFALVRRHRLSLPPELVQLLRMLIIVDGIGRRLHPGFDYTRVLD +PFALRLVGEHLDPRRVAGRIGRATIAAAELGIDLPEYARKVMERIDDGGIDVTVRASELE +PLVTRLERTGDRVVAAMVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLA +WISRPRRRPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001298.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001298.fa new file mode 100644 index 0000000000000000000000000000000000000000..e1ff4c0b3657ebc34f9943692d01b57c522b3506 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001298.fa @@ -0,0 +1,45 @@ +>PROKKA_01595 +MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF +CEHRMLETPPEKSRIVSTRADDGAPAWQILRHPAAERLEETIPAFRRVPNLFEILSYDYW +RLNHGYELPPDACRRRDEYLATEAGRAHVRAVVTAKLRASGRSAEEAAAMSEAELIGASA +AFFGGTHDVVIARRHFVDGAVDDHQLASSGTLTPDEHHAFMALTADAMRDLYATTPAVRY +VSVFQNWLKPAGASFDHLHKQLVAIDEVGAQNVAALDRLREDPQVFNQAALDVAVAHDLM +IAANEHAVMFAGFGHRYPTVEVYSTSPVGQPWRQTAAELRAVSDLLHAAHAATGPDVPSN +EEWHTRPPGVADPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELWAA +GALADGMRIGADARVRPGMLRYAD +>PROKKA_01307 +MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF +CEHRMLETPPEKSRIVSMRADDGAPAWQILRHPAAERLEETTPAFRRVPNLFEILSYDYW +RLNHGYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSAEEAAAMSEAELIGASA +AFFGGTHDVVIARRHFVDGAVDDHQLASSGTLTPDEHHAFLALTADAMRDLYATTPAVRY +VSVFQNWLKPAGASFDHLHKQLVAIDEVGAQNVAALDRLREDPQVFNHAALDVAVAHDLM +IAANEHAVMFAGFGHRYPTVEVYSTSPVGQPWRQTAAELRAVSDLLHAAHAATGPDVPSN +EEWHTRPPGVASPMPWRVMLKWRVSTLAGFEGATKINVNTISPWDVRDRVLARLRELRAA +GALADGMRIGADARVRPGALRYADGAARLTPPRGR +>PROKKA_01301 +MPRTRPPAQDFLAELPDGTVKQRNPFSGTEVWTVPGRGHRPLGIARPAAQPLDPDDDGRH +CAFCSARLLETPPEKSRVVRTEDGEHAILRDVPAEALFDTVPEFRRVPNLFEILSYEYWR +LNHGFVPAPGVADRRAAYLATETGRAHVLAVVGNKLRAAGRSAEEVEAMPEEERIEAASG +FFGGGHDVIIARRHFADGAQDDHALAGSGTLSPEEHRRFIALTVDSMRDLYAANPHARYV +SVFQNWLKPAGASFDHLHKQLVAIDEVGVQNEAAIARVRRNPDAFAQDALGYAAKQGLMI +ARNEHAAMFAGFGHRYPTVEIHSLSPTCEPWEQTDAERDAMADLIHAAHAATGADVPSNE +EWHTRPTGVAEPLPWRVCLKWRVSTLAGFEGATKIYLNTVSPGSVRERVATRLQELQAAG +AIADGIRIDDDGHGAV +>PROKKA_01214 +MSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAFCEHR +MLETPPEKARIVPTRADDDAPAWQILRHPAAERLGETTPAFRRVPNLFEILSYDYWRLNH +GYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSAEEAAAMSEAELIAASAAFFG +GTHDVVIARRHFVDGAVDDHQLASSGTLTLDEHHAFLALTADAMRDLYATTPAVRYVSVF +QNWLKPAGASFDHLHKQLVAIDEVGAQNAAALDRLREDPQVFNHAALDVAVAHDLVIAAN +EHAVMFAGFGHRYPTVEVYSTSPVGQPWRQSAAELRAVSDLLHAAHAATGPDVPSNEEWH +TRPPGFASPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELRAAGALA +DGMRIGADARVRPGALRYAD +>PROKKA_01522 +MHPSVSEPLTRLPDGTVKQRNPFTGTEVWTVPGRGHRPLGLVRPAPQPLDPAQHGRHCAF +CEHRMLETPPEKSRIVSMRADDGAPAWQILRHPAAERLEETTPAFRRVPNLFEILSYDYW +RLNHGYELPPDARRRRDEYLATEAGRAHVRAVVAAKLRASGRSTEEAAAMSEAELIAASA +AFFGGTHDVVIARRHFVDDAVDDHQLASSGTLTPDEHHAFLALTADAMRDLYATTPAVRY +VSVFQNWLKPAGASFDHLHKQLVAIDEIGAQNAAALDRLREDPQVFNHAALDVAVAHDLV +IAENEHAVMFAGFGHRYPTVEVYSTSPVGEPWRQDPAELRGMSDLLHAAHAATGPDVPSN +EEWHTRPPGVADPMPWRVMLKWRVSTLAGFEGATKINVNTLSPWDVRDRVLARLRELRAA +GALADGMRIGADARVRPGMLRYAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001299.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001299.fa new file mode 100644 index 0000000000000000000000000000000000000000..e56176b62811ab2f812d9e8b8b5f6e1869172216 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001299.fa @@ -0,0 +1,50 @@ +>PROKKA_01597 +MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE +EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQT +VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH +DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSPFKPADADSIA +IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML +DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN +GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH +VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH +TPHLLGESLSWHQRFLETGTMRQG +>PROKKA_01309 +MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE +EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQT +VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH +DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSPFKPADADSIA +IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML +DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN +GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH +VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH +TPHLLGESLSWHQRFLETGTMRQG +>PROKKA_01298 +MSSRIQHAGLRAKVMSAQEAAAFIRPGTTVGMSGFTGSGYPKAVPLALAERISAAHARGE +DFRIDLHTGASTSSEMDGALAESGGVALRTPFQSDPTMRAKINAGEVEYIDTHLSHLAQT +VWNGFYGPMHTAVVEVSAIREDGTLVPSSSVGNNKSWLDLADEVILEVNSWQSEELEGLH +DVYYGTALPPHRQPVMITDPADRIGQPYFECDPAKVVAVVETHGPDRNSAFKPADADSIA +IAQHLVEFFEHEVAAGRYDERLLPLQSGVGNIANAVMAELVKSRFRGLTAFTEVVQDGML +DALDSGTLSMASATAFSLSTEAAERFNSTVAQYKDKLILRTQEISNHPELVRRLGVLAMN +GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSVAKGGDISCIVPMVSH +VDHTEHDVHVLVTEQGLADLRGLSPKQRARTIIAKCAHPDYRDQLQDYFDRAMRGSDGLH +TPHLLGEALSWHQRFLETGTMRHG +>PROKKA_01207 +MSSRIHHPGLRAKVMSAEEAAAFITPGMTVGMSGFTGSGYPKAVPMALAERIKSAHARGE +DFRIDLHTGASTSVEMDGALAEADGVRLRTPFNTDPTMRAKINDGSVDYIDTHLSHLAQT +VWEGFYGPMDAAVIEVSAIREDGTLVPSSSVGNNKSWLQLADKVILEVNSWQSEDLDGIH +DVYYDTALPPHRKPVPVNHPSDRIGRTEFVVDLDKVVAVVETHGPDRNSPFKPADADSIA +IAQHLVEFFEHEVKAGRYDEHLLPLQSGVGNVANAVMAELVKSRFHGLTAFTEVVQDGML +DALDSGTLAMASCTAFSLSTEVAERFNDNVLQYKDKLIIRTQEISNHPELVRRLGILAMN +GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH +VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYREQLRDYFDRAMRGSDGLH +TPHLLGEALSWHQRFLETGTMRQG +>PROKKA_01524 +MSSRIHHPGLRSKVMSAAEAAAFIQHGTTVGMSGFTGSGYPKAVPTALAERAKELHARGE +EFRINLHTGASTSAEMDGALAEADAVALRTPFQSDPTMRAKINAGAIEYIDTHLSHLAQA +VWNGFYGPMTTAVIEVSGIREDGRLVPSSSVGNNKSWIDLADQVILEVNSWQSEDLEGLH +DVYYGTALPPHRTPIMLTHPADRIGETYLRCDPAKVVAVVETHAPDRNSAFKPADADSIA +IAQHLVEFFEHEVAQGRYDERLLPLQSGVGNIANAVMSELVKSRFTGLSAFTEVVQDGML +DALDSGTLATASATAFSLSTEAAERFNDNAAKYRDKLILRTQEISNHPELVRRLGILAMN +GMLEADLYGNVNSTHLMGTKMMNGLGGSGDFARNAFTSFFLTPSTAKGGDISCIVPMVSH +VDHTEHDVHVVVTEQGLADLRGLSPKQRARTIIDTCAHPDYRDPLRDYFDRAMRGSDGLH +TPHLLGEALSWHQRFLETGTMRHG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001300.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001300.fa new file mode 100644 index 0000000000000000000000000000000000000000..efced170619d2840a3c47a9199fe009f85b5be85 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001300.fa @@ -0,0 +1,18 @@ +>PROKKA_01598 +MTKHRQPVPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA +EIGLGAALLALPGQRRLTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP +ALIAAALWAAGIPEREQGGRG +>PROKKA_01310 +MTKHRQPVPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA +EIGLGAALLALPGQRRLTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP +ALIAAALWAAGIPEREQGGRG +>PROKKA_01295 +MTKRRQSVPLSQTAARLGLGAALWAAGIPEREHGGRG +>PROKKA_01204 +MTKRRQSVPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA +EIGLGAALLALPGQRRRTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP +ALIAAALWAAGIPEREHGGRG +>PROKKA_01525 +MTKRRQSAPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA +EIGLGAALLALPGQRRLTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP +ALIAAALWAAGIPEREQGGRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001301.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001301.fa new file mode 100644 index 0000000000000000000000000000000000000000..8988e2f75be3423fad9ea8e18b87c565f555a1c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001301.fa @@ -0,0 +1,20 @@ +>PROKKA_01599 +METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGTNPEQLFAAGYAACFHS +ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVLPNVPADQARALMEQAHQVC +PYSNATRGNIDVVLELGEA +>PROKKA_01311 +METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGTNPEQLFAAGYAACFHS +ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVIPNVPADQARALMEQAHQVC +PYSNATRGNIDVVLELGEA +>PROKKA_01294 +METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGANPEQLFAAGYAACFHS +ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVLPHVPADQARALMEQAHQVC +PYSNATRGNIDVVLELGEA +>PROKKA_01203 +METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGSNPEQLFAAGYAACFHS +ALQMVARASRADITDSSVGARVGIGRQGEGFGLEVTLEVVLPHVPADQARALMEQAHQVC +PYSNATRGNIDVVLELGEA +>PROKKA_01526 +METIYTAEALSTGAGRDGHVRTTDGRVDLDLAVPTEMGGSGQGTNPEQLFAAGYAACFHS +ALQMVARASRADITDSSVGVRVGIGRQGEGFGLEVTLEVVLPNVPADQARALMEQAHQVC +PYSNATRGNIDVVLELGEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001303.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001303.fa new file mode 100644 index 0000000000000000000000000000000000000000..f2bb5d0fa3d881a2dfa31026ac4059221454ce11 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001303.fa @@ -0,0 +1,34 @@ +>PROKKA_01602 +MSTPTRTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV +ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF +SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS +AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD +GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA +GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL +>PROKKA_01314 +MSTPTHTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV +ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF +SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS +AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD +GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA +GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL +>PROKKA_01292 +MSVDPYMRGRMNDVKSYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGLGWREHAV +LDGDTVQAVDTSQFPDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAG +QIARLLGASRVVGSAGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVG +GDHLEAAIAALRVDGRVAMCGAIAQYNSTEPPAAPRNLALAIGKRLTLRGFVLQKYAAQV +RPEFLERVGPWVAAGKIQWDETVREGLENAPQAFIDLLDGANTGKMLVRL +>PROKKA_01200 +MSTPTHTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV +ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGLGWREHAVLDGDTVQAVDTSQF +SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSTAGQIARLLGASRVIGS +AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD +GRVAMCGAIAQYNSTEPPAAPRNLALAIGKRLTLRGFVLQKYAAQVRPEFLERVGPWVAD +GKIQWDETVREGLENAPQAFIDLLEGANTGKMVVRL +>PROKKA_01529 +MSTPTRTREIHLASRPHGAPTPENFRLTEVELPELAEGQVLVRNTVMSVDPYMRGRMNDV +ESYVPPFQLDAPLDGGAVGTVIASRHADVPEGTSVLHGRGWREHAVLDGDTVQVVDTSQF +SDSTYLGVLGMTGLTAYTGLVHVAEMQEGDAVFISGAAGAVGSVAGQIARLLGASRVVGS +AGTPEKVARVKELGFDAAFDYHDGSPTDLLAEAAPEGIDVYFDNVGGDHLEAAIAAMRVD +GRVAMCGAIAQYNSTEPPAAPRNLALAIGKCLTLRGFVLQKYAAQVRPEFLERVGPWVAA +GKIQWDETVREGLENAPQAFIDLLEGANTGKMLVRL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001304.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001304.fa new file mode 100644 index 0000000000000000000000000000000000000000..5d03fb1549e0ba23ab0c2adfcf189207aa1d32c3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001304.fa @@ -0,0 +1,26 @@ +>PROKKA_01603 +MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK +PEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII +LDSDAAGRPLGLVCHAPGILHPITAADGTPFVRGRQVTGFTNGEEEAAQLTDVVPFLVED +SLIAAGADYRKGPDGESFVVTDGTLVTGQNPASSADAARRLLDLLAR +>PROKKA_01315 +MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK +PEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII +LDSDAAGRPLGLVCHAPGILHPITAADGTPFVRGRQVTGFTNGEEEAAQLTDVVPFLVED +ALIAAGADYRKGPDGESFVVTDGTLVTGQNPASSGDAARRLLDLLAR +>PROKKA_01291 +MRLVGTVTLARDSVVYDHKSSVPTNERAPDMSRILMILTSHDQLGDTGRKTGFWLEEFAS +PYYVFTDAGHEVTLASPRGGQPPIDPTSSKPEMQTEATRRFDQDDEAKAALAHTTPLAQV +DVDGFDAVFYPGGHGPLWDLVSDADSTRIILDSDAAGRPLGLVCHAPGILHPITAADGTP +FVRGRQVAGFTNGEEDAAQLTDVVPFLVEDSLIAAGADYRKGPDGESFVVTDGTLVTGQN +PASSADAARRLLDLLAR +>PROKKA_01199 +MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK +SEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII +LDSDAAGRPLGLVCHAPGILHPITTADGTPFVRGRQVAGFTNGEEEAAQLTDVVPFLVED +SLIAAGADYRKGPDQESFVVTDGTLVTGQNPASSADAARRLLDLLAR +>PROKKA_01530 +MSRILMILTSHDQLGDTGRKTGFWLEEFASPYYVFTDAGHEVTLASPRGGQPPIDPTSSK +PEMQTEATRRFDQDEEAKAALAHTTPLAQVDVDGFDAVFYPGGHGPLWDLVSDADSTRII +LDSDAAGRPLGLVCHAPGILHPITAADGTPFVRGRQVTGFTNGEEEAAQLTDVVPFLVED +SLIAAGADYRKGPDGESFVVTDGTLVTGQNPASSADAARRLLDLLAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001305.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001305.fa new file mode 100644 index 0000000000000000000000000000000000000000..e1233860dad9568978efbc33fbdf2ad8057fd9fa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001305.fa @@ -0,0 +1,30 @@ +>PROKKA_01610 +MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTGGRIAAVPVAAVVASPLERC +AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQTQPSAVVFPGG +ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV +GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTGAGAVDERTPRIV +A +>PROKKA_01321 +MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTADRIAAVPVAAVVASPLERC +AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATESLWATVQTQPSAVVFPGG +ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV +GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTGTGAVDERTPRIV +A +>PROKKA_01288 +MATVLLVRHGRTTANASGLLAGRTPGVSLDEHGREQAARTADRIAAVPVTAVVASPLERC +AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQSRPSAVVFPGG +ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGMHLDMFQRLDV +GPASVSIVSYGSSRPRVLTVNTDAGDLSWLATKGPSGDAPVGGGAGTDPVADSANGRTPR +IDA +>PROKKA_01193 +MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTADRVAAVPVAAVVASPLERC +AQTARALLDRQSGAVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQTQPSAVVFPGG +ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV +GPASVSIVSYGPSRPRVWATNTDAGDLSWLSSLGPSDDAPVGGGAGTGPGAVDEQTPRIV +T +>PROKKA_01536 +MATVLLVRHGRTTANASGLLAGRTPGVSLDDHGREQAARTADRIATLPVAAVVASPLERC +AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATESLWATVQTQPSAVVFPGG +ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV +GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTGTGAVDEQTPRIV +T diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001306.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001306.fa new file mode 100644 index 0000000000000000000000000000000000000000..85f2e9c69e56ddcf65b58fac7361824ccd776da6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001306.fa @@ -0,0 +1,20 @@ +>PROKKA_01611 +MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI +LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLVDAHPLTD +DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPVCSDCGQPIDPDGHDCTFPDS +>PROKKA_01322 +MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI +LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGGIGLGWDPTTAQVLIDAHPLSD +DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPFCSDCGQPIDPDGHDCTLPDS +>PROKKA_01287 +MTESPAHVHEFDWPDRVVIGTIGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMLDEI +LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLSD +DDADPALEVDAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS +>PROKKA_01192 +MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI +LDDLMALDGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLTD +DDADPVLETDAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS +>PROKKA_01537 +MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI +LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLSD +DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001307.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001307.fa new file mode 100644 index 0000000000000000000000000000000000000000..1668a271c05ae01e3e9f39df7df646bae562d0ba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001307.fa @@ -0,0 +1,30 @@ +>PROKKA_01612 +MSAADVPAGELMSGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAATLAR +REVAASLVSEALGWDIVPRTWLRDGPFGKGMVQLWQEQDPEQDAVDLFPADEVPASGWLT +VLEGEDEGGNRLVLAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH +VQDKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGQGLAELLGAEEVEALAARCAQLL +DDGIFPAPSGLTPAVPWPLF +>PROKKA_01323 +MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR +REVAASLVSEALGWDIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPAGQVPASGWLT +ILEGEDADGNRLVLAHEDSAALRRMAVFDVIVNNADRKGAHILAMPGGHRHGVDHGLTFH +VADKLRTVLWGWLGEELSEEERDGVGRVLDGLDGELGRGLAELLSAEEVQALAERSAGLL +DDGRFPAPSGLTPAVPWPLF +>PROKKA_01286 +MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTSVVYKPVAGEAPLWDFPAGTLAR +REVAAYLVSEALGWDIVPRTWLREGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT +ILEGEDEGGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRYGVDHGLTFH +VADKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGRGLVQLLSAEEVEALAERCAQLL +DDGVFPAPSGLTPAVPWPLF +>PROKKA_01191 +MSAADVPAGELVDGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR +REVAAHLVSEALGWEIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPAAGWLT +ILEGEDEEGRRLALAHENSAALRRMAVFDVIVNNADRKGAHILAMPGGHRYGVDHGLTFH +VAGKLRTVLWGWLGEALSEEERDGVGRVLDGLDGELGRGLAELLSAEEVEALAERGARLL +DDGIFPAPSGRTPAVPWPLF +>PROKKA_01538 +MSAADVPAGELVSGELTLTGRITTASNATFLGAVGDTPVVYKPVAGEAPLWDFPAGTLAR +REVAAHLVSEALGWDVVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT +ILEGEDEDGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH +VEDKLRTVLWGWLGEALSDEERDGVARVLDGLDGELGRGLAELLSAVEIGALAERSAGLL +DDGTFPAPSGLTPAVPWPLF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001311.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001311.fa new file mode 100644 index 0000000000000000000000000000000000000000..c658403711fda1340f22d53359e6f13925a6cb95 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001311.fa @@ -0,0 +1,19 @@ +>PROKKA_01629 +MSTPTPTGPTPTPPGGELLPLISLAVEHVFNTLGRQPVFAPTILAVTADGQRGMWEHPDL +QPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV +AAAGIAARVDGDPQVVANGPNPLFG +>PROKKA_01334 +MSTPTPTGPTPTPPGGELLPLISLAVEHVFDTLGRQPVFAPTILAVAADGQRGMWEHPDL +EPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV +AAAGIAARVDGDPQVVANGPNPLFG +>PROKKA_01267 +MEHVFDTLGRRPVFHPTILAVTADGQRGMWEHPDLEPEQAAAEVAKISPRPARAVAVFEG +EAATEDGPRPAVAVEAFDAAALASVRLVFTYLPGVPGAGIAAQVDGDPQVVANGPNPLFG +>PROKKA_01175 +MTPPTHEILPLVSLAVDHVFDTLTRQAVFDPTILAVTADGARGMWTLPDLAPEQAAAEVG +RIQPLPQRAVAVFDGEVQTPQGPRPAVAVEAFDAGAVQSVRLVFEYVPGIPGTEITGRIE +GEPHIVANGHNPLFGQIS +>PROKKA_01558 +MSTPTPTGPTPTPPGGELLPLISLAVEHVFDTLGRQSVFAPTILAVTADGQRGMWEHPDL +EPEQAAATVAKISPRPTRAVAVFDGEIETADGPRPAVAVEAFDAAALASTRMVFPYLPGV +AAAGIAARVDGDPQVVANGPNPLFG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001314.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001314.fa new file mode 100644 index 0000000000000000000000000000000000000000..6a0dae6f3749275e18a7acae544140a8521c3f03 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001314.fa @@ -0,0 +1,40 @@ +>PROKKA_01632 +MEGMSAPSVSARPSAVGLGMPQVPRVRRSREEVEAAAPVSGEKRVLLAAPRGYCAGVDRA +VVAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVDELDEVPEGALTVFSAHGVSP +AVVEEAAQRNLRTIDATCPLVTKVHREAVRFAKQDKRILLIGHDGHEEVEGTFGEAPEHT +TVINDVAEARTVQVEDPDNLIWLSQTTLSVDETLEIVSVLRERFPNLQDPPSDDICYATS +NRQAAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFANQVDESWFEGVA +TVGLSSGASVPEVLVQEVLALLAEYGYGQVDEVVTAEEDIIFSLPKELRAEMKRVGDDGR +ALGGRRRAAEA +>PROKKA_01337 +MEGMSAPSVSARPSAVGLGMPQVPRVRRSREEVEAAAPVSGEKRVLLAAPRGYCAGVDRA +VVAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVDELDEVPEGALTVFSAHGVSP +AVVEEAAQRNLRTIDATCPLVTKVHREAVRFAKQDKQILLIGHEGHEEVEGTFGEAPEHT +TVINDVAEAQTIQVEDPDNLIWLSQTTLSVDETLEIVSVLRERFPNLQDPPSDDICYATS +NRQAAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFTNQVDESWFEGVA +TVGLSSGASVPEVLVQEVLALLAEYGYGQVDEVVTAEEDIIFSLPKELRAELKRVGDESR +SLGGRRRDAEA +>PROKKA_01263 +MGGMSAPSVSARPSAVGLGMPQVPRVRRTREDVEAAAPVSGDKRVLLAAPRGYCAGVDRA +VVAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVEELDEIPEGALTVFSAHGVSP +AVVQDAERRSLRTIDATCPLVTKVHREAVRFAKQDKQILLIGHEGHEEVEGTYGEAPEHT +TVINDVAEARAVQVADPDNLIWLSQTTLSVDETLEIVAVLRERFPNLQDPPSDDICYATS +NRQAAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFASQVDESWFEGVS +TVGLSSGASVPEVLIQDVLALLAEYGYGQVDEVVTAEEDIMFSLPKELRAELKRVGDDSR +GLGGRRQTEG +>PROKKA_01172 +MDGMSVPTASAPSTVGLGMPQVPRTRRSREEVEAAAPVAGDKRVLLAAPRGYCAGVDRAV +VAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGAVFVQELDEVPAGALTVFSAHGVSPA +VVAEAAERDLQTIDATCPLVTKVHREAVRFARQDKRILLIGHTGHEEVEGTYGEAPEHTT +VINDVEEARTVQVDDPDNLIWLSQTTLSVDETLEIVAVLRERFPNLQDPPSDDICYATSN +RQAAIKRISPQCDLVIIVGSANSSNSVRLKEVALEYGAARAERVDFASQVDESWFEGVAT +VGLSSGASVPEVLVQDVLALLADYGYGQVEEVVTAEEDIIFSLPKELRAQLKQAGDEERS +LGGRRRPAE +>PROKKA_01561 +MSAPSVSARPSAVGLGMPQVPRVRRSREEVEAAAPVSGEKRVLLAAPRGYCAGVDRAVVA +VEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVDELDEVPEGALTVFSAHGVSPAVV +EEAAQRNLRTIDATCPLVTKVHREAVRFAKQDKQILLIGHEGHEEVEGTFGEAPEHTTVI +NDVAEAQTIQVEDPDNLIWLSQTTLSVDETLEIVSVLRERFPNLQDPPSDDICYATSNRQ +AAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFANQVDESWFEGVATVG +LSSGASVPEVLVQEVLALLAEYGYGQVDEVVTAEEDIIFSLPKELRAEMKRVGDDGRALG +GRRRDAEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001315.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001315.fa new file mode 100644 index 0000000000000000000000000000000000000000..45bd5ddb8cd46e9afdd09a91e1415a72d49296ac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001315.fa @@ -0,0 +1,38 @@ +>PROKKA_01633 +MRTTLSLLVAALAGLLAVLATAGALVDEATHRPELLRGVTEQVAVDPEVRAAVPGVIDDV +VHDAVPEQVPDPLAQAAEDLLRPLAQRVADDPQVVQGWSDTADEARRAWLAQLEDPQGAD +EPGSGADVTIPFGPVAQSGITAALGDIERDLREDRFDLPGQALLETIAGADVGDWAADTL +LAPLYDRAADLRDSTALRMDARIDALAGTDRATVHRWVDASAHWRWAAAASVLALVGALL +LAPRGRRGLAVAVAGAVALAGGLIGGARLGPDAVHLTAPEGASPGVAAFVQQMEEAARPA +FAAAVAPYPQTLTTLGWIVLAAGLLLALAELWVARRGRVRAARADGPPAVGRSHTAADVT +SR +>PROKKA_01338 +MRTTLSFLVAALAGLLAVLATAGALVDEATHRPELLRGVTEQVAVDPEVRAAVPGVIDDV +VHDAVPEQVPGPLAQVAEDLLRPLAQRVADDPQVVQGWSDTADEARRAWLAQLEDPQGAD +EPGSGADVTIPFGPVAQSGITAALGDIERDLREDRFDLPGQALLETIAGADVGDWAADTL +LAPLYDRAAELRDSTALRMDARIDALAGTDRATVHRWVDASAHWRWAAAASVLALVGALL +LAPRGRRGLAVAVAGAVALAGGLIGGARLGPDAVHLTAPEGASPGVAAFVQQMEEAARPA +FAAAVAPYPQTLTTLGWIVLAAGLLLALAELWVARRGRVRAARADGPPAVGRSHTAADVT +SR +>PROKKA_01262 +MRQLTAVLLALVAGVLAVLATAGALVDEAAHRPALVRQAAEQVASDDDVRAAIPGAVADA +VGDAVPEGVPGPLRGLAQDLVRPMAESAAQDEGVVRGWSDTADEARRAWLHDLREASDAT +GPVPGGDFTIPFGPVAQSGVAAALGDLETDLREDRLNLPGQQLVERLLGVDFGDWAVDTL +VGPLHERAAELRDRTDLTMTVTVDALRDVDRSEVARWVSASVHWRWAAGGAVVLLAAAVL +IAPLRWRGVAVLLSAATALVGGYLLANATRAEAFAVAAPEGAPAGIARLVERVEQALRPA +VDAALAPYADGLTTAGWIALAVGAALLVAELVLSAARAGRTTPPRARGGSRAAADPASR +>PROKKA_01171 +MRSLLSLLSAVLAALLAVLATAGALVDRTAHQPDTVRQVAERIAADDAVRAAVPRAVTDS +IEGAVPESVPAPLTQLAQDIVRPIAEDVAKDPDVATGFADTADEARRAWLMDLERARDGG +EHAPGGEFRIPFGPVAQSGVASAVGDLETRLRSDQLNLPGQSIVEAIVGVDVGTWAADTL +VKPLYDRAAELRDSTDLTMTVRVDALAGTDRATVARWVDASAHWRWAAGGSVLALVASLL +LARRGRRGLALAVAGVTVLLAVLLASSAVDSSRWSLAAPDGATGGVAALARAAEAAFRPA +VADVLAPWLGGLTTWGTVALLAGLVLMAIEVLAGPVRRRLARTRPSGTGSHTGR +>PROKKA_01562 +MRTTLSFLVAALAGLLAVLATAGALVDEATHRPELLRGVTEQVAVDPEVRAAVPGVIDDV +VHDAIPEQVPGPLAQTAEDLLRPLAQRVADDPQVVQGWSDTADEARRAWLAQLEDPQGAD +EPGSGADVTIPFGPVAQSGITAALGDIERDLREDRFDLPGQALLETIVGADVGDWAADTL +LAPLYDRAAELRDSTALRMDARIDALDGTDRATVHRWVDASAHWRWAAAASVLALVGALL +LAPRRRRGPAVAVAGAVALVGGLIGGARLGPDAVHLTAPEGASPGVAAFVQQMEEAAGPA +FAAAVAPYPQTLTTLGWIVLAAGLLLALAELWVARRGRVRAARVDGPPAVGRSHTAADVT +SR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001317.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001317.fa new file mode 100644 index 0000000000000000000000000000000000000000..dd2f97399d1f68dbbc4db004066e41d077ad1505 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001317.fa @@ -0,0 +1,15 @@ +>PROKKA_01635 +MSEQGMEQTQDAGRPSGVEGFTSADVSDVARMSYEQARAELVETVGRLEAGGAGLEESLA +LWERGEALADRCQAWLDGARARLDQVRGEAAPDAD +>PROKKA_01340 +MSEQGMEQTQDPGRPSGVEGFTSADVSDVARMSYEQARAELMETVGRLEAGGAGLEESLA +LWERGEALADRCQAWLDGARARLDQVRGEAAPDVD +>PROKKA_01260 +MSEQQQEQTGAPVEGFTSADTSDVAGMSYEQARAELVETVTRLEAGGGRLEESLALWERG +EALAARCQAWLDGARARLDEVRGAADSPTA +>PROKKA_01169 +MSEQEQQGTAVGGFTSADTSDVARMSYEQARAELVEVVGQLEAGGAGLEESLALWERGEA +LADRCQAWLDGARARLDQVRGEAAPDAD +>PROKKA_01564 +MSEQGMEQTQDAGRPSGVEGFTSADVSDVARMSYEQARAELVETVGRLEAGGAGLEESLA +LWERGEALADRCQAWLDGARARLDQVRGEAAPDAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001318.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001318.fa new file mode 100644 index 0000000000000000000000000000000000000000..8f7e2666e477f03b69fcb3ed4c39af0a17e3c704 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001318.fa @@ -0,0 +1,34 @@ +>PROKKA_01637 +MADTPATEAGRPARATDDGVFGAPARELFAARRGDEVRGPADVDAAATPGYGGDKAKGKK +DLAARGAVLADLQELLFAQSVRDAPVGEVPSLLVVLQGMDTAGKGGIMRHVIGAMDPLGV +HVHAFKAPTPEERAHDFLWRIRPHLPRPGLVSVFDRSHYEDVLVHRVRGLSPLAEVEERY +GAIREFEAAVRAAGTRIVKVMLRISPEEQAKRLLARLDDPTKHWKFSESDLDDRAYWDQY +MDAYRIAIERTDTEDAPWFIVPADRKWFARLAVQQLIIETLQGMGLDWPKADFDVAAARR +RLLAG +>PROKKA_01342 +MADTPATEAGRPARATDDGVFGAPARELFAARRGDEVRGPADVDAAATPGYGGDKAKGKK +DLAARGAVLADLQELLFAQSVRDAPVGEVPSLLVVLQGMDTAGKGGIIRHVIGAMDPLGV +HVHAFKAPTAEERAHDFLWRIRPHLPRPGLVSAFDRSHYEDVLVHRVRGLSPLAEVEERY +GAIREFEAAVRAAGTRIVKVMLRISPEEQAKRLLARLDDPTKHWKFSESDLDDRAYWDQY +MDAYRIAIERTDTEDAPWFIVPADRKWFARLAVQQLIIETLQGMGLDWPKADFDVAAARR +RLLAG +>PROKKA_01258 +MAENGTAETVRPDDAEGAETGVFSAPARELFAARRGDAVADPADVDASATPGYTGGKAQG +KQDLADRADVLADLQELLFAQSTREAPSGEVPSLLLVIQGMDTAGKGGIMRHVIGAMDPQ +GVHLHAFKAPTAEERAHDFLWRIRPHLPRPGRVSVFDRSHYEDVLVHRVRELSPLAEVEE +RYGAIREFESRVRAAGTRIVKVMLRISAEEQAERLLARLDDPTKHWKFNEGDLDDRAYWD +DYMDAYRIAIERTDTEDAPWFVVPADRKWFARLAVQQLLIETLQGLDLDWPEADFDVEAA +RRRLLAG +>PROKKA_01167 +MADTPENRFTEPVRTLLRARRADGAPVGPADVDPHGKPGFDGGKSEGRAVLAARSERLGQ +LQELLYAQSTREADGGLPAPSVLLVVQGMDTAGKGGIMRHVVGQMDPQGVDVHAFKRPTP +EEARHDFLWRVRPHLPMPGTLSVFDRSHYEDVLIQRVRSLAPAEEIERRYTAIREFEAEA +VAAGIRVVKVMLHISPEEQKARLSERLERADKHWKFNPGDLDERELWDEYQEAYRVALHR +TDATDAPWFIVPADRKWYARVAVQELMIETLEAMGLTWPEADFDVAAARRRLLAG +>PROKKA_01566 +MADTPATAAGRPARATDAHGVFDAPARELFAARRGDEVRGPADVDAAATPGYGGDKAKGK +KDLAARGRELADLQELLFAQSVRDAPVGEVPSLLVILQGMDTAGKGGIMRHVIGAMDPQG +VHLHAFKVPTPEERAHDFLWRIRPHLPRPGLVSVFDRSHYEDVLVHRVRGLSPLAEVEER +YGAIREFEAAVRAAGTRIVKVMLRISPEEQAERLLARLDDPTKHWKFSEGDLDDRAYWDQ +YTDAYRIAIERTDTEDAPWFIVPADRKWFARLAVQQLIIETLQGMGLDWPEADFDVAAAR +RRLLAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001319.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001319.fa new file mode 100644 index 0000000000000000000000000000000000000000..79096f0d99213361523bbbd3881722c055ddcc71 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001319.fa @@ -0,0 +1,40 @@ +>PROKKA_01638 +MPTPHPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAVL +AAMHQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDIGVDDVFIGNGVSEMITMVLQAL +VDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWEPDLEHIESLVTERTKGIVLI +NPNNPTGAVYSRAVLQGIVDVARRHNLVLMADEIYEKITYDGARHINAAGLSDDVLTLTF +SGLSKAYRVAGYRSGWVAVSGPKHRAADFLEGLTLLANMRMCANVPAQHAIQVALGGYQS +INDLVLPGGRLLEQRNLAQDRLNAIPGVSVQPAHGALYLFPRLDPEVYAIDDDEAFVIEL +LRAKKILVSHGGAFNYPHSDHFRLVTLPSVKDLDVALDRLEDFLEDWRERHG +>PROKKA_01343 +MPTPHPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAVL +AAMHQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDIGVDDVFIGNGVSEMITMVLQAL +VDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWEPDLEHIESLVTERTKGIVLI +NPNNPTGAVYSRAVLQGIVDVARRHNLVLMADEIYEKITYDGARHINAAGLSDDVLTLTF +SGLSKAYRVAGYRSGWVAVSGPKHRAADFLEGLTLLANMRMCANVPAQHAIQVALGGYQS +INDLVLPGGRLLEQRNLAQDRLNAIPGVSVQPAHGALYLFPRLDPEVYAIDDDEAFVIEL +LRAKKILVSHGGAFNYPHSDHFRLVTLPSVKDLDVALDRLEDFLEDWRERHG +>PROKKA_01257 +MPTPRPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAIL +QAMYRHLPHAQGYSDSQGIYSARTAVSQYYESRGIRDIGVEDVFIGNGVSEMISMVLQAL +VDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWAPDLEHIESLVTERTKGIVLI +NPNNPTGAVYSRQILQGIIDVARRHGLVLMADEIYEKITYDGARHINAAGLSDDVLTLTF +SGLSKAYRVAGFRSGWVAVSGPKHRARDFLEGLTLLANMRMCANVPAQHAIQVALGGYQS +IDDLVLPGGRLLEQRNLAQKRLNDIPGVSVQPAQGALYLFPRLDPEVYAIEDDQEFVIDL +LRAKKILVSHGGAFNYPHTDHFRLVTLPSVEDLDVALDRLEDFLEDWRERRG +>PROKKA_01166 +MAPSTPREFRQSSKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAIL +QAMYQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDISVDDVFIGNGVSEMITMVLQAL +VDDGDEILVPSPDYPLWTGATTLSGGRAVHYRCVEEEGWAPDLEHLESLITERTKGLVII +NPNNPTGAVYSREVLNGVVDIARRHNLVLLADEIYEKITYDGARHINAAGLSDDVLTLTF +SGLSKAYRVAGYRSGWVAVSGPKHRAKDFLEGLTLLSNMRMCANVPAQHAIQVALGGYQS +IEDLILPGGRLLEQRNLAQKRLNDIPGVSVQPAHGALYLFPRLDPEVYAIDDDEKFVIEL +LQAKKILVSHGGAFNYPQPDHFRLVTLPSVKDLDIALDRLEDFLEDWRERRG +>PROKKA_01567 +MGGMPTPHPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPD +AVLAAMHQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDIGVDDVFIGNGVSEMITMVL +QALVDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWEPDLEHIESLVTERTKGI +VLINPNNPTGAVYSRAVLQGIVDVARRHNLVLMADEIYEKITYDGARHINAAGLSDDVLT +LTFSGLSKAYRVAGYRSGWVAVSGPKHRAADFLEGLTLLANMRMCANVPAQHAIQVALGG +YQSINDLVLPGGRLLEQRNLAQDRLNAIPGVSVQPAHGALYLFPRLDPEVYAIDDDEAFV +IELLRAKKILVSHGGAFNYPHSDHFRLVTLPSVKDLDVALDRLEDFLEDWRERHG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001322.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001322.fa new file mode 100644 index 0000000000000000000000000000000000000000..e9f5da08412f9a639ea5b2369ca7ede6bee4e661 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001322.fa @@ -0,0 +1,60 @@ +>PROKKA_01641 +MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA +ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR +HLGRPRQAELESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH +RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA +AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA +GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL +VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA +GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL +LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA +ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE +LDALREGLGAD +>PROKKA_01346 +MDTPQDPPRRDDPSGGPVEPAVDAALDRVHALLRQARVIAAPDAPTALDARGWWELSLEA +ALRDEPRESARLADSGLAALVPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR +HLGRPRQAGLESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH +RVHTGDLDTALELTRRVIAVLGGLRAAGALLPIGSWSSAHLLLARLHLWRGEHAEADAAA +AVVTVLPAARAVLASATTVRAIAAHELDRPTAALDLAFEAAERMASVGLRRGAASAAALA +GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL +VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA +GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL +LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA +ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE +LDALREGLGAD +>PROKKA_01254 +MDAPQQTPAPADVGPTAVLARVRTLLAEARTSGAPEDAVDAAPVDHDARQWWELSLEAAL +RDEPRESARCAESGLAALGPGEDGVRLSLLRALAVAADRLGDETGLTRWVEARAALLRTL +GRPRQAALETQLGASLVREPDGFEAAVLAGVVEEEPGVPGEDPGDTVLPEAALALAVHRV +HASDLDGALAAARRAVESLRGLRAAGAVLPVGSWSSAHLLLSRLHLWRGEHAEADEAAAV +VTSLPAARAVLASATTVRAIAAHEQDRPTAALALALDAADRMARVGLRRGAASAAALAGR +VAGDLEGHEEAAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRPDEAEPLLARLVR +REAAQGHDVEQARALVDLGHAHHDQDRSENALPLWREAAGLFEAHGRWEDAARTLLAAGA +LVNRERDELTRPSALDLFERAVAAARRAVDEDPAVLPAALHAHGYLLCESGRPEGLELLD +EAVALVREAEAPWQVADYTDTRARALWSLEQGAEAVSTALHAADLFTAAQDPEGAAQAEL +FAASVVAEDGSPEQAATLFRLVSESTQSTLVRLGALTGLHQCLSAVGDHDGAARVRDDLD +AVREQLGAD +>PROKKA_01163 +MAEDAPALLAGRDPLAAVEALLAAARDDAALPLPAGSDAPSLRERALEALLREDPASAAR +AAEDGLDAPGGQDPALRLALLRLRATAAAHAGDEPALEEWTARRADLLRRLGRPRQADLE +VQLGASLLREPDAFEATVLAGVAEDERGRITADPAALEDTVLPDALLALCAQRVQAHDLD +AALEAAEEALAVIRAQETAGVVLGEAAEPHALLMLARLHLWREEHRASDDAARAVLARPC +AAVVRASATLVRALAAHGQDRPEAALDFALRAAEAMSRAGLRRGAASAAALVGRVAGARA +DRQDLAVAAWELSCVHAEKAEAPEAPSLAYWWAHQLLIAGRAEEAEPVLTALVRREAAAG +DEAAQARALVDLGHACHELDRPSEALPLWREAAELFTRRGHHADAAHTLLAAGALCHRDP +HDAAHAGALDLFEQAVDAARRSEGDSAVLASALHALGYLRCETGRGDGLELIDEAIALAE +GSGAAWQKADYLDTRARSLWALHRGDDAVSAALTSADLFTDAGDPSGAAQAELFAAHVVA +EDGRPEQAATLFRLVSESTHSDLVRLGALTGLQQCLAALGEHAEADRVRADADAVRRALG +GRD +>PROKKA_01571 +MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA +ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR +HLGRPRQAGLESQLGGALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH +RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA +AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA +GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL +VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA +GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL +LEEALALVRYAGADWQVANYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA +ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE +LDALREGLGAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001323.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001323.fa new file mode 100644 index 0000000000000000000000000000000000000000..d2f4f3d3d0e973677e9433b3335fd4b66cf9ccff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001323.fa @@ -0,0 +1,40 @@ +>PROKKA_01642 +MSIDRAAARQAVRASGERWLRTRADALHLQRGRRLARVLDLDVMTGRAGDARVRSRTLVL +ARDPRHPDVPAAACPPVPGERGILEDGTLWWWAPADPVLPGLTLTADPDALAALLGTAPG +RARLTWRGYRPRDRAVLAVEATGDDGVAARTFLKVLPPARAARVARRQAAAGAAGVPVPA +VLATPEHGVLPLASVPGLPWRALLAGPEAAGLDPARVAALLDRLPPVPEEPPGPAGPTAG +AAGCADTDDGGPAILLEHATWAAVVLDPEAQDEVAARADRLRAALAAGDPGPRVPVHGDL +HPGNLHVDAAGERITGVLDADDLGMGHRVDDWAVLIAHLEAGAVDLGAGGAALRAVAARF +RRHARSEVDEVALAARVATVLAALAAQPTAPRAVRSARRAAADAALARVGL +>PROKKA_01347 +MSIDRAAARQAVRASGERWLRTRADALHLQRGRRLARVLDLDVMTGRAGDARVRSRTLVL +ARDPRHPDVPAAACPPVPGERGFLEDGTLWWWAPADPVLPGLTLTADPDALAALLGTAPG +RARLTWRGYRPRDRAVLAVEATGDDGVVGRTFLKVLPPARAARVARRMAAAGAAGVPVPA +VRAAPEHGVLPLASVPGLPWRALLAGPEAAALDPARVAALLDRLPPVPEEPPGPAGPPAV +AAGGADADDGGPAVLLEHATWAAVVLDPEAQDEAAARADRIRAALAAGDPGPRVPVHGDL +HPGNLHVDAAGERITGVLDADDLGMGHRVDDWAVLIAHLEAGAVDLGAGGAALRAVAARF +RRHARSEVDEVALAARVATVLAALAAQPTAPRAVRAARRAAADAALARVGL +>PROKKA_01251 +MSIGRASAPLAVRASGLRWLRTRADALHLQRGRRLARVLDVDVMEGRAGDARVRTRTLVL +ARDPRTGPDAAPPGSARTSERGVLEDGTLWWWAAADPALPGLALTENDAGLAALLGTAPG +RVRLTWRGYRPRERAVIALDAADAGLAGSRAYLKVLAPAAAEAVAARLSAARAAGVPVPD +LLAAPERGTLLLGNVPGLPWGALLGDARADALDPARVAEVLDRMPAPPGEAGPAPDAAAA +LLEHAAWAAVVLDPERQAESAARADRLRAALAAGDPGPPVPVHGDLHPGNLHVDASGGRV +TGLVDCDGLGLGHRVDDWATLLAHLEAAAADLGPGGGAVRAVAERVRAHARTETDEVALA +ARAAVVLAALGADPSVPRAARTARRAAADAALARVSR +>PROKKA_01162 +MVLLEGPPGAGVARERVLVLRGPVEPAVAVPGPPGPPVPASGPAPRRRGRGRLPDGTRWW +LLPHDPALPGLDLALDHERLDAWLPGLGRAGEPAWVAYRPGERAVLRVPLDAVPARPDEP +GSSLHLKVLPPARLHGMHGRLLAARAAGLPVPPPLAPPDLGVLALGTLPGEPWRARLGAD +APQPAPAAVAALLDALPDALAAHDDGPSRTPAWSALLAHAVRAGTLLDPGAAEELRERAR +RLEESLAAADPGPRVPVHGDLHPDNLLLAPGTDRIVGVLDPDSLGPGHRVDDWAVLVGHL +AVAAADAAVPGPSHDPERARRTAALAAEFTGHACGVVDEEALRARADVTALALAAAPDLP +AAVRAARRSAR +>PROKKA_01572 +MSIDRAAARQAVRASGERWLRTRADALHLQRGRWLARVLDLDVMTGRAGDARVRSRTLVL +ARDPRHPAAPGAACPPVPGERGILEDGTLWWWAPADPVLPGLTLTADPDALVALLGTAPG +RARLTWRGYRPRDRAVLAVEATGDDGVVARTFLKVLPPSRAARVARRMAAAGAAGVPVPA +VRAAPEHGVLPLASVPGLPWRALLAGSEAAALDPARVAALLDRLPPVPEEPPGPAGPTAG +VAADADADDGGPAVLLEHATWAAVVLDPEAQDEAAARADRLRAALAAGDPGPRVPVHGDL +HPGNLHVDAAGERITGVLDADDLGTGHRVDDWAVLIAHLEAGAADLGAGGAALRAVAARF +RRHARSEVDEVALAARVATVLAALAAQPTAPRAVRSARRAAADAALARVGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001326.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001326.fa new file mode 100644 index 0000000000000000000000000000000000000000..2a736508fd18efb0ba131d2cd01cfcfac0ae4a18 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001326.fa @@ -0,0 +1,25 @@ +>PROKKA_01645 +MRTPPPVPEPAATGPVAGVDDVVDAKAALRARLRTARRDRSPARRAAESAAAVEHLWAWL +GPRVAAATADGTAPVVATVLPMATEPDTGGLRTRLLAAGARVLVPVIEPERRLSWASWHP +GVATARAANAPVDEPVGERLGTDALAAATAVVMPALAVAEDGMRLGQGGGYYDRFLAELP +RSVPTVALVFEDELLPAGAIPAEPTDRPVDGVVTAAGLRWV +>PROKKA_01350 +MRTPPPVPEPASTGPVAGVDDVVDAKAALRARLRTARRDRSPARRAAESAAAVEHLWAWL +GPRVAAATADGTAPVVATVLPMATEPDTGVLRTRLLAAGARVLVPVIEPERRLSWAPWHP +DVATARAANAPVDEPVGERLGTDALAAATAVVMPALAVAEDGMRLGQGGGYYDRFLAELP +RSVPTVALVFEDELLPAGAIPAEPTDRPVDGVVTAAGLRWV +>PROKKA_01248 +MRTPPPAPEPASTGPVAGVDDVVAAKAALRARLRAARRERSPERRAAESAAAVEHLWAWL +GPRVAQAARDGEAVVATVLPMPTEPDTGPLRERLVAAGARVLVPVIEPQRRLNWTAWHPG +VATARAAAAPVDEPVGERHGVEALAEAVAVVMPALAVAEDGMRLGQGGGYYDRFLARLPR +SVPTVALVFEDELLPAGSVPAEPTDRPVDALVTAAGLRHV +>PROKKA_01159 +MPAAAPAPHPDDAAAALASTEAKAALRTRLRAARRGLDPAVRARQAEAAAEHLWTWLGPH +LEERTADGPPVVATVLPMPTEPDTGPVRERALAAGARVLVPVIEPGRHLSWTAWRPGVAV +ARAANAPLDEPVGPREPGSVLDGAALVLMPGLAVDLTGARLGQGGGYYDRFLATLPSSVT +TVAFVHPSEVLEPGVIPLEPTDRPVDGVLTADGLLWCEPASAGPQ +>PROKKA_01575 +MRTPPPVPEPAATGPVAGVDDVVDAKAALRARLRTARRDRSPARRAAESAAAVEHLWAWL +GPRVAAATADGTAPVVATVLPMATEPDTGGLRTRLLAAGARVLVPVIEPERRLSWAPWHP +DVATARAANAPVDEPVGERLGTDALAAATAVVMPALAVAEDGMRLGQGGGYYDRFLAELP +RSVPTVALVFEDELLPAGAIPAEPTDRPVDGVVTAAGLRWV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001327.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001327.fa new file mode 100644 index 0000000000000000000000000000000000000000..e9dd3c93948c170e91eafab6eccabf87932c183d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001327.fa @@ -0,0 +1,15 @@ +>PROKKA_01646 +MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRKQYGSVGVSFKGSGFYRTDSRSG +TGGTGSAGGSTSDSAAGSSTSSTSSSSSPAAD +>PROKKA_01351 +MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRNQYGSVGVSFKGSGFYRTDSRSG +TGGTGSAGGSTSDSAAGSSTSSTSSSSSAAAD +>PROKKA_01247 +MPTYAYRCRDCGHAFDAVQSFTDDALTQCPECGGVLRKQYGSVGVSFKGSGFYRTDSRSA +GSASSGSASSAGSASSSTSAGGSGTSSTSSGGSGSSGSSSSSSGSKD +>PROKKA_01158 +MPTYAYRCKDCGHAFDAVQSFSDDALTECPVCGGVLRKQYGSVGVSFKGSGFYRTDSRGG +APSSTPAAPSSGAASSTGTSSGSSD +>PROKKA_01576 +MPTYAYRCKDCGHAFDVVQAFTDDALTECPACGGVLRKQYGSVGVSFKGSGFYRTDSRSG +TGSAGGSTSDSAAGSSTSSTSSSSSAAAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001329.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001329.fa new file mode 100644 index 0000000000000000000000000000000000000000..d2bdfd7dd7613d36215a0f44ce159e0a69173a7a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001329.fa @@ -0,0 +1,110 @@ +>PROKKA_01648 +MTEQEFPRLARARAAARPDEGQTRPDPAAWVSSLGSGAENDTMLRFAPSAANSIDLTEAN +SSGVSQLLLGRRTRLSTLLPAGPELDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW +TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL +DPEAYQQAAYATARLEPAPAFARLREETAAIADLHIQDCLLVSTFADLGETASLPASLED +LPVVQALYDAGTGMVPRPAALQPTGAPAEDDVAPADERLVVDVDAAQARVLEHAAAGESL +VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN +ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA +MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR +VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL +TEFTPEVFSLDVPQLVAATATSSWRRLHLVEMSSVTRSRLRRAAKDAVRPGVQPTDLHGA +LVDAAAVLEDWNRHAAEPGTPPQVPDQGEHVMGQVGQVRERLRRLEGVLAPEAVAEAPLE +ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRDHGLAELLEDLRDREVPTEALTAEL +ELAWWQSALEAMISGDDFLAMMSGTDLAEVERGFRDLDRAHLERGGARLSAALAARWREA +LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV +LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALD +EVLPTLPLRTVHRPLERRLVRLLSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP +MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA +HEFLARGRGEDAADAEPFVIVPVVRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPDG +ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGDDAADPVGMVGDP +LLADLRDRLEEHGARVLPRYAGVMDLAVLDPRADQDEAPRPLALAGDGGEVYRALTVRQR +SRTLPEGLEARGWEPRTLWSIDVFADPESVARELADRLGVEPADETDETDDDAR +>PROKKA_01353 +MTEQEFPRLARARAAARPDEGQTRPDPAAWVASLGSGAENDTMLRFAPSAANSIDLTEAN +SSGVSQLLLGRRTRLSTLLPAGPELDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW +TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL +DPEAYQQAAYATARLEPAPAFARLREETAAIADLHVEDCLLVSTFADLGETASLPASLED +LPVVQALYDAGTGMVPRPAALQPTGAPAEDDVAPADERLVVDVDAAQARVLEHAAAGESL +VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN +ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA +MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR +VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL +TEFTPEVFSLDVPQLVAATATSSWRRLHLVEMSSVARSRLRRAAKDAVRPGVQPTDLHGA +LVDAAAVLKDWNRHAAEPGTPPQVPDQGEHVMGHVGQVREHLRRLEGVLAPEAVAEGPLD +ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRDHGLAELLEDLRDREVPTEALTAEL +ELAWWQSALEAMISGDDFLAMMSGTDLTEVERGFRDLDRAHLERGGARLSAALAARWREA +LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV +LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALD +EVLPTLPLRTVHRPLERRLVRLLSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP +MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA +HEFLARGRGEDAADAEPFVIVPVVRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPDG +ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGEDAADPVGMVGDP +LLADLRDRLEEHGARVLPRYGGVMDLAVLDPRAEQDEAPRPLALAGDGGEVYRALTVRQR +SRTLPEGLEARGWEPRTLWAIDVFADPESVARELADRLGVEPADETDETDDDVR +>PROKKA_01245 +MREQEFPRLARARAAARPEEGQTRPDPAAWVASLGSGAENDTMLRFAPSAANSIDVTAAN +SSGVSQLLLGRRTRLSTLLPAGPALQAAEEVAAGLRAKVRELSEERGIDVGALAVGVATW +TAEEDGRRERRSAPVLLARVALTVRRGARGRGELEVQITEPARLNPALVRNLRRHHGIAL +DPEAYRQAAYATARLEQRPALARLREEAAALTGLQVEDRMLVSTFADLGETATLPASLEH +LPVVEALYDAGTGMVPRPPALQPTEAPGEDDVAPADERLVLDLDAAQRRVVEHSAAGESL +VVAAAPGTGQTQTAVAVAARLAWEGRRVLVVAERSAALADVHARLDEIGLRAAALDVPAH +ADPEQLRRQLVQAVLRAERAEAPDAARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA +MQALAALTGLPTPPATTVRLKRSVLDSTVNRQAVAEQLVRAGELGAFSAAATESRWFGAR +VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL +TEFTPEVFALDVPQLVAATATSTWRRTHLVEMSSVARSRLRRAAKDAVRPGVQPTDLHGA +LVDAAAVLEDWNRHAAEPGTPPQVPDQGERVMGVVGDVRERLRRLERILAPEAVAEQPLA +ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLKDHGLTELLTDLRDREVPTEALAAEL +ELAWWQSALEAMISGDDFLAMMSGADLAEVERGFRELDRAHLERGADRLSAALGARWKEA +LRTFRADAAVLRGLLKQGRPTVEALTTLAPEVLQPLVPVVTTSPMALSEFPSDWGADVVV +LLEADATALATAVGALTRAPQVVAFGDPVIGRPQSFQVSVDPTATAGPLRPLRSAHDALA +EVLPTVALRTVHRPLERRLVRMLSALAYEGALEALPTAGEATGRDRTVTAEYLQEGTGIP +MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEPHARRVAAAVQATAARASWA +LDFLSRGRGEDAEGAEPFVIVPVTRAASVVRDAVILTPGYGRTPHGRVVHHFGAFSDPGG +ERMVAVALTRARQRLHLVSALRAADLDEDRLDGGAQWFLRLLEAYLGDGAPDPVGRVSDP +LLADLRERLEERGARVLPRHGGVMDLAVVDPHPEDEDEDGDAPRPLALAGDGGDVYRALT +VRERTRTLPERLEARGWDPRTLWAIEVFADPESVAQELADRLGVRPADESERDADDDGR +>PROKKA_01156 +MTEQEFPRLARARAAVRPAEQDQERPDPAAWVASLGSGAESDTMLRFAPSAANSIDLTGA +GTSGLSQLLLGRRTRLSTLLPAGPELDAAQEVAAALRAKVRELGEERGIDVGALALGVAT +WSAVEDGRRERRTAPVLLARLAFSVRSGARGRDEVELQIVEHAHLNPALVRNLRRHHGLR +LDPEAYQHAAYATSRLEPGPALALLREEAAGVEGLEVQETLLVSTFADLGDTATLPESLE +HLPVVQALYDVGTGMVPRPAELRPTGRPDEDELPPADERLVLDADPSQLRALDHAAAGES +LVVRTAPGTGQTQTAVNLAARLAWEGRRVLVVAERSSALADVHARLAQAGLRDAALDVPA +HADPEDLRRQLVAAVLRAERASAPDRAAADAELEELRRRLREHVDSLHHVRPRWGCSPFQ +AMQALASLTALDTPPATTVRLKRSVLDSTVDRHAVAGRLTRAGELGAFDRDATASRWFGA +RVRNVQETEAAGELVEHLAGTLYTTRRAVEAAADQAGLRRPRTVDGWAEQSDLFARVERA +LTAMDPSVFSLDVPQLVTATASSQWRRSNAVEMSSVQRSRLRRAAKDAVKPGVQVPDLHQ +ELMEVEGILEDWRRWTAIPGSTPMVPDMADHARPAVRDVLDALDRLSQVLAPEATAGTPL +AEQDVDDLMAAVDGLVADRPTLATLPERTLVLDELREHGLNELLEDLHAREVPVAALPAE +LELAWWQSALEAMISGDDFLAMMSGADLTAVEQGFRAADRTLLDSGGARLAASLGAAWKA +ALGTYRADAAVLRSLLKQGRPSVESLATITPGLLQALVPIVTTSPMALTEFPPDWDADVV +ILLEADATALATVAGALTRAPQVVAFGDPAIGRPQSFQVSVDPTATAGPLRPLRSALSAL +AEVLPVLDLRHVHRPLPRSLVRLVSHVAYEGAVDALPTAAEFTGRGRTLTAEYVAEGVGI +PMTGGDVVESTDAEVARTVERVFEHIRDRPEESLAVVTVSEQHARRVAGAVQATAARAPW +AADFLARGRTDGDEREPFVIVPVLRASTVTRDAVILTPGYGRTPHGRVVHHFGALSDPDG +ERMLTVALTRARARMHVVTALRAADLDADRLDGGALAFRRMLEVALDDAEAAPAGRLSDP +LLLDLRDRLAAEDALVAAHYGGAMDLAAADAAGERGRVRPLALVSDGGDAYREQSVRERS +RRLPERLEARGWDTDTLWAIDVFADPESVAARLVGRLGLPLEEVDEDGEDDADGES +>PROKKA_01578 +MTEQEFPRLARARAAARPDEGQTRPDPAAWVSSLGSGAENDTMLRFAPSAANSIDLTEAN +SSGVSQLLLGRRTRLSTLLPAGPVLDAAHEVSLGLRAKVRELAEERGIDVGALAVGVATW +TAEEDGRRERRSAPVLLARVALTVRRGARGRDELEVQITEPARLNPALVRNLRRHHGIAL +DPEAYQQAAYATARLEPAPAFARLREETAAIADLHIQDCLLVSTFADLGETASLPASLED +LPVVQALYDAGTGMVPRPAALQPTGAATEDDVAPAEERLVLDVDAAQARVLEHAAAGESL +VVAAAPGTGQTQTAAALAARLAWEGRRVLVVAERSAALADVLDRLEEADLRSIALDVPAN +ADPELLRRQLVQAVLRSERAVDPDTARDEAALTERRRRLQEHVGSLHHVRPRWGCSPFQA +MQALAALTGLETPPATTVRLKRSVLDSTVNRQAVGEQLVRAGELGAFSAAATESRWFGAR +VRNVQETEAASELADELAAALHTTRRAVDTAAAQAGLRPERTVAGWAEQADLYRRVARTL +TEFTPEVFSLDVPQLVAATATSAWRRLHLVEMSSVTRSRLRRAAKDAVRPGVQPTDLHGA +LVDAAAVLEDWNRHAAEPGTPPQVPDQGEHVMGQVGQVRERLRRLEGVLAPEAVAEGPLD +ERDVDDLVAAVDGLVADRDTLATLPERTLVLDSLRGHGLAELLEDLRDREVPTEALTAEL +ELAWWQSALEAMISGDDFLAMMSGTDLAEVERGFRDLDRAHLERGGARLSAALAARWREA +LRTYRADAAVLRTLLKQGSPTVESLATITPELLQPLVPVVTTSPMALSEFPPEWRADVVV +LLEADATALATAMGALTRAPQVVALGDPVIGRPQSFQVSVDPTATAGPLRPLRSAYDTLD +EVLPTLPLRTVHRPLERRLVRLVSALAYDGALDALPTAGEATGRDRAVTAEYLPEGTGIP +MTGGDVVESTNAEVARTVERVFEHIRDRPEQSLAVVTVSEQHARRVAAAVQATAAQAPWA +HEFLARGRGEDAAEAEPFVIVPVVRAASVTRDAVILTPGYGRTPHGRVVHHFGAFSDPDG +ERMVTVALTRARRRLHLVSALRAADLDEDRLDGGALWFLRLLEAYLGDDAADPVGMVGDP +LLADLRDRLEEHGARVLPRYAGVMDLAVLDPRAEQDEAPRPLALAGDGGEVYRALTVRQR +SRTLPEGLEARGWEPRTLWSIDVFADPESVARELADRLGVEPADETDETDDDVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001331.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001331.fa new file mode 100644 index 0000000000000000000000000000000000000000..ef19303b41cde5aac7dfc3408188b3702cb4b90f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001331.fa @@ -0,0 +1,24 @@ +>PROKKA_01650 +MSTQHPGPEPVDPASLPDPEDITEADLPEPPPRPGREQRRFAGTQQQIRSATRLYVVCAW +ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG +WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFVVEKRMTRVVRDELHRFPDAAR +RY +>PROKKA_01355 +MSTQHPGPQPVDPASLPDPEDITEADLPEPPPRPGREQRRFSGTQQQIRSATRLYVVCAW +ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG +WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFMVEKRMTRVVRDELHRFPDAAR +RY +>PROKKA_01243 +MSHTEPVDPAALPDPEDITEADLPEAPPRPGRERRRFAGTQQQIRSATRFYVVCSWITGV +MLLLLVAEMVFKYAWGQELFAGGTTVDGEQNILGLHPEDSVTGGVNLSLFILIAHGWMYV +VYLLACFRLWSLMRWQPMRLLAMAGGGVVPFLSFVVEKKVTKVVRDDVHRFPDAARRY +>PROKKA_01154 +MSQPHHDAGREAARAGEAPVDPATLPDPEDITEADLPAPPPRPGRAVRRFAGTRQQIVSA +DRIYKVCAYITGVMLLLLVAEMVFKYGLHQELFAGGTTVDGEPHGFGLAPEKSVTGGVNL +SLAILIAHGWMYVVYLLACFRLWSLMRWAPGRLLAMAGGGVVPFLSFVVERKVSGQVREE +LAQFPDAARRY +>PROKKA_01580 +MSTQHPGPQPVDPASLPDPEDITEADLPEPPPRPGREQRRFAGTQQQIRSATRLYVVCAW +ITGIMLLLLVAEMVLKYGMHVELYAGGTTLDGDANGLGLHPTDSVTGGVNLSLFILIAHG +WMYVVYLLASFRLWSLMRWEPLRLLAMAGGGVVPFLSFVVEKRMTRVVRDELHRFPDAAR +RY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001332.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001332.fa new file mode 100644 index 0000000000000000000000000000000000000000..a7c5811bf23b3abd5a3e71b7d4a6f9f249a3ef75 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001332.fa @@ -0,0 +1,35 @@ +>PROKKA_01651 +MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTEHAVPFLEHVRPYE +ALLGSQADQVVTVEGEFVPGTDVLVGPRLLNGRDGYWTVTALRVAGAPDGEVVPVVRGWS +ADADVVDPAPAGQVTVTGRLLPPDGPLPREATAEDTADRLLYRSLAPAQLVNVWDEPSYA +AYVAAFEMVDAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW +WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAVAAQAAAHPRQDHDDD +GAARPDPRDPGPRGPREEQSR +>PROKKA_01356 +MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTENAVPFLEHVRPYE +ALLGSQADQVVTVEGEFVPGTDVLVGPRLLDGRDGYWTVTALRVAGAPDGEVVPVVRGWS +ADADVVDPAPAGQVTVTGRLLPPDGPLPREAAAEDTADRLLYRSLAPAQLVNVWDEPSYA +AFVAAFEMADAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW +WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAFAAQAAAHPRQDHDDD +GAARPDPRDPGPRGPREEHRR +>PROKKA_01242 +MLRTALKPVWLATLVLALVAAGLFVALSKWQFETAETNAPPPRTQTEQPVPLTDHVRPYE +PLLARDADQVVTVPGEFLPDTDVLVGPRLLRGDEGFWTVSAFRVAGAPDGEVIPVVRGWS +AGADVVDPAPQGDVTVTGRLLPPDGPLPRTAAEADTADRLLYASLAPGQLVNVWDEPSYA +AFVAAFEVADAAGAEVGAGASEGGLEPVWVAPQPEETEVIWLNVFYAVEWILFAGFALFL +WWRFVRDDHLRDERERELDEEWAAQWRAEELARRREEARLAKERAYAAQAAARPSTDPEE +NRP +>PROKKA_01153 +MLRTALKPKWLATLVLALVAATAFVLLSRWQFASSETAAPPPRTQTENAVPLTEHVRPGE +PLLASQADQVVSARGEFVPGTDALVGPRLSDGREGWWTVTAFRVAGAPDGETVPVVRGWS +EAADVVDPAPTGEVTVTGRLLPPDGPVSPADAGEDTAGRPAFSTLSPGQLVNAWDVPAYA +AYVAAFGVTDAAGADVSAGARDGGLQPVWVPPQPEESQVVWLNVFYGVEWLLFAGFALFL +WWRFVRDDHLRDEQEAELDAQWAARWRAEELERRRERARREKEAAARAYAAWQAGETAPD +AAHQEPQDGPAGPRKEGQA +>PROKKA_01581 +MLRTALKPVWLATLVLALVAAAVFVALSKWQFESAETNAPPPRTQTENAVPFLEHVRPYE +ALLGSQADQVVTVEGEFVPGTDVLVGPRLLNGRDGYWTVTALRVAGAPDGEVVPVVRGWS +ADADVVDPAPAGQVTVTGRLLPPDGPLPREAAAEDTADRLLYRSLAPAQLVNVWDEPSYA +AFVAAFEMVDAAGAETGAAGPGGLEPVWVAPQPEETQIIWLNVFYAVEWMLFAGFALFLW +WRFVRDDHVRDEHERRLDEEWAAQWRAEELERRRAAAREAKERAFAAQAAAHPRQDHDDD +GAARPDPRDPGPRGPREEQSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001333.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001333.fa new file mode 100644 index 0000000000000000000000000000000000000000..b5e7693a5df3f905856745745cc8c089c202b512 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001333.fa @@ -0,0 +1,40 @@ +>PROKKA_01652 +MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPQDVSLTWRIDAYTFDMPVIGAPMDSVM +SPEAAIAMGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALQAGPAGTEATRKLQEAYAAPI +RPDLITERLAQIREAGVVVAGSLTPQNTQEFYRTVVAAGVDLFVIRGTTVSAEHVSSTQE +PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA +TAISDIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKAIAMGADAVVLGAALARATDAP +GGGWHWGLEAAHPELPRGHRTQVGQVAPLEEVLWGPGRHADGTSNLMGGLKRAMATCGYT +ELKDFQKVEVLVTPTQTV +>PROKKA_01357 +MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPQDVSLTWRIDAYTFDMPVIGAPMDSVM +SPETAIAMGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALEAGPAGTEATRMLQEAYAAPI +RPDLITERLAQIREAGVVVAGSLTPQNTQEFYRTVVAAGVDLFVIRGTTVSAEHVSSTQE +PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA +TAISDIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKAIAMGADAVVLGAALARATDAP +GGGWHWGLEAVHPELPRGHRTHVGQVAPLEEVLWGPGRHADGTSNLMGGLKRAMATCGYT +ELKDFQKVEVLVTPTQTV +>PROKKA_01241 +MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPKDVSLTWRIDAYTFEMPVIGAPMDSVM +SPETAIALGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALEAGPDGTEATRRLQEAYAAPI +RAELITERLAQIREAGVVVAGSLTPQNTQEFYKTVLAAGVDLFVIRGTTVSAEHVSSSHE +PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGSSTTTRRAMGIRVPMA +TAIADIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKALAMGADAVVLGAALARATDAP +GGGWHWGLEAAHPELPRGHRTHVGQVAPLEEVLWGPGHHADGTSNLMGGLKRAMATSGYT +ELKEFQKVEVLVTPTQTV +>PROKKA_01152 +MTNQIEIGRGKRGRQAFSFDDVSVVPSRRTRDPKDVNLSWRIDAYTFDMPVMGAPMDSVM +SPETAIALGRLGGLGVLNLEGLWTRHEDPEPLLEEIAAMEAEAGSPEVTRRLQEIYSAPI +RADLITERLAQIRESGVVVAGSLTPQNTQQFSQTVLAAGVDLFVIRGTTVSAEHVSSTHE +PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA +TAIADIAEARRDYMDESGGRYVHVIADGGVGTSGEIVKAIAMGADAVTLGTALARATEAP +GRGWHWGLEAAHPELPRGHRTRVGQVAPLEEVLWGPGHTTDGTSNLMGALKRAMATSGYT +ELKDFQKVEVLVTGARTH +>PROKKA_01582 +MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPQDVSLTWRIDAYTFDMPVIGAPMDSVM +SPETAIAMGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALEAGPAGTEATRKLQEAYAAPI +RPDLITERLEQIREAGVVVAGSLTPQNTQEFYRTVVAAGVDLFVIRGTTVSAEHVSSTQE +PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA +TAISDIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKAIAMGADAVVLGAALARATDAP +GGGWHWGLEAAHPELPRGHRTHVGQVAPLEEVLWGPGRHADGTSNLMGGLKRAMATCGYT +ELKDFQKVEVLVTPTQTV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001335.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001335.fa new file mode 100644 index 0000000000000000000000000000000000000000..89e1397f25ceb68f716e3bf5e0805789b222e180 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001335.fa @@ -0,0 +1,46 @@ +>PROKKA_01654 +MSTAQSSPAPAPRRRLPAWTSNFGWQIAAALVLGLVLGLIARATGHTAEHPTWLGETLAT +VGSIYISLLKAAVVPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG +VVLQPGVGTGQTAPASYQAKDVGWLDFLTSLVPANFLGLTVKTTAGEDGALASSPTFNVL +QILVIAIVVGVAALKVGEKAAPFLTFSRSVLAIIQKLLWWIIRLAPIGTIGLLGNAVASY +GWSTMGTLAKFVVAVYVGLALVMLVVYPLLARLHGLSVKQFFTGVWPAFQLGFVSRSSLG +TLPVTQRVAERNFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFIAQFYGIEMSLSQY +ALVALVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGMALLLAVDPIVDMGRTALNVSGQ +ALIPALVASQEGILDRDRYDAPRGDIFGEDEEEIVEARAHATADSRAELVGTPEPRA +>PROKKA_01359 +MSTAQSSPAPAPRRRLPAWTSNFGWQIAAALVLGLVLGLIARATGHTSEHPTWLGETLAT +VGSIYISLLKATVVPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG +VVLQPGVGTGQTAPASYQAKDVGWLDFLTSLVPANFLGLTVKTTAGEDGALASSPTFNVL +QILVIAIVVGVAALKVGEKAAPFLTFSRSVLAIIQKLLWWIIRLAPIGTIGLLGNAVASY +GWSTMGTLAKFVVAIYVGLALVMLVVYPVLARLHGLSVKQFFTGVWPAFQLGFVSRSSLG +TLPVTQRVAERNFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFIAQFYGIDMSLSQY +ALVALVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGMALLLAVDPIVDMGRTALNVSGQ +ALIPALVASQEGILDRDRYDAPRGDIFGEDEEEIVEARAHATADSRAQLVGTSEPRA +>PROKKA_01239 +MSTTQSSPEPAPRRRLPAWTGNFGWQIVAALVLGLVLGLVARSMGHTPDSPTWLGETLAT +IGSVYISILKATVIPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG +VVMQPGVGTGQSAPESYQARDVGWLDFLTSMVPANFLGLTVKSTVGEDGAVASSPTFNVL +QILVIAIVVGIAALKVGEKAAPFLTFSRSVLAVIQKLLWWIIRLAPIGTVGLLGNAVASY +GWSTMGTLAKFVVAIYVGLAIVMFVVYPVLARLHGLCVKQFFTGVWPAVQLGFVSRSSLG +TLPVTQRVAERNFGVPTGYAAFAVPLGSTTKMDGCAAIYPAIAAVFVAQFYGIEMSLGQY +ALVVLVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGLALLLAVDPIVDMGRTATNVAGQ +ALVPALVAKQEGILDQARYDAERVDIMGEDEEEIVEARAQDRDDDQDQMVGAAARPARD +>PROKKA_01150 +MTSHPSSPASGASTPARRRRLPAWTGNFGWQIAAALVLGLLLGLAARAMGHTPDSPTWLG +ETLALIGSIYVQLLKATVVPLVFFAVVASVANLAQVTNAARLAAKTLLWFAITSFIAVLI +GLAVGVVMQPGVGTGQSAPEGYQARTVTWLDFLTSMVPVNMLGLTVKTTAGDDGALTSTP +SFQVLQILVIAIAVGVAALKVGEKAEPFLAFSRSVLAVIQKVLWWIIRLAPLGTVGLLGN +AVASYGWSTMGTLVKFVVAVYVGLALVMLVVYPLLARVHGLSVKQFFTGVWPAFQMGFVS +RSSLGTLPVTQRVAERSFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFVAQFYGIDM +TLGQYALVVLVSVLGSAATAGTTGATVMLTLTLSTTGLPLEGMALLLAVDPIVDMGRTAV +NVSGQALIPALVAQQEGILDRTRYDAERGDVMADEDETIVEARHDDARGASRADLTEAGS +AR +>PROKKA_01584 +MSTAQSSPAPAPRRRLPAWTSNFGWQIAAALVLGLVLGLIARATGHTSEHPTWLGETLAT +VGSIYISLLKATVVPLVFFAVVASIANLAQVTNAARLAAKTLLWFAITSLIAVLIGLAVG +VVLQPGVGTGQTAPASYQAKDVGWLDFLTSLVPANFLGLTVKTTAGEDGALASSPTFNVL +QILVIAIVVGVAALKVGEKAAPFLTFSRSVLAIIQKLLWWIIRLAPIGTIGLLGNAVASY +GWSTMGTLAKFVVAIYVGLALVMLVVYPVLARLHGLSVKQFFTGVWPAFQLGFVSRSSLG +TLPVTQRVAERNFGVPTGYASFAVPLGATTKMDGCAAIYPAVAAVFIAQFYGIDMSLSQY +ALVALVSVLGSAATAGTTGATVMLTLTLSTAGLPLEGMALLLAVDPIVDMGRTALNVSGQ +ALIPALVASQEGILDRDRYDAPRGDIFGEDEEEIVEARAHATADSRAQLVGTPEPRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001336.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001336.fa new file mode 100644 index 0000000000000000000000000000000000000000..60e774f423eb163562d9c6828620446d5caf7e7d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001336.fa @@ -0,0 +1,15 @@ +>PROKKA_01657 +MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD +VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVAK +>PROKKA_01362 +MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD +VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK +>PROKKA_01237 +MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD +VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK +>PROKKA_01148 +MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGTRVPVD +VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK +>PROKKA_01587 +MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD +VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001337.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001337.fa new file mode 100644 index 0000000000000000000000000000000000000000..3d845fe01a7113e1020c69bd5d815b61961cdb4f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001337.fa @@ -0,0 +1,30 @@ +>PROKKA_01659 +MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV +GGHDITTTPSRRIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI +DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR +AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV +DGPHGPLAVYY +>PROKKA_01364 +MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV +GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI +DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR +AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILCPEVLERIFKTPCSVV +DGPHGPLAVYY +>PROKKA_01235 +MIELRGVVKRHSDEVCIGPVDLDIEAGGITALVGPNGAGKSTVLTMIGRLQDVDAGTIAV +GGQDITSTPSRRIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERYVSEAI +DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR +AADMLGRTVVIVLHDINFAARYADHIVAMGDGQVVETGTPGEILRPEVLERIFRTPCSVV +DGPHGPLAVYY +>PROKKA_01146 +MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV +GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI +DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR +AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV +DGPHGPLAVYW +>PROKKA_01589 +MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV +GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTCGRLTLEDERHVSDAI +DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR +AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV +DGPHGPLAVYY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001338.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001338.fa new file mode 100644 index 0000000000000000000000000000000000000000..3cf4aba651179eec929284351e3c2f30ff524480 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001338.fa @@ -0,0 +1,39 @@ +>PROKKA_01660 +MAEPLATAPGRLPAPLGGATAAGPVDADAPRRSGAFVTAAERRRYAVVVAVLAAVAVLST +AGILLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVTFHTVTGNRIITPSIMG +FEALYTAVSTVAVYVLGAAGVAVLTGVGPFLAQAALMVALTTALYSWLLSRPYGSVHLML +LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW +LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY +SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLVVVMRKG +RL +>PROKKA_01365 +MAEPLATAPGRIPAPPGGATAAGPVEADAPRRSGAFVTAADRRRYAVVVAVLAAVAVLST +AGILLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVTFHTVTGNRIITPSIMG +FEALYTAVSTVAVYVLGAAGVAVLTGVGPFLAQAALMVALATALYSWLLSRPYGSVHLML +LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW +LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY +SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLVVVMRKG +RL +>PROKKA_01234 +MVAVLAVVAVLSTAGILLWGNEAEPGSRAFWMIAGMRLDSLGVIAIVALCHSFATVSFHT +VTGNRIITPSIMGFEALYTAVQTGAVYVLGAAGIGVVTGTGPFLAQAALMVVLATVLYSW +LLSRPYGSIHLMLLVGVVLGGGLAALSTFMQRLLDPNSFDVLSARLFGNISNARSEYVAI +AAPIVVVVCLVLWLRSRRMNVLALGADSATNLGLHHRRELMVTLLLVSVLMAMTTALVGP +MTFLGFLVATLAYSLVDTHDHRMVLPVAALGAYAVLTLAYFVLRHVFYAGGAVTVIIELV +GGITFLIVVMRKGRL +>PROKKA_01145 +MAEPLATAPGRIPAPSGGATAAGPVDADAPRRSGAFVTAADRRRYALVVAVLAAVAVLST +AGILLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVSFHTVTGNRIITPSIMG +FEALYTAVSTAAVYVLGAAGVAVLTGVGPFLAQAALMVALATALYSWLLSRPYGSVHLML +LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW +LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY +SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLIVVMRKG +RL +>PROKKA_01590 +MVEPLATAPGRIPAPPGGATAAGPVDADAPRRSGAFVTAADRRRYAVVVAVLAVVAVLST +AGVLLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVSFHTVTGNRIITPSIMG +FEALYTAVSTAAVYVLGAAGVAVLTGVGPFLAQAALMVALATALYSWLLSRPYGSVHLML +LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW +LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY +SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLVVVMRKG +RL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001344.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001344.fa new file mode 100644 index 0000000000000000000000000000000000000000..096938ac10d482717c79b3f1117deaeffbc5ccbd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001344.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001347.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001347.fa new file mode 100644 index 0000000000000000000000000000000000000000..4b186f7d6125443b3a6a7d277f620e31fb4671c4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001347.fa @@ -0,0 +1,40 @@ +>PROKKA_01670 +MTGPLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP +EIAARAHLEALVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGT +PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISAEVELLGST +IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPHR +HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM +LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF +GADPGQPVEVVSV +>PROKKA_01375 +MPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIPEIAARAHLEA +LVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGTPLYGINHLVA +HVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGSTIDDAAGEAYD +KVARLIGAGYPGGPVIDRLAAEGDPTAFRFPRGLTAGKFVGSAEEPGPHRHDWSFSGLKT +AVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLMLGGGVAANSR +LRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWFGADPGQPVEV +VSV +>PROKKA_01208 +MTGPLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP +EIAARAHLEALVPTVRRALEAADVGLKDLDAIAVTSGPGLAGALMVGVAGAKALATALDT +PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGST +IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPHR +HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM +LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF +GADPGQPVEVVSV +>PROKKA_01136 +MAPMSATATAPLVLGIESSCDETGVGIARGTALLAHEVASSVEEHVRFGGVIPEIAARAH +LEALVPTVRRALDAAGVTLDEVDAIAVTSGPGLAGALMVGVAGAKALAVAADKPLYGINH +LVAHVGVGLLDGVRPADWDDLPRDLGALLVSGGHTEILQVDRISSDVTLLGSTIDDAAGE +AYDKVARLIGAGYPGGPVIDRMAQEGDPKAFRFPRGLTAGKFVGTAEEPGPHRHDWSFSG +LKTAVSRAVEQFEAQGLEVPRTDIAASFQEAVADVITAKAVRACREHGLTHLLLGGGVAA +NSRLRGLLADRCRSAGIELVVPPVNLCTDNGAMVAALGARLVADGVAPSDLAFGADPGQP +VSAVSAA +>PROKKA_01600 +MTGLLTRLEPMPTATAAPLVLGIESSCDETGVGVVRGTALLAHEVASSVEEHVRFGGVIP +EIAARAHLEALVPTIRRALDTADVTLADLDAIAVTSGPGLAGALMVGVAGAKALATALGT +PLYGINHLVAHVGVGMLDGVRPAQWDDLPADLGALLVSGGHTEILRVGRISSEVELLGST +IDDAAGEAYDKVARLIGAGYPGGPVIDRLAAQGDPTAFRFPRGLTAGKFVGSAEEPGPQR +HDWSFSGLKTAVSRAVEQFEARGLEVPRADIAASFQEAVADVITAKAVRACREHGLTHLM +LGGGVAANSRLRALLADRCRSAGIELTVPPVNLCTDNGAMVAALGARLVRDGVAPSDAWF +GADPGQPVEVVSV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001348.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001348.fa new file mode 100644 index 0000000000000000000000000000000000000000..d93fa7155022706f33796f0e796492c280c48539 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001348.fa @@ -0,0 +1,25 @@ +>PROKKA_01671 +MSPAEPDPAGDGRPAEDAHGLPPGYLLRPMTVWDIPEVLAHEATLFPLDAWPAHFYEEEL +AQTGPAGGRDAHGRPPTRDYRVVVRDVAAPGSADDDGPAPGEIVGYGGIMVVGDVADVQT +VGTVAAAQGRGIGAAQLRWMAAEAAARGASSLMLEVRASNAAARRLYARHGFEELHVRRR +YYPGGEDAVIMRKVL +>PROKKA_01376 +MSPAEPAPTDDGRPAEDEHGLPPGYLLRPMTVWDIPEVLAHEATLFPLDAWPAHFYEEEL +AQTGPAGGRDAHDRPPTRDYRVVVRDVPAPGSADDDGPAPGEIVGYGGIMVVGDVADVQT +VGTVAAAQGRGIGAAQLRWMAAEAAARGASSLMLEVRASNAAARRLYARHGFEELHVRRR +YYPGGEDAVIMRKAL +>PROKKA_01207 +MSPVEPAPGGDERPAEDEHGLPPGYLLRPMTVWDIPEVLAQEATLFPLDAWPARFYEEEL +AQTGPAGGRDAHGRPPTRDYRVVVRDVPAPVAPDEDGPAPGEIVGYGGIMVVGDVADVQT +VGTVAAAQGRGIGAAQLRWMAAEAAARGASALMLEVRASNAAARRLYARHGFEELHVRRR +YYPGGEDAVIMRKAL +>PROKKA_01135 +MSLPDATDPGDDAAPAHGLPAGFLLRPMTVWDVPEVLEHEETLFPLDAWPGHFYAEELAQ +AGPAGALDAHGRPTTRDYRVVVRQDTGEIVGYGGIMAVGDTADVQTIGTAAAVQGRGIGA +AQLRWMVAAARERGAESLLLEVRESNAAARRLYARHGFEPIAVRRGYYPGGEDAVVMRRA +L +>PROKKA_01601 +MSPAEPAPAGDGRPAEDGHGLPPGYLLRPMTVWDVPEVLAHEATLFPLDAWPAHFYEEEL +AQTGPAGGRDAHGRPPTRDYRVVVRDAAAPSSADDDGPAPGEIVGYGGIMVVGDVADVQT +VGTVAAAQGRGIGAAQLRWMAAEAAARGAGFLMLEVRASNAVARRLYARHGFEELHVRRR +YYPGGEDAVIMRKTL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001350.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001350.fa new file mode 100644 index 0000000000000000000000000000000000000000..619872bb594d0c375f6e7f29c65b2c6c703dcf55 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001350.fa @@ -0,0 +1,25 @@ +>PROKKA_01673 +MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF +TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS +VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAASAGEGEDGIVTDFS +DEDGGQAEELRSAVVTGRGPRWAGVVLP +>PROKKA_01378 +MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF +TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS +VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAAPAGEGEDGIVTDFS +DEDGGQAEELRSAVVTGRGPRWVGVVLP +>PROKKA_01205 +MSRHEPPAPDPALPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF +TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAT +VDRSVTVVEWGRGLAESLAGFPEDPDASWLDVEIVRARGGEDPAPAGPGADDGGIVTDFS +DEDGEQAEELRSAVVTGYGPRWAGVRLP +>PROKKA_01133 +MIAGRRAEQPLPAPVWERRVPLDGAAGTREFGAALAGVLRAGDVLILTGELGAGKTTLTQ +GLGAGLGVREGVISPTFVLSRIHPSLADGPDLVHVDAYRLRSAGELTDLDLEATADRSVT +VVEWGRGMAESLAGFPEDPEASWLDVEVLRARGGADLPDGPAGGDAAPDAPVIVTDFSDE +EGEAAEEVRTAVVRAHGPRWAAVALP +>PROKKA_01603 +MSDHEFPAPGPTLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF +TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS +VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDGPAASAGEEDGIVTDFSD +EDGGQAEELRTAVVTGRGPRWAGVVLP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001351.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001351.fa new file mode 100644 index 0000000000000000000000000000000000000000..12413a6dc845e5158946cc0fae278df181e6f314 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001351.fa @@ -0,0 +1,40 @@ +>PROKKA_01674 +MSRADVAPADTERAVRIDLAAVRHNVGVLQERIRRPDGSRPLLTAVVKADAYGHGAVAVA +RAAAAAGADRLGVAHVREALALRAAGVRLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD +AVADAVRGLRARGGAGPEARADLHLKADTGLGRHGCTPERWPALVARAAELEAAGLVRVE +GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM +VRVGLGLYGLSPFADVTAAEFGLRPAMSFVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG +LVPLGYADGVPRVVEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS +GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP +>PROKKA_01379 +MSRADVNPADTERAARIDLAAVRHNVGVLRERIRRPDGGRPLLTAVVKADAYGHGAVAVA +RAAAAAGADRLGVAHVREALALRAAGVPLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD +AVADAVRGLRARGGAGPEARAVLHLKADTGLGRHGCTPERWPALVARAAELEAAGLVRVE +GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM +VRVGLGLYGLSPFADVTAAEFGLRPAMSFVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG +LVPLGYADGVPRVVEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS +GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP +>PROKKA_01204 +MTQQDRSAGPAERTARIDLAAVRHNVAAVRARTVRQDGTRPLLTAVVKADGYGHGAVAVA +RAAQAAGADRLGVAHVREALELRGAGLRLPILAWLHTVGTDFAAALEADVTLGVSGWDLD +AVAAAVRALRPAPGTADSGPVRARVHLKADTGLGRHGCTPERWPAFVARAAELEAAGLVR +VEGVFSHLGVADDPERAEETTAQLRRFEEAAAAAAAALGRPLLRHLANTPATLSRPDTHL +DMVRVGLGLYGLSPFEGVDAAGLGLRPAMSLGTTLANVKPVPAGQGVSYGFRHVAPAPTT +LGLVPLGYADGVPRIAEGARVHVGGRTVPVVGRIAMDQFVVDLGPDARDRPGDAVELFGP +ASGIPADEWAAAAGTINYELVTRIGARVDRAHEGGEAPDAQEARA +>PROKKA_01132 +MDDAPDLTPSAAEAAPAERRALVDLAAVRSNVAALRARLGRPDGASTALMAVVKADAYGH +GAVPVARAALEAGADRLGVAHVTEALALRAAGVTAPILAWLHTRDTPFRAAVETDVALGV +SGMWDLEAVAQAARAAGRRATVHVKADTGLGRNGCLLADLPALAARAAALQDEGVVDVEG +LFSHLAVADELDRAAETDAQAAAFGEATVALDAAGLRPRVRHLANTPAALTRPDLHHDMV +RVGLGLYGLSPFPDRAPAEFGLRPAMSLQTTLAAVKAVPAGQGVSYGFRHRTAEPTVLGL +VPLGYADGVPRIAEGAPVAVAGRRVPHVGRVAMDQLVVDLGPGAAERVGDPVELFGPASG +IPADAWAEAAGTINYELVTRISPRVPRVHVDGAAAGEVAA +>PROKKA_01604 +MSLADVNPADTERAVRIDLAAVRHNVGVLRERIRRPDGSRPLLTAVVKADAYGHGAVAVA +RAAAAAGADRLGVAHVREALALRAAGVRLPVLAWLHTGATDFAAAVEAEVTLGVSGWDLD +AVAAAVRGLRARGGAGPEARAVLHLKADTGLGRHGCTPERWPAFVARAAELEAAGLVRVE +GVFSHLGVADEPDRAAETTAQLLRFERMAAEAAETLGHPLLRHLANTPAALARPDTHLDM +VRVGLGLYGLSPFADVTAAELGLRPAMSLVTVLANVKAVPAGQGVSYGFRHVTAEPTTLG +LVPLGYADGVPRVAEGTRVHVGGRTVPVVGRIAMDQFVVDLGPDAADAPGDAVELFGPAS +GIPVEEWAAAAGTINYELVTRIGGRVDRQHVDPTPTQEARP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001354.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001354.fa new file mode 100644 index 0000000000000000000000000000000000000000..2ca979f5e7e6e398b5762cd5e5b3574684b74976 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001354.fa @@ -0,0 +1,30 @@ +>PROKKA_01677 +MNERVDRGRVRRGLPRWARALCATVATLAALALAFGAGWATHAVTDPHPDDAPRVDALLV +LYSQPRVYDAAIELAASGLTDRLFVSAYLGPDGHEKLCGGPEERDPRLAGVTVECFAPDP +VTTQGEVIHAGERMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR +LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA +GAA +>PROKKA_01382 +MNERVDRGRVRRGLPRWARALCATVATLAALALAFGAGWATHAVTDPHPDDAPRVDALLV +LYSQPRVYDAAIELAASGLTDRLFVSAYLGPDGHEKLCGGPEERDPRLAGVTVECFAPDP +VTTQGEVIHAGDRMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR +LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA +GAT +>PROKKA_01201 +MSEGSDRARARRGARGVPRGVRALLSAAAGTATLALAFGVGWAAHAVTSPRPDDPERVDA +LLVLYSQPRVYDAAIELAADGVADRLFVSAHLGPDGHERLCGPEERRDPRLAGVSVECFA +PDPLTTQGEAMHAAARMRELGLEHLGVLTFHQHLERSRLLVERCWTPQEGRVSMFAFDAG +LDRWGRVRHGAYGVLAYGKAMATPGCDQELPGVLQWPLDLAKRLRGQPVGAEAGAAGPAG +AVSAAPAAATPAAPARGEGPA +>PROKKA_01129 +MSRPAGSAPAVDGDAQAAPRGPQAGRRVQADRGRGRRRRRILGAVLAAAALVLAAAFGPG +LMRAADMTLHPRPDDPPRVDALLVLYSQPAVYDAALELLDRGVADRVFVSAHLGPDGFEK +FCGTPAQRDPRTRGVEVECFSPDPVTTQGEVMFAADRMRALGLRRLGVLTFDQHLERARL +LAERCLPAADGSVSMYRFDGGYTGAEKVRQDVYGTAAFAKVALTTDCSGELPDVLQWPLD +LVKRTAGMPVGAVAESAAGVGRAGAGVRP +>PROKKA_01607 +MSAQADRGRVRRGLPRWARALCATVATLAALGLAFGAGWATHAVTEPHPDDAPRVDALLV +LYSQPRVYDAAIELAASGVTDRLFVSAYLGPDGHEKLCGGPGERDPRLAGVSVECFAPDP +VTTQGEVIHAADRMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR +LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA +GAV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001356.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001356.fa new file mode 100644 index 0000000000000000000000000000000000000000..521d7c4048882569d9ffdd8f014d85dcfabd5740 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001356.fa @@ -0,0 +1,60 @@ +>PROKKA_01680 +MRRSRARSGILVRMCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQ +LYHRKKAGKLANLAEELAEHPVPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLAFIHN +GIIENYAELREELLAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAF +TLLAVHVDHPDRVVASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITA +DAVEISDFRGGPAEGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGA +LMLDELRIDPEELKAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPI +IDPHTLVVSISQSGETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEI +AVASTKAFLAQITAAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAGKDQVKE +LARSMADATSVLFLGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPV +FVVMPSPLDRHSLHAKVVSNIQEVRARGARTFAVAERGDAAVRAQAEVVFEVPETQPMLM +PLLTTVPLQIFALELATAKGYDVDQPRNLAKSVTVE +>PROKKA_01384 +MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL +AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL +LAKGVEFLSETDTEVAAHLLADVYRHAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV +VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA +DGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL +KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS +GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT +AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF +LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPLDRHSL +HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL +ELATAKGYDVDQPRNLAKSVTVE +>PROKKA_01198 +MCGIVGYIGQPSSTREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGELYHRKKAGKLANL +AQELEEHPVPTGLVGIGHTRWATHGGPTDVNAHPHVADEGRLAMIHNGIIENYAELREEL +LAKGAEFLSETDTEVAAHLLTDVYRNAGGQDLTRSLQLASQRLEGAFTLLAVHVDHPDRV +VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITAEGVEITDFAGSPA +EGKRFTVDWDASAAEKGGYETFMEKEIHDQPQAVQDTLLGRMDAAGTLVLDELRIDPEEL +KAVNKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPNTLVVSISQS +GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT +AAYLLGLYLAQLNKKLFSGQIKDILADLHAIPGKIQEILDDKEQVKELARSMADTSSVLF +LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQAVFVVMPSPMDRHSL +HAKVVSNIQEVRARGARTFVVAERGDQAVRSHAEVVIEVPETQPMLMPLLTTVPLQIFAL +ELASAKGYDVDQPRNLAKSVTVE +>PROKKA_01127 +MRMCGIVGYIGQPSSTREHDALEVLMEGLRRLEYRGYDSAGVAVVADGELYHRKKAGKLA +NLAAELEAEPVPSAQVGIGHTRWATHGGPTDVNAHPHVADEGRLALIHNGIIENYAELRA +ELLEKGVTFLSETDTEVAAHLLADVYRGAGEGDLTRTMQLASQRLEGAFTLLAVHVDHPD +RVVASRRNSPLVVGVGEGENFLGSDVSGFIDFTKEAIELEQDQVVTITADAVEITDFQGA +PAQGKAFTVDWDASAAEKGGFDTFMEKEIHDQPQAVQDTLLGRTDATGALVLDELRIDPE +ELKAVRKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDDHTLVVSIS +QSGETMDTLMAVRYAKEQGARTLSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQ +ITAAYLLGLYLAQLNKKLFTGQIKDILADLAEIPGKIQEILDSSTPVRELARSMADTSSV +LFLGRNVGFPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDEGQAVFVVMPSPLDRH +SLHAKVVSNIQEVRARGARTFVVAERGDEAVRDHAEVVFEVPETQPVLMPLLTTVPLQIF +ALELASAKGYDVDQPRNLAKSVTVE +>PROKKA_01609 +MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL +AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL +LAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV +VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA +EGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL +KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS +GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT +AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF +LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPMDRHSL +HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL +ELATAKGYDVDQPRNLAKSVTVE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001357.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001357.fa new file mode 100644 index 0000000000000000000000000000000000000000..551447b7c061dea96f26da2c92c349d9b973ca4e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001357.fa @@ -0,0 +1,36 @@ +>PROKKA_01682 +MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER +LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA +VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR +FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS +VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW +DSINGPNLEQNVRPTRGRARLVLTKNAQHEVTRVLLRKV +>PROKKA_01386 +MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER +LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA +VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR +FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS +VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW +DSINGPNLEQNVRPTRGRARLVLTKNAHHEVTRVLLRKV +>PROKKA_01196 +MKDSTQPAPSVPEDLEDDLVSDHHRSPFVELERQTWARLATEMAQPFDQGDVERLRGLGE +HLSLREVAEVYLPLSRLLSINVEASGALRSATNAFLGERTGRTPYVIGVAGSVAVGKSTT +ARVLQEMLRRWPTTPRVELITTDGFLHPNAVLQERGIMARKGFPESYDRRALLRFMVDVK +SGAQEVRAPVYSHITYDIVPGEEQVVRRPDVLIVEGLNVLAPPVTRADGTAGLSVSDFFD +FSVYVDARADWIRSWYIERFMGLRSGAFADPRSYFHRYATLSDAEAQGTAESIWDSINGP +NLQQNVQPTRGRARLVLTKNAQHEVTRVLLRKV +>PROKKA_01125 +MRADAPPPPPPPCAVVLAGRRDAVAGRRPRACHDGPVKDTRDGGGGAPTAPADAPGPASA +GDPHLSPFVELERQTWARLADQLDQPFDQDDVERLRGLGETLSLREVAEVYLPLSRLLGI +HVEAAGALRRATNEFLGERTGRTPYVIGVAGSVAVGKSTTARVLQEMLRRWPSTPRVELI +TTDGFLHPNAVLQERGIMDRKGFPESYDRRALLRFMADVKSGAAEVSAPVYSHVTYDIVP +ERRQVVHRPDVLIVEGLNVLAPPLLRADGTPGLSVSDFFDFSVYVDARADWIRDWYVERF +MGLRSSAFRDPDAFFHRYASLSDEEARETARSIWDRINGPNLAQNVQPTRGRARLVLTKN +RQHEVTRVLMRKV +>PROKKA_01611 +MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER +LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA +VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR +FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS +VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW +DSINGPNLEQNVRPTRGRARLVLTKNAQHEVTRVLLRKV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001358.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001358.fa new file mode 100644 index 0000000000000000000000000000000000000000..fcbb13c48b7e275523ed92c49c0bb1bf2da178bd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001358.fa @@ -0,0 +1,20 @@ +>PROKKA_01684 +MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV +NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMIEARNRRLGIDPAEEEVPADVAVLT +EIRDLLAERRGGPTSGTTTL +>PROKKA_01388 +MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV +NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMIEARNRRLGIDPAEEEVAADVAVLT +EIRDLLAERRGGPTSGTTTL +>PROKKA_01194 +MKGNVIDLAVAVVIGAAFGAVINAVVDSVLMPLIAALFAAPSFDDWLVLDINGVLVKFGV +VLTAVVNFLLIAAAIYFAIVLPMNKMIERRNRRLGIDPAEEEVPEDVALLTEIRDLLSAQ +RGGAAGTTHTTL +>PROKKA_01124 +MKGNVVDLAVAVVIGAAFGKVVTALVDSVLMPLIAALFKAPSFDSWLVLNLNGVDVKFGV +VLTAIVNFLLIAAAVYFCIVLPMNTMIERRNRRLGITPAEDEVAPDVAVLTEIRDLLARQ +NGAPRV +>PROKKA_01613 +MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV +NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMVEARNRRLGIDPAEEEVPADVAVLT +EIRDLLAERRGGPTSGTTTL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001361.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001361.fa new file mode 100644 index 0000000000000000000000000000000000000000..a1e8217cf12923477f596742141e471d5f8be26e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001361.fa @@ -0,0 +1,26 @@ +>PROKKA_01688 +MAENTSPTPDPRTRGEHGTEHTAQAPFAVTRDYAAEVDEIRELGRKLGGEKKTPTPDPQA +WREGYPYKTKLSRKSYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGGAIKRF +NEHLNPRGARTVALEKPTEEEASQWYFQRYIQHLEFMRETPELERMLLNSGVHIIKFWFS +VSQREQLNRFAARETDPVRRWKLSPTDLASLDKWDDYTNAKEAMFFYTHTADAPWTVVKS +NDKKRARLEAIRHVLHTLPYPDKDERIVHRPDPQICGPANELAEYGEVSGGSFPRVR +>PROKKA_01392 +MGSFSWPLTAIKRFNEHLNPRGARTVALEKPTEEEASQWYFQRYIQHLEFMRETPELERM +LVNSGVHIIKFWFSVSQREQLNRFAARETDPVRRWKLSPTDLASLDKWDDYTNAKEAMFF +YTHTADAPWTVVKSNDKKRARLEAIRHVLHTLPYPDKDERIVHRPDPQICGPANELAEYG +EVSGGSFPRVR +>PROKKA_01190 +MTGRSPVRCAVRSNTTSGAAAAENTSTTTETTPAGGHAMEDTADAPWTVVKSNDKKRARL +EAIRHVLHTLPYPDKDERIVHRPVPHICAPATELFETGEDSGGSFPRVR +>PROKKA_01120 +MAENTTTPPTDPSADGVLAGEHPLESGRREQPFAVTEDYAAEVDEIRELGRTLHGDSLPS +PDPTAWREGYPYKTKLSRKTYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGG +AIKRFNEHMNPRGARTVALEKPTEAEASQWYFQRYIQHLPSGGEIVMFDRSWYNRAGVER +VMGYCTPQQYLEFMRETPELERMLSNSGIHIIKFWFSVSRREQLNRFAARETDPVRRWKL +SPTDLASLDKWDDYTNAKEAMFFYTHTADAPWTVVKSNDKKRARLEAMRHVLYTLPYPNK +DERIVHLPDPQICASADVLSEIDEADGGSFPRVR +>PROKKA_01617 +MQLWVKQTGQKVLIIVEGRDAAGKGGAIKRFNEHLNPCGARTVALEKPTEEEAPQWYFQC +YIQHLEFMRETPELERMLVNSGVHIIKFWFSVSQREQLNRFAARETDPVRRWKLSPTDLA +SLDKWDDSTNAKEAMFFYTHTADAPWTVVKSNDEKRARLEAIRHVLHTLPYPDKDERIVH +RPDPQICGPANELAEYGEVSGGSFPRVCGGGFSRAPPPRTPG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001362.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001362.fa new file mode 100644 index 0000000000000000000000000000000000000000..a18472d0475b9fc84fcf8e54a8d6682d60f7015e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001362.fa @@ -0,0 +1,20 @@ +>PROKKA_01689 +MSINENDDVELTSYTSESTATAEAPAASERPALTVPGSAVGRRKEAVARVRLVPGSGQWT +INGRALENYFPNKLHQQEVSDPFTLLELTGAYDVIARIHGGGPSGQAGALRLGISRALNE +IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR +>PROKKA_01396 +MSINENDDVELTSYTSESTAAAEAPVASERPALTVPGSAVGRRKEAVARVRLVPGSGQWT +INGRALENYFPNKLHQQEVSDPFTLLELTGAYDVIARIHGGGPSGQAGALRLGISRALNE +IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR +>PROKKA_01189 +MSINEHDDVELTSYTSESTSAGTEAPAASERPALTVPGSAVGRRKEAVARVRLVPGSGQW +TINGRTLENYFPNKLHQQEVNDPFTLLELAGAYDVIARIHGGGPSGQAGALRLGISRALN +EIDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR +>PROKKA_01119 +MSINQNDDVELTSYTSESTAASETAAVSERPALTVPGSAVGRRKEAVARVRLVPGSGQWS +VNGRTLENYFPNKLHQQEVNDPFTLLELNGAYDVIARIHGGGPSGQAGALRLGISRALNE +IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR +>PROKKA_01618 +MSINENDDVELTSYTSESTATAEAPAASERPALTVPGSAVGRRKEAVARVRLVPGSGQWT +INGRALENYFPNKLHQQEVSDPFTLLELTGAYDVIARIHGGGPSGQAGALRLGISRALNE +IDREHNRPALKKAGFLTRDARVIERKKAGLKKARKASQFSKR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001363.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001363.fa new file mode 100644 index 0000000000000000000000000000000000000000..c9089b238223cc4d433195d083e190cfd6976336 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001363.fa @@ -0,0 +1,20 @@ +>PROKKA_01690 +MRTYSPKPGDADRQWHIIDATDVVLGRLASHTATLLRGKHKPTFAPHMDMGDYVIIVNAE +KVALTGAKLEKKRAYRHSGYPGGLKSQSYAELLETNPVRAVEKAVKGMLPKNSLAAQQLS +KLKVYKGAEHPHTAQQPQTFEIGQVAQ +>PROKKA_01397 +MRTYSPKPGDADRQWHIIDATDVVLGRLASHTATLLRGKHKPTFAPHMDMGDYVIIVNAE +KVALTGAKLEKKRAYRHSGYPGGLKSQSYAELLETNPVRAVEKAVKGMLPKNSLAAQQLS +KLKVYKGAEHPHTAQQPQTFEIGQVAQ +>PROKKA_01188 +MRTYSPKPGDADRQWHIIDATDVVLGRLASHTATLLRGKHKPTFAPHMDMGDYVIIVNAE +KVALTGAKLEKKRAYRHSGYPGGLKSQSYAELLETNPVRAVEKAVKGMLPKNSLAAQQLT +KLKVYRGAEHPHAAQQPQTFEIGQVAQ +>PROKKA_01118 +MRTYTPKPGDADRQWHIIDATDVVLGRLATHTATLLRGKHKPTFAPHTDMGDYVIIINAE +KVALTGAKLEKKRAYRHSGYPGGLKSESYAELLEKNPVRAVEKAVKGMLPKNSLAAQQLT +KLKVYRGAEHPHAAQKPATFEIGQVAQ +>PROKKA_01619 +MRTYSPKPGDADRQWHIIDATDVVLGRLASHTAALLRGKHKPTFAPHMDMGDYVIIVNAE +KVALTGAKLEKKRAYRHSGYPGGLKSQSYAELLETNPVRAVEKAVKGMLPKNSLAAQQLS +KLKVYKGAEHPHTAQQPQTFEIGQVAQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001364.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001364.fa new file mode 100644 index 0000000000000000000000000000000000000000..64f8a33e7eeafcf964d6eb0565d4364f8cfd8ce4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001364.fa @@ -0,0 +1,31 @@ +>PROKKA_01691 +MSEQHRPDAPTAPGEPPSVRVRLGLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV +RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLIRRLGGVLSGWGGAVV +VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV +LGLHDFLSFCRPRAGATTIREVQHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVG +EGAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELHRRAEGTRAKRTL +>PROKKA_01398 +MSEQHRPDAPSAPGEPASVRVRLDLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV +RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLTRRLGGVLSGWGGAVV +VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV +LGLHDFLSFCRPRAGATTIREVTHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVG +ERAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELHRRAEGTRAKRTL +>PROKKA_01187 +MTEQPAPSAPRPSAAGEEPVRVRLDLAYDGGAFRGWARQPGLDSVQGALEDGLERILRRP +VRTVVAGRTDAGVHARGQVVHLDLAEGEWAGLTRGRPDLEPGASLARRLGGVLSGWDGAV +VVHGARRAPAGFDARFSALWREYEYRIDDAPDRRDPRTRAFTHWHGAALDERLMALEADA +VLGLHDFLSFCRPREGATTIREVQDLRVARDEDGSVRVRIRADAFCHNMVRAVVGALLQV +GEGSREPGWLGLRVATPARDSQVRLAPPRGLTLLAVGYPEDGEGLRRRAEGTRARRTL +>PROKKA_01117 +MVGMPDDALPAAPVEPRPEPTTGLPREGEVRLRLDLAYDGSDFRGWAAQPGLATVQGALE +GALETIVRRPVRTVVAGRTDAGVHARGQVVHCDLTEAEWSALARGRADVDPADALVRRLQ +GVLRPWQGAVVVRGARRAPDGFDARFSALWRAYEYRISDRPETRDPLARHGVLWHGARVD +ERLMAVEAGALLGLHDFLSFCRPREGATTVREVQDAEVVRTPDGLVRVRLRADAFCHSMV +RTIVGALLEVGEGRRTPGWTAARVAGPVRDSAARLAPAHGLTLLEVGYPETGEELRARAE +GTRARRAPLADLG +>PROKKA_01620 +MSEQHRPDAPSAPGEPASVRVRLDLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV +RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLIRRLGGVLSGWGGAVV +VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV +LGLHDFLSFCRPRAGATTIREVKHLEVRRDEDGVVRIRIRADAFCHNMVRAIVGALLQVG +EGAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELRRRAEGTRAKRTL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001366.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001366.fa new file mode 100644 index 0000000000000000000000000000000000000000..24eee7908c26c3620d42fe9923ce598f2cb9ce6c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001366.fa @@ -0,0 +1,35 @@ +>PROKKA_01693 +MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL +HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEVHN +PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA +TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPDV +VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK +LQELGLSLKDSPAGYDPQAHARQMDDDPFSDF +>PROKKA_01400 +MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL +HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHN +PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA +TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEV +VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK +LQELGLSFKDSPAGYDPQAHARQMDDDPFSDF +>PROKKA_01185 +MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL +HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEVHN +PDLHIATLNAKGKFDMELTVERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA +TRVEQRTDFDRLILDVETKESMLPRDAVASAGSTLVELFGLARSLNVEAEGVDLGDEPQT +AEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK +LYELGLSLKDSPAGYDPQAHARQMDDDPFSDF +>PROKKA_01115 +MLIAQRPTLTEEVVSDHRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL +HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGSGVVTAADITAPAGVEIHN +PDLHIATLNAKGKFDMELTVERGRGYVTAAQNKSADQEIGRIPVDSIYSPVLKVTFKVEA +TRVEQRTDFDRLILDVETKESMLPRDAVASAGSTLVELFGLAKGLNVEAEGIDLGEAPAE +ADGSADLAQPIEDLELTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKEK +LYELGLSLKDSPAGFDPQAHASQDDDPFSDF +>PROKKA_01622 +MLIAQRPTLTEEVVSDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL +HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHN +PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA +TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEV +VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK +LQELGLSLKDSPAGYDPQAHARQMDDDPFSDY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001368.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001368.fa new file mode 100644 index 0000000000000000000000000000000000000000..9b242ac54c2994d608c61da1475877cce6dd0c49 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001368.fa @@ -0,0 +1,20 @@ +>PROKKA_01695 +MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI +EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK +KK +>PROKKA_01402 +MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI +EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK +KK +>PROKKA_01183 +MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI +EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK +KK +>PROKKA_01113 +MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDRDIRVKDLTDDQLVQLRDHI +EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK +KK +>PROKKA_01624 +MARLAGVDIPREKRVIIALTYIYGVGKTRAEETLAATGIDPNIRVKDLSDEQLVQLRDHI +EGSYKVEGDLRREVAADIRRKVEIGSYEGLRHRRGLPVRGQRTKTNARTRKGPKKTVAGK +KK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001369.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001369.fa new file mode 100644 index 0000000000000000000000000000000000000000..bdab200a6525048e772d086a50e7c73076d178bb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001369.fa @@ -0,0 +1,10 @@ +>PROKKA_01696 +MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG +>PROKKA_01403 +MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG +>PROKKA_01182 +MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG +>PROKKA_01112 +MKVQPSVKRICDKCQVVRRKGRVLVICENPRHKQRQG +>PROKKA_01625 +MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001373.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001373.fa new file mode 100644 index 0000000000000000000000000000000000000000..0130307e03b7665c4d91c8e3da72d9af3a5618b6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001373.fa @@ -0,0 +1,45 @@ +>PROKKA_01700 +MLKAIARIVRTPDLLRKIAFTLALIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF +VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL +TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE +NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP +VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPSILIQFNTPQDGSAPAPW +ITWLSRYFGPGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP +TERYLQYVISRITLVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ +VSAQMEQRHYEGLLR +>PROKKA_01407 +MLKAIARIVRTPDLLRKIAFTLALIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF +VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL +TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE +NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP +VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPSILIQFNTPQDGSAPAPW +ITWLSRYFGPGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP +TERYLQYVISRITLVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ +VSAQMEQRHYEGLLR +>PROKKA_01178 +MFKAIARIVRTPDLLRKIAFTLGIIAVYRMGAFVPSPGVDYPAVQQCLAAGNAQGGLYSF +VNMFSGGALLQVSIFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQSTLTQYTRYL +TLALSLLQATTMASLARTGALLGCQLPLLRNDSILTVLLVVVVLTAGCIIVMWLGERVTE +NGVGNGMSLLIFASIAAGFPAGLGQVVQTQGWRVFAIVMLIGLLTMLAIVFVEESQRRIP +VQYAKRQIGSRTVGGSSTFIPIKVNMANVIPVIFASSVLMLPGILIQFNTPQDGTAPAPW +IAWLSRYFGNGDHPVYMAVYFLMIIGFTYFYVSITFNPQEISDNMKRYGGFIPGVRAGRP +TERYLQYVISRITLAGALYLGIVAMIPLIAFVVIGASQNFPFGGTSILIMVGVGLQTVKQ +VNAQMEQRHYEGLLR +>PROKKA_01108 +MFKAIARIVRTQDLRRKILFTLALVAVYRLGAFIPAPGVDYAAVRQCLAAGSAQGGLYSF +VNMFSGGALLQVSIFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL +TIALAVLQGTTMASLARTGALLGCRVPLLHDQSIATVLLVVVVLTTGCVIVMWLGERITE +NGIGNGMSLLIFASIAAGFPAGIGQVLQTQGWRTFAIVMVVGLLTMLAVVFVEESQRRIP +VQYAKRQIGTRTVGGTSTFIPIKVNMANVIPVIFASSVLMLPGILAQFNTPQDGSAPPAW +VSFLSTYFVGGDHPLYMALYLLMIIGFTYFYVSITFNPQEISDNMKRYGGFIPGVRAGRP +TERYLQYVISRITLPGALYLGIVAMIPLIAFVLIGANQNFPFGGTSILIMVGVGLQTVKQ +ISAQMEQRHYEGLLR +>PROKKA_01629 +MLKAIARIVRTPDLLRKIAFTLGLIAVYRMGAFVPAPGVDYPAVQQCLAAGNAQGGLYSF +VNMFSGGALLQVSVFALGIMPYITASIIVQLLRVVIPRFEQLHQEGPQGQATLTQYTRYL +TLALALLQATTMASLARTGALLGCSLPLLRDGSILTVLLVVIALTTGCLIVMWFGERITE +NGVGNGMSLLIFTSIAAGFPAGLGQVVQTQGWRVFAIVMGIGLLTMLAIVFVEESQRRIP +VQYAKRQIGSRTVGGSSTYIPVKVNMANVIPVIFASSVLMLPGILIQFNTPQDGSAPAPW +ITWLSRYFGSGDHPVYMALYFLLIIGFTYFYVSITFNPVEISDNMKRYGGFIPGVRAGRP +TERYLQYVISRITFVGALYLGIVAMIPLIAFAVIGTSQNFPLGGTSILIMVGVGLQTVKQ +VSAQMEQRHYEGLLR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001374.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001374.fa new file mode 100644 index 0000000000000000000000000000000000000000..5fcca602bee5f68b2e53b863fadeb781c7f55198 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001374.fa @@ -0,0 +1,20 @@ +>PROKKA_01701 +MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL +QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE +ITSAVQVKANAFSSSAVEKIQAAGGSTETL +>PROKKA_01408 +MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL +QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE +ITSAVQVKANAFSSSAVEKIQAAGGSTETL +>PROKKA_01177 +MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL +QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE +ITSAVQVKVDAFSASAVEKIQAAGGSTETL +>PROKKA_01107 +MAENDAIKVHDLRPAPGAKTAKTRVGRGEGSKGKTAGRGTKGTKARYQVRAGFEGGQLPL +QMRLPKLRGFKNPFRTEYQVVNLDKLSEMFPEGGEVTVETLVSKGLVRKNQPVKVLGTGE +ITSAVQMKADAFSASAIEKIKAAGGSAETV +>PROKKA_01630 +MADNDAIKVHDLRPAPGAKTAKTRVGRGEASKGKTAGRGTKGTKARYQVRAGFEGGQLPL +QMRLPKLRGFKNPFRTEYQVVNLDKLSAHFPEGGEVTVDALVSKGLVRRGQPVKVLGTGE +ITSAVQVKANAFSSSAVEKIQAAGGSTETL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001375.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001375.fa new file mode 100644 index 0000000000000000000000000000000000000000..e2372e2c107c059523acb3816cfc4f57785fb69c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001375.fa @@ -0,0 +1,15 @@ +>PROKKA_01702 +MFEPTRKNIQPSDATLVITQTRGVTGSKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN +TVPHLVSVEEVNNG +>PROKKA_01409 +MFEPTRKNIQPSDATLVITQTRGVTGSKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN +TVPHLVSVEEVNNG +>PROKKA_01176 +MTEPTRKNIQPSDATLVITQTRGVTGTKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN +TVPHLVSVEEVNNG +>PROKKA_01106 +MLQTTRKNIQPSDATLVITQTRGVTGTKQNQRDTLRSLGLKRIGHQVTRKADAATVGMVN +TVPHLVSVEEVNHG +>PROKKA_01631 +MFEPTRKNIQPSDATLVITQTRGVTGSKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN +TVPHLVSVEEVNNG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001376.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001376.fa new file mode 100644 index 0000000000000000000000000000000000000000..33b1bddff7a69df8ffab8ea6989772475068b9ef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001376.fa @@ -0,0 +1,30 @@ +>PROKKA_01703 +MTENINQKDTQVTESTETTVSETGSGSASQTTERATGGRGGRDGGRGGRDGDRRGGRRDD +RNRRGAQDDEKDQFLERVVGINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP +AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC +AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR +AQKSAKAGA +>PROKKA_01410 +MTENINQKDTQVTESTETTVSETGSGSASQTTERATGGRGGRDGGRGGRDGDRRGGRRDD +RNRRGAQDDEKDQFLERVVGINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP +AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC +AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR +AQKSAKAGA +>PROKKA_01175 +MTENNNQKDTQVTESTETTVSETASGSSSQTTERSAGGRGGRDGGRGGRDGDRRGGRRDD +RNRRGAQDDEKDQFLERVVAINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP +AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC +AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR +AQKSAKAGA +>PROKKA_01105 +MTETNDQKDTQVSETTETTVSETSAGSAGQSTERSGGRGGRDGGRGGRDGDRRGGRRDDR +NRRGAQEDEKDAFLERVVAINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVPA +AIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLECA +GIHDVLSKSMGSANAINIVRGTVDALKRLEEPQAVAARRGKALDEVAPHAMLRTMENDRA +SKGAQKAGV +>PROKKA_01632 +MTENINQKDTQVTESTETTVSETGSGSASQTTERATGGRGGRDGGRGGRDGDRRGGRRDD +RNRRGAQDDEKDQFLERVVGINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP +AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC +AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR +AQKSAKAGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001377.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001377.fa new file mode 100644 index 0000000000000000000000000000000000000000..182e5b35c35bf45c72186c238ff11d8e888b964a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001377.fa @@ -0,0 +1,20 @@ +>PROKKA_01704 +MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA +STMEADVRALEGDKTAKAKRVGELVAERAKAAGIDAVVFDRGGNKYHGRVAAVADGAREG +GLQL +>PROKKA_01411 +MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA +STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG +GLQL +>PROKKA_01174 +MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAWA +STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG +GLKL +>PROKKA_01104 +MSTLKVKGKGKFNARTRRHLRVRKRISGTAVRPRLVVNRSARHMFVQVVDDTQSRTLAYA +STMEADVRAFDGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG +GLQL +>PROKKA_01633 +MSTLKVKGKGKFNARTRRHLRVRKRISGTTVRPRLVVNRSARHMFVQVVDDTQSRTLAYA +STMEADVRALEGDKTAKAKRVGELVAERAKAAGIEAVVFDRGGNKYHGRVAAVADGAREG +GLQL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001378.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001378.fa new file mode 100644 index 0000000000000000000000000000000000000000..d423ef5059af39a2bf18673f2aba78b9f6bb6853 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001378.fa @@ -0,0 +1,20 @@ +>PROKKA_01705 +MSRIGRLPITIPAGVDVTIDGDRVSVKGPKGQLEHSLPTPITATLEEGQVTVARPDDERE +SRSLHGLTRTLISNMVEGVTNGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG +ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK +>PROKKA_01412 +MSRIGRLPITIPAGVDVTIDGDRVSVKGPKGQLEHSLPTPITVTLEEGQVTVARPDDERE +SRSLHGLTRTLISNMVEGVTNGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG +ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK +>PROKKA_01173 +MSRIGRLPITIPSGVDVTIDGDRVSVKGPKGQLEHSLPTPITATLEEGQVTVARPDDERE +SRSLHGLTRTLISNMVEGVTTGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG +ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK +>PROKKA_01103 +MSRIGRLPITVPSGVDVTIDGARISVKGPKGQLEHTLPSPITATLEEGQVIVARPDDERE +SRSLHGLSRTLINNMVLGVTEGFTKALEVVGTGYRVQAKGQDLEFALGYSHPVPVKCPEG +ISFTVEGNKVTVAGIDKQKVGETAANIRKLRKPDPYKGKGVRYAGEQIRRKAGKAGK +>PROKKA_01634 +MSRIGRLPITIPAGVDVTIDGDRVSVKGPKGQLEHSLPTPITVTLEEGQVTVARPDDERE +SRSLHGLTRTLISNMVEGVTNGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG +ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001379.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001379.fa new file mode 100644 index 0000000000000000000000000000000000000000..03d8a9cf49c40d0bdd7144c09ddeca38963e9a34 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001379.fa @@ -0,0 +1,20 @@ +>PROKKA_01706 +MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKAEGYIQDWREEEAEVGKKL +TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK +KGVGGEVLAYVW +>PROKKA_01413 +MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKAEGYIQDWREEEAEVGKKL +TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK +KGVGGEVLAYVW +>PROKKA_01172 +MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKSEGYIQDWREEEAEVGKKL +TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK +KGVGGEVLAYVW +>PROKKA_01102 +MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKVRVAEILKAEGYIQDWREEEAEVGKKL +TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTDRQASQ +KGVGGEVLAYVW +>PROKKA_01635 +MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKAEGYIQDWREEEAEVGKKL +TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK +KGVGGEVLAYVW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001382.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001382.fa new file mode 100644 index 0000000000000000000000000000000000000000..a850ea79cae91b26a86a3ed9afb85540b31276dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001382.fa @@ -0,0 +1,20 @@ +>PROKKA_01709 +MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA +VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE +VI +>PROKKA_01416 +MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA +VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE +VI +>PROKKA_01169 +MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA +VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE +VI +>PROKKA_01099 +MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA +VVVRTRKQSRRPDGSYIRFDENAAVILKNDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE +VI +>PROKKA_01638 +MIQQESRLKVADNTGAKEILTIRVLGGSGRRYAGIGDTIVATVKDAIPGGNVKKGDVVKA +VVVRTRKQSRRPDGSYIKFDENAAVILKTDGEPRGTRIFGPVGRELRDKKFMKIVSLAPE +VI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001384.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001384.fa new file mode 100644 index 0000000000000000000000000000000000000000..c80af35e3f7721e00b5124e1a6e43e038dd65039 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001384.fa @@ -0,0 +1,15 @@ +>PROKKA_01711 +MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNASRLKAVKRDIARI +YTILRERELGIRGDVAAEAQAEKNEEAAK +>PROKKA_01418 +MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNASRLKAVKRDIARI +YTILRERELGIRGDVAAEAQAEKNEEAAK +>PROKKA_01167 +MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNSSRLKAVKRDIARI +YTILRERELGIRGDVAAEAQADNNEEAAK +>PROKKA_01097 +MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLEDSSRLKAVKRDIARI +YTILRERELGIRGDVETAGAEKNEEAAK +>PROKKA_01640 +MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNASRLKAVKRDIARI +YTILRERELGIRGDVAAEAQAEKNEEAAK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001386.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001386.fa new file mode 100644 index 0000000000000000000000000000000000000000..572052436e347f882ba33c658ad2b903c4e6ec50 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001386.fa @@ -0,0 +1,30 @@ +>PROKKA_01713 +MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE +IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV +AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH +TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGVRRSGGERR +RRNDRAERAPRQENAGAGAETPAAAPAEGGNA +>PROKKA_01420 +MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE +IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV +AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH +TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGGGERR +RRNDRAERAPRQENAGAGAETPAAAPAEGGNA +>PROKKA_01165 +MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE +IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV +AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCAGRLGGAEMSRSEFYREGRVPLH +TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGDRRGGGGGE +RRRRNDRAERAPRQENAGAGAETPAAAPAEGGNA +>PROKKA_01095 +MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTDGMERAGISKVE +IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV +AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH +TLRANIDFGKFEAKTTYGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGPGGGE +RRRRNDRAERAPRQENAGAGAEQSAAAPAEGGNA +>PROKKA_01642 +MGQKINPNGFRLGITTDHVSHWFADSHKEGQRYADFLKEDVKIRELMTTGMERAGISKVE +IERTRDRVRVDIHTARPGIVIGRRGAEADRIRGELEKLTGKQIQLNILEVKNPETDAQLV +AQGVAEQLASRVAFRRAMKKAIQSAMRAGAQGIRIQCSGRLGGAEMSRSEFYREGRVPLH +TLRANIDFGKFEAKTTFGRIGVKVWIYKGDLTAKELAAKEAAQPSGRGRGGERRGGGERR +RRNDRAERAPRQENAGAGAETPAAAPAEGGNA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001387.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001387.fa new file mode 100644 index 0000000000000000000000000000000000000000..85d6e602d25da95d0078bd60afa80f9309e69c4a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001387.fa @@ -0,0 +1,20 @@ +>PROKKA_01714 +MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV +KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG +N +>PROKKA_01421 +MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV +KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG +N +>PROKKA_01164 +MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV +KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG +N +>PROKKA_01094 +MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV +KADREGVAFNEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASQDEKGG +N +>PROKKA_01643 +MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV +KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG +N diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001388.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001388.fa new file mode 100644 index 0000000000000000000000000000000000000000..92a1b3a9d26a511e86e4cdd5119f061fcd9ff621 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001388.fa @@ -0,0 +1,15 @@ +>PROKKA_01715 +MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV +FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR +>PROKKA_01422 +MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV +FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR +>PROKKA_01163 +MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV +FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR +>PROKKA_01093 +MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV +FVTESMVGHKLGEFAPTRTFRGHVKDDKKGKRR +>PROKKA_01644 +MPRSLKKGPFVDQHLYLKVLAENEKGSKNVIKTWSRRSMIIPDMLGHTIAVHDGRKHVPV +FVTESMVGHKLGEFAPTRTYRGHVKDDKKGKRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001389.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001389.fa new file mode 100644 index 0000000000000000000000000000000000000000..d5bb36303447c79eb1ac44de87c2d8e6ee1cd48a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001389.fa @@ -0,0 +1,30 @@ +>PROKKA_01716 +MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR +QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG +PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG +EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT +SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR +>PROKKA_01423 +MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR +QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG +PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG +EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT +SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR +>PROKKA_01162 +MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR +QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG +PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG +EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT +SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR +>PROKKA_01092 +MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR +QYRLIDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLQQGDVVEAG +PNADIKPGNNLPLRNIPVGTTIHAVELRPGGGAKMARSAGASIQLVAREGKYAQLRLPSG +EIRNVDVRCRATVGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT +SGGRHPVNPNGKPEGRTRRPNKESDKLIVRRRRTGKNKR +>PROKKA_01645 +MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR +QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG +PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG +EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT +SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001392.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001392.fa new file mode 100644 index 0000000000000000000000000000000000000000..ddee3c699fc995b621052e753b2c8379602512e3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001392.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001394.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001394.fa new file mode 100644 index 0000000000000000000000000000000000000000..2148de7e0955fffb6b97623d9ef82144e8b5d613 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001394.fa @@ -0,0 +1,20 @@ +>PROKKA_01721 +MSLPSPRRLFAVTAMAEMFTWAGLLIAMGLKYGGVTERVVPIAGGVHGFVFLCYLVVTVA +VWIDGRWPVARGLLGLGSTIVPFMTVPFERAQRRRGEPASRWQVVDRAPGERRPLERLLV +VVLRHPVVSALLAVAVVAVVFTLLLNAGPPTEWGR +>PROKKA_01428 +MSLPGPRRLFAVTAMAEMFTWAGLLIAMGLKYGGVTERVVPIAGGVHGFVFLCYLVVTVA +VWIDGRWPVARGLLGLGSTIVPFMTVPFERAQRRRGEPASRWQVVDRAPGERGPLERLLV +VVLRHPVVSALLAVAVVAVVFTLLLNAGPPTEWGR +>PROKKA_01157 +MSLPSPRSLFRVTAAAEMVTWAGLLTAMALKYTGVTDAVMPIAGGIHGFVFLCYFVVTVA +VWIDGRWPAARGLLGLGSAVVPFMTVPFERAQLRRGEPARHWRVLEGEPGERTGAQRVLA +AVLGRPLVSALVALIAVVVVFTLLLNAGPPTEWGR +>PROKKA_01087 +MRVPGPRSLYRATAVAEMATWTLLLLAMALKYGGVTAALMPAAGGVHGFVFLCYAAVVVA +VWIDGRWGVGRGLLALGSAVVPYMTVPMERALLRRGEPAPRWRVLEEAGRTSATDRLLRT +VLRRPRVSALAVLVAVVVVFSLLLRAGPPTEWFSR +>PROKKA_01650 +MSLPSPRRLFAVTAMAEMFTWAGLLIAMGLKYGGVTERVVPIAGGVHGFVFLCYLVVTVA +VWIDGRWPVARGLLGLGSTIVPFMTVPFERAQRRRGEPASRWQVVDRAPGERRPLERLLV +VVLRHPVVSALLAVAVVAVVFTLLLNAGPPTEWGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001397.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001397.fa new file mode 100644 index 0000000000000000000000000000000000000000..676e1073c20740942555941de07313d390fca656 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001397.fa @@ -0,0 +1,65 @@ +>PROKKA_01724 +MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE +RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET +VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL +LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG +EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV +NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI +GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESMTFPEPVISVAI +EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE +ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT +GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF +KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS +EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE +>PROKKA_01431 +MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE +RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET +VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL +LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG +EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV +NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI +GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESITFPEPVISVAI +EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE +ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT +GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF +KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS +EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE +>PROKKA_01154 +MAQDVLTDLNKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGASTTDWMEQEKE +RGITITSAAVTCFWNDNQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET +VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVNRLGARPLVMQLPIGAENDFVGVVDL +LSMKAFVWPGDAKGDVTMGAEYETREIPAELQEKAEEYRAQLVEAVADTSEELMEKYLEG +EELTTEEIQAGVRHLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGAVKGHDV +KDEEVELEREASKDAPFSALAFKIASHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI +GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDAAHPIILESMTFPEPVISVAI +EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE +ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTADGEIYEFENAVT +GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF +KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVKALVPLS +EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE +>PROKKA_01084 +MAQDVLTDLNKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGASTTDWMEQEKE +RGITITSAAVTCFWKNNQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET +VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGAKPLVMQLPIGSESDFIGVVDL +LTMKAFVWPGDAKGDVTMGAEYETQEIPADLQEKAEEYRTQLLEAVADTSEELMEKYLEG +EEISEEEIVAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGAVKGHAV +GDEEQVLEREPSKEAPFSALAFKIASHPFFGTLTFIRVYSGRLEGGAQILNATKGKKERI +GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPQNPIILESMTFPEPVISVAI +EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNDETGQTEIGGMGELHLDVFVDRMRREFKVE +ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT +GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF +KEGVRKANPVLLEPLMAVEVRTPEEFMGDVVGDLNSRRGQIQSMEDATGVKVVNALVPLS +EMFGYIGDLRSRTQGRAVYSMTFHSYSEVPKNVADEIIQKSQGE +>PROKKA_01653 +MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE +RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET +VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL +LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG +EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV +NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI +GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESMTFPEPVISVAI +EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE +ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT +GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF +KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS +EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001398.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001398.fa new file mode 100644 index 0000000000000000000000000000000000000000..e895bfe0281bb072ebe722a3cf8828dd9bd7fb5e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001398.fa @@ -0,0 +1,20 @@ +>PROKKA_01725 +MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLVDGKKSTAERIVYGALEGARAKNGADPVA +TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL +MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW +>PROKKA_01432 +MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLVDGKKSTAERIVYGALEGARAKNGADPVA +TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL +MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW +>PROKKA_01153 +MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLIDGKKSTAERIVYGALEGARAKNGADPVA +TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL +MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW +>PROKKA_01083 +MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLIDGKKSTAERIVYGALEGVRAKNGADPVA +TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL +MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW +>PROKKA_01654 +MPRKGPAPKRPLVVDPVYGSPLVTQLINKVLVDGKKSTAERIVYGALEGARAKNGADPVA +TLKKAMDNIKPALEVRSRRVGGATYQVPVEVKPGRSTALALRWLVGFSKARREKTMTERL +MNEILDASNGLGGAVKRREDTHKMAEANKAFAHYRW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001399.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001399.fa new file mode 100644 index 0000000000000000000000000000000000000000..4e5aef09d3feeefe7e7a4d51a5115dc7413ec7a9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001399.fa @@ -0,0 +1,20 @@ +>PROKKA_01726 +MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG +IEVTAYIPGEGHNLQEHSIVLVRGGRVRDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK +KEKK +>PROKKA_01433 +MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG +IEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK +KEKK +>PROKKA_01152 +MPTIQQLVRKGRSPKVVKTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG +IEVTAYIPGEGHNLQEHSIVLVRGGRVRDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK +KEKK +>PROKKA_01082 +MPTIQQLVRKGRSPKVVKTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG +VEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK +KEKK +>PROKKA_01655 +MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG +IEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK +KEKK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001401.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001401.fa new file mode 100644 index 0000000000000000000000000000000000000000..b20cd8b740591a65d8225200a330fb43200cd7d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001401.fa @@ -0,0 +1,105 @@ +>PROKKA_01728 +MVASSTSNETATVSPRSGASAGRVSFAKISEPLDVPDLLALQTESFDRLIGNERWAARVD +AALAADDHSVPVTSGLTDIFEEISPIEDFQGTMSLSFAEPEFADAKMTEEECKDRDATFS +APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT +PDKTSDKEIFSAKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILE +EFGHYDSIRATLEKDGTADQDEALLDIYRKLRPGEPAAVDAAQTLLNNLYFTPKRYDLAK +VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGETVIKGTRDGEPVDVRVE +IDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA +IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI +ETPEGPNIGLIGSLATFGRINSFGFIETPYRRVVDGRVTDTVDYLTADDELAFQIAQANA +PVDEDGRFEEEFVLCRQRGGDGEPVLSTVDEIDYMDVSPRQMVSAATALIPFLEHDDANR +ALMGANMQRQAVPLLRSEAPYVGTGMEKYVAVDAGDSVTATQGGVVTEVAADLVTVMNDD +GTTTHYPIMKFARSNQGNAYNQRVRVSEGERVEPLSIIADGPATDNGELALGKNLLVAFM +PWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL +DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES +GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM +PFLADGTPVDIVLNPLGVPGRMNLGQVMELHLGWAASRGWDIQGEPEWIKDLPNFPRQSG +PVNVATPVFDGAEAYEITGLLGHVNVTRDGDRLMSDSGKAQLFDGRTGEPFPDPVSVGYM +YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL +LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQAIEMR +DAEDEVYRAAEELGIDLSHAEPSSVEEV +>PROKKA_01435 +MVASSTSNETATVSPRSGASAGRVSFAKISEPLDVPDLLALQTESFDRLIGNERWAARVD +AALAADDHSVPVTSGLTDIFEEISPIEDFQGTMSLSFAEPEFADAKMTEEECKDRDATFS +APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT +PDKTSDKEIFSAKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILE +EFGHYDSIRATLEKDGTADQDEALLDIYRKLRPGEPAAVDAAQTLLNNLYFTPKRYDLAK +VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGETVIKGTRDGEPVDVRVE +IDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA +IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI +ETPEGPNIGLIGSLATFGRINSFGFIETPYRRVVDGRVTDTVDYLTADDELAFQIAQANA +PVDEDGRFEEEFVLCRQRGGDGEPVLSTVDEIDYMDVSPRQMVSAATALIPFLEHDDANR +ALMGANMQRQAVPLLRSEAPYVGTGMEKYVAVDAGDSVTATQGGVVTEVAADLVTVMNDD +GTTTHYPIMKFARSNQGNAYNQRVRVSEGERVEPLSIIADGPATDNGELALGKNLLVAFM +PWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL +DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES +GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM +PFLADGTPVDIVLNPLGVPGRMNLGQVMELHLGWAASRGWDIQGEPEWIKDLPNFPRQSG +PVNVATPVFDGAEAYEITGLLGHVNVTRDGDRLMSDSGKAQLFDGRTGEPFPDPVSVGYM +YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL +LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQAIEMR +DAEDEVYRAAEELGIDLSHAEPSSVEEV +>PROKKA_01150 +MVASSTSNETATVSPRSGASAGRISFAKISEPLDVPDLLALQTESFDRLIGNERWVARVE +EAQAADDHSVPVTSGLTDIFEEISPIEDFQGTMSLSFSEPEFADAKMTEEECKDRDATYA +APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT +PDKTSDKEIFSAKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILE +EFGHYDSIRATLEKDGTADQDEALLDIYRKLRPGEPAAVDAAQMLLNNLYFTPKRYDLAK +VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGEKTVKGVRDGEAVDVRVE +IDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA +IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI +ETPEGPNIGLIGSLATFGRINSFGFIETPYRRVVDGRVTDTVDYLTADDELAYQIAQANA +PVAEDGTFEEELVLCRQRGGDGEPVLSTVDEIDYMDVSPRQMVSAATALIPFLEHDDANR +ALMGANMQRQAVPLLRSEAPYVGTGMEKYVAVDAGDSVTATAAGVVTEVAADLVTVMNDD +GTTTHYPIMKFARSNQGNAYNQRVLVSEGDRVEPLSVIADGPATDNGELALGKNLLVAFM +PWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL +DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES +GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM +PFLADGTPVDIVLNPLGVPGRMNLGQVMELHLGWAASRGWDIQGEPEWIKDLPNFPRQSD +PVNVATPVFDGAEAYEITGLLGHVNATRDGDRLMGENGKAQLFDGRTGEPFPDPVSVGYM +YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL +LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQTIEMR +DAEDEVYRAAEELGIDLSHAEPSSVEEV +>PROKKA_01079 +MVASSTSNETAAVSPRSAASAGRISFAKIHEPLDVPDLLALQTESFDRLIGNERWAARVD +AAVAADDHSVSVTSGLTDIFEEISPIEDFQGTMSLSFSDPEFADAKMTEEECKDRDATFA +APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT +PDKTSDKEIFSARIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKALGWTESRILE +EFGQYDSIRATLEKDGTADQNEALLDIYRKLRPGEPAAVDAAQNLLNNLYFTAKRYDLAK +VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGEKTIKGARDGEPVEVRVE +VDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA +IKEFFGTSQLSQFMDQNNPLAGLTHKRRLNALGPGGLSRDRAGMEVRDVHPSHYGRMCPI +ETPEGPNIGLIGSLATFGRINPFGFIETPYRRVVDGRVTDQLDYLTADDELAFQIAQANA +PVDEDGRFVEELVLCRQRGGGGEPVLSTVDDIDYMDVSPRQMVSAATALIPFLEHDDANR +ALMGANMQRQAVPLLQSEAPYVGTGMEKYVAVDAGDSVTAAQPGVVTEVAADLVTVMNDD +GSTTHYPIMKFSRSNQGNAYNQRVRVSEGDRVERLSIIADGPATDNGELALGKNLLVAFM +PWEGLNYEDAIILSQRMVSDDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL +DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES +GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM +PFLADGTPVDVVLNPLGVPGRMNLGQVMEIHLGWAASRGWDIEGEPEWIKDLPDFPRQSG +PVNVATPVFDGAEAYEITGLLGHVNKTRDGDRLMGTTGKAQLFDGRSGEPFPDPVSVGYM +YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL +LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQTIEMR +DAEDETYRAAEELGIDLSHAEPSSVEEV +>PROKKA_01657 +MVASSTSNETATVSPRSGASAGRVSFAKISEPLDVPDLLALQTESFDRLIGNERWAARVD +AALAADDHSVPVTSGLTDIFEEISPIEDFQGTMSLSFAEPEFADAKMTEEECKDRDATFS +APLYVKAEFMNNTTGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERT +PDKTSDKEIFSAKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILE +EFGHYDSIRATLEKDGTADQDEALLDIYRKLRPGEPAAVDAAQTLLNNLYFTPKRYDLAK +VGRYKLNRKLGVDVHLGDPNASVLTEDDIVQMVHFIAALHAGETVIKGTRDGEPVDVRVE +IDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAA +IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI +ETPEGPNIGLIGSLATFGRINSFGFIETPYRRVVDGRVTDTVDYLTADDELAFQIAQANA +PVDEDGRFEEEFVLCRQRGGDGEPVLSTVDEIDYMDVSPRQMVSAATALIPFLEHDDANR +ALMGANMQRQAVPLLRSEAPYVGTGMEKYVAVDAGDSVTATQGGVVTEVAADLVTVMNDD +GTTTHYPIMKFARSNQGNAYNQRVRVSEGERVEPLSIIADGPATDNGELALGKNLLVAFM +PWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQL +DERGIIHIGAEVEAGDILVGRVTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGES +GTVIGVRIFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDM +PFLADGTPVDIVLNPLGVPGRMNLGQVMELHLGWAASRGWDIQGEPEWIKDLPNFPRQSG +PVNVATPVFDGAEAYEITGLLGHVNVTRDGDRLMSDSGKAQLFDGRTGEPFPDPVSVGYM +YMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEL +LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSADGQAIEMR +DAEDEVYRAAEELGIDLSHAEPSSVEEV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001404.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001404.fa new file mode 100644 index 0000000000000000000000000000000000000000..218c4527919980c00b12f3a54bf26fd458f5601c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001404.fa @@ -0,0 +1,25 @@ +>PROKKA_01731 +MAQRSKAYKAAKAAIGEDLYSPVEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG +SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM +GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE +AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL +>PROKKA_01438 +MAQRSKAYKAAKAAIGEDLYSPVEAIRLAKETNPSKIDATVEVALRLSVDPRKADQMVRG +SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM +GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE +AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL +>PROKKA_01147 +MAQRSKAYKAAKAAIGEDVYSPVEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG +SVSLPHGTGKTARVVVFATGERAEAARAAGADVVGDDDLIAKISEGWVDFDAAVASPELM +GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVTDIKGGKIDFRVDKHSNLHFIIGKTSFE +AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVSMDPNVTSVDSSEL +>PROKKA_01076 +MAQRSKAYKAAKAAIGDTVYAPAEAIALAKETNPSKTDATVEVALRLSVDPRKADQMVRG +SVSLPHGTGKTARVVVFATGERAEAARAAGADHVGDDDLIAKIADGWTDFDAAVASPELM +GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE +ANQLVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVQMDPNAAPPKDEAQA +>PROKKA_01660 +MAQRSKAYKAAKAAIGEDLYSPAEAIRLAKETNPSKTDATVEVALRLSVDPRKADQMVRG +SVSLPHGTGKTARVVVFATGDRAEAARAAGADVVGDDDLIARISEGWVDFDAAVASPELM +GKVGRLGKVLGPRNLMPNPKTGTVTPDVAKAVADIKGGKIDFRVDKHSNLHFIIGKTSFE +AKALVENYAAALEEVLRLKPSSSKGRYISKATVATTFGPGVPMDPNVTSVDSSEL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001407.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001407.fa new file mode 100644 index 0000000000000000000000000000000000000000..e6700d8d1681e80266b9fd21e335645e8c6c87e9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001407.fa @@ -0,0 +1,15 @@ +>PROKKA_01734 +MAANGGGPAPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI +LLVMGLDWVFGTVAGLLFGAGGL +>PROKKA_01441 +MAANGGGPTPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI +LLVMGLDWVFGTVAGLLFGAGGL +>PROKKA_01144 +MTDIAANGGGSTPAPDRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVA +FMILLVMGLDWVFGTVAGLLFGGGGGL +>PROKKA_01073 +MTANHGSSASGPESRRRGPFGRIALFLRQVLDELRKVVTPTGDELLKMTGVVLAFVAVMI +LLVMGLDWVFGTLAGLLFGAGPA +>PROKKA_01663 +MAANGGGPAPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI +LLVMGLDWVFGTVAGLLFGAGGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001408.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001408.fa new file mode 100644 index 0000000000000000000000000000000000000000..57bfc624b48a2c8d6a197b19475bff84fe23262a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001408.fa @@ -0,0 +1,41 @@ +>PROKKA_01736 +MAAPARRVSARLSAIAPSATLAVDARAKELKAAGRPVIGFGAGEPDFPTPDYIVEAAVAA +ARDPKNHRYSPASGLPELREAIADKTLRDSGVSLEAAQVLVTNGGKQAVYNAFAALLDPQ +DEVLVPAPYWTTYPEAIRLAGGVPVEVFAGPEQGYKVTVDQLDESVTDRTKVLLFVSPSN +PTGAVYSPEETAAIGQWARERGLWVVTDEIYEHLTYDGMPFTSIVRAVPELAEQSVILNG +VAKTYAMTGWRVGWMAGPLDVVKAATNLQSHATSNVANVSQRAALAAIAGPLDAVAEMKT +AFDRRRRAMVEAMDAVPGFHCPTPQGAFYAYVDVREALAKTYRGGVTPATSAELAAFILD +EAEVAVVPGEAFGPSGYLRLSYALGDADLAEGVERIRALLSA +>PROKKA_01443 +MAAPARRVSARLSAIAPSATLAVDARAKELKAAGRPVIGFGAGEPDFPTPDYIVEAAVAA +ARDPKNHRYSPAAGLPELREAIAAKTLRDSGVSLEAAQVLVTNGGKQAVYNAFAALLDPQ +DEVLVPAPYWTTYPEAIRLAGGVPVEVFAGPEQGYKVTVDQLDESVTDRTKVLLFVSPSN +PTGAVYSPEETAAIGQWARERGLWVVTDEIYEHLTYDGMPFTSIVRAVPELAEQSVILNG +VAKTYAMTGWRVGWMAGPLDVVKAATNLQSHATSNVANVSQRAALAAIAGPLDAVAEMKT +AFDRRRRAMVEAMDAVPGFHCPTPQGAFYAYVDVREALAKTYRGGVTPATSAELAAFILD +EAEVAVVPGEAFGPSGYLRLSYALGDADLAEGVERIRALLSA +>PROKKA_01142 +MIGFGAGEPDFPTPAYIVEAAVAAAKDPKNHRYSPAAGLPELREAIAAKTLRDSGVAIDV +AQVLVTNGGKQAVYNTFAALLDPQDEVLVPSPYWTTYPEAIRLAGGVPVDVFAGPEAGYK +VSVEQLEAAVTERTKALLFVSPSNPTGAVYSPEETEAVGRWALDRGLWVITDEIYEHLTY +DGMPFTSILKAVPELAEQAVILNGVAKTYAMTGWRVGWMAGPLDVIKAATNLQSHATSNV +SNVSQRAALAAVAGPLDAVDEMKVAFDRRRRAMVEAMNAVPGFHCPTPQGAFYAYVDVRE +ALGRTYRGGVTPTTSAELATFILDEAEVAVVPGEAFGPSGYLRLSYALGDDDLAEGVERI +RALLSE +>PROKKA_01071 +MTRAPSNRAGTSAPDGGSVGWPHGRRVRVRRPPEQMRKVPMATPAHRVSARLSAIAPSAT +LAVDAKAKALKAAGRPVIGFGAGEPDFPTPDYIVEAAVAAARDPKNHRYSPAAGLPELRE +AIAAKTLRDSGVELDASQVLVTNGGKQAVYNAFAALLDPQDEVLVPSPFWTTYPEAIRLA +GGVPVDVFAGPDQGYKVTVDQLEAAHTERTKVLLFVSPSNPTGAVYSPEETRAIGEWALA +KGLWVVTDEIYEHLTYDGVPFTSILKAVSGLAEQGVILNGVAKTYAMTGWRVGWLAGPLD +VVKAATNLQSHATSNVANVSQRAALAAVAGPLDAVEEMKTAFDRRRRAMVEALNRVPGFH +CPTPEGAFYAYVDVREALGRTYTGGVTPATSAELADFILDQAEVAVVPGEAFGPSGYLRL +SYALGDEDLAEGVERIRALLSA +>PROKKA_01665 +MAAPARRVSARLSAIAPSATLAVDARAKELKAAGRPVIGFGAGEPDFPTPDYIVEAAVAA +ARDPKNHRYSPAAGLPELREAIAAKTLRDSGVSLEAAQVLVTNGGKQAVYNAFAALLDPQ +DEVLVPAPYWTTYPEAIRLAGGVPVEVFAGPEQGYKVTVDQLDEAVTDRTKVLLFVSPSN +PTGAVYSPEETAAIGRWARERGLWVVTDEIYEHLTYDGMPFTSIVRAVPELAEQSVILNG +VAKTYAMTGWRVGWMAGPLDVVKAATNLQSHATSNVANVSQRAALAAIAGPLDAVAEMKT +AFDRRRRAMVEAMDAVPGFHCPTPQGAFYAYVDVREALGKTYRGDVTPTTSAELAAFILD +EAEVAVVPGEAFGPSGYLRLSYALGDADLAEGVERIRALLSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001411.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001411.fa new file mode 100644 index 0000000000000000000000000000000000000000..806bc75afdbc2789d31d65fc8bfdf73530985b1c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001411.fa @@ -0,0 +1,36 @@ +>PROKKA_01739 +MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG +VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDPDGRVQFGRLRRGEWQDATV +AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG +RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA +TRLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP +TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG +>PROKKA_01446 +MTSTHDPFTGPGPHVAPDGAASGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG +VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDADGRVQFGRLRRREWQDATV +AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLLGLGALAVLVWWLVTRWDGRAQARVAPG +RAPDADQPSHAVPRPAWYVGGGPRERAAEVTDPHGFHPEWIDPATGTWRDHVHSRERRAA +ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP +TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG +>PROKKA_01139 +MRRSDSSWVGGVLAGVAERYRVDPLLARGVFVALCVVSAGFGLLAYAVAWALLPDGDGTV +HYGRLRRGEWQDATVAIAVIGGIGVLNVVLGAGFTLLAPVVGGPGSLLGLAAVAVLVWWL +VTRWDGSTQSRVGPAPASEPEASGRAAARPAWYLRRDDARAAASRQDAHGFRADWLDPET +GTWRSPVHSRELRAAARLAEEEQAAPAGPSGRGSAVVAAPRRLSPAVQAVTYAVAALAAA +AAVGASLLVGVGSLTLLAVPAIVAALAVIAPVMLAALLTGRRPGSLAPASGILVGAAALQ +VAVAVAVL +>PROKKA_01068 +MDTAHDPFPAPRSSPATRPLPPGPASDARSRSAGTDGPAPDGLEVLPVWLRRPVEGWGVR +RSRSSWVGGVLAGVAERYRIDPLLSRGVFVALCVVSAGIGLLGYALAWAVLPDADGRVHY +GRLRRGEWSDAPVAIAAIAAIGALNVVLGAGFTLIAPVLGGPGSLIGLTALAVLVWWLVT +RWDGEGERRMAPAQPARDAAARPAAEPSWYLRRHRPESATVDAHGFRSDWIDPETGSWRE +QPHSREHRAAARLAEAQVRAAGQAAGRRPAGTGRGSHSAVKPLLGRGTRIATCVVAAGVA +LAVSLAMVLGNVSTSATLFPVWPALAALGVMAAVMTAGLLRGRRPGLLAPLSGILVGVVA +LQVCAHLLFTPLP +>PROKKA_01668 +MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG +VAERYRIDPLLARGVFVAVCMISAGLGLLAYAAAWAVLPDADGRVQFGRLRRGEWQDATV +AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG +RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA +ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP +TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001412.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001412.fa new file mode 100644 index 0000000000000000000000000000000000000000..7d5ee42c2fc2139bbaafebee812adcf725992d92 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001412.fa @@ -0,0 +1,35 @@ +>PROKKA_01740 +MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL +ARTGGTILGTSRTHPYNAEGGGPENMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI +VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH +SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFIPEGHDDPLAEAGVEA +SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ +RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR +>PROKKA_01447 +MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL +ARTGGTILGTSRTHPYDAEGGGPENMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI +VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH +SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFVPEGHDDPLAEAGVEA +SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ +RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR +>PROKKA_01137 +MRVGMLTSGGDCPGLNAVIRSAVLHGIKTYDMEMVGIRNGWSGLIEKDVEELPRTRVRGL +ARNGGTILGTSRTHPYDTEGGGPENMRRNMRELGLDAVIAIGGEGTLAGANRLAADGLPI +VGVPKTIDNDLRGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH +SGMAAGAHAILIPEVRTPMEQVAEWVKQVHDRGRSPLVVVAEGFIPEGHDDPLSEAGVED +SGRPRLGGIGEWVTREIEAMTGVETRNTVLGHIQRGGAPTATDRVLSTRFGMGAVDLAAQ +KRWGQMVAANGTDIISIPMSAALKGLKEVPVERYEEAKVLFGR +>PROKKA_01066 +MRVGLLTSGGDCPGLNAVIRAAVLHGIKTYDMEMVGIRNGWAGIIEQDVEDLPRTRVRGL +ARTGGTILGTSRTHPYDADGGGPENMARNLRELGIDAVVAIGGEGTLAGANRLAQDGLPV +VGVPKTIDNDLQGTDYTFGFDTAVEIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH +SGMAAGAHAILIPEVRTPMSQVAEWVTQVHEKGRSPLVVVAEGFIPEGHDDPLADAGMEA +SGRPRLGGIGEWVTREIEEMTGIETRNTVLGHIQRGGAPTARDRVLSTRFGMGAIDLAAQ +HRWGSMVAARGTDIITIPMSAALKGLKEVPRERYDEAKVLFGR +>PROKKA_01669 +MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL +ARTGGTILGTSRTHPYNAEGGGPKNMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI +VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH +SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFVPEGHDDPLAEAGVEA +SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ +RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001413.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001413.fa new file mode 100644 index 0000000000000000000000000000000000000000..a6ba197a57233487371500cf82501c641882bf96 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001413.fa @@ -0,0 +1,30 @@ +>PROKKA_01741 +MRPDHPAVGVLALGLARRLGLPDTALLPDDAPAAGAEPRRIEVARQGVAEAEVLALPWAT +VVAGPAWFTRACRGVPAEALGVESALLRTAVRAAAGEAVRSRGEFTLYAAEEPPPVDPSR +TVAVSDDPAHVHAVVAQAPADDVAEAGVPSWESSVALVPDDGAGRAIEAAVAAAGHRVTG +GVLASLGTLTPPRLRGRGLGRYAVAVAMDRAALEGLLPFAEVPAGHTAAHHVAIAVGLEA +AGTRTVLALD +>PROKKA_01448 +MRPDHPAVGVLALGLARRLGLPDTALLPGDAPAAGAEPRRIEVARQDVAEAEVLALPWAT +VVAGPAWFTRACRGVPAEALGVESALLRTAVRAAAGEAVRSRGEFTLYAAEEPPPVDPSR +TVAVSDDPAHVHAVVAQAPADDVAEAGVPSWESSVALVPDDGAGRAIEAAVAAAGHRVTG +GVLASLGTLTPPRLRGRGLGRYAVAVAMDRAALEGLLPFAEVPAGHTAAHHVAIAVGLEA +AGTRTVLALD +>PROKKA_01136 +MSGAPSFAGVLALGLARRLGLPDTALLPDDDGATKPRRLEAVREDAAEAEVLALPWATVV +AGPAWFAAACRNVPAEVLGVESALLRTAAGAAPGAGSGGGAAVRSRGEFTLYAAEEPPVL +EPSRSVAVSEDPAHALAVAAQAPADDLAEAAAQAWTSSASLVPDDGAGHGLEAPVAAAGH +RVSGGILAELGVLTVPRLRGHGLGRYAAAVAMDRATLEGLLPVAHLRAGHTAAHHVAIAV +GLEPVGSRTVLALG +>PROKKA_01065 +MTAAEPLPEHVRELVALAWGRALGVPDDVAALARATGRRVALPRPAGPETDILLLEAAGL +EVLAGPEPLLAAAADRATEELALESTLLRLASGWGPRSRGEHTLLHLDEPPEVAPSGRVA +VSDDPADAAALARECPADDARAAGLDELHALRTLVPDDGAGRATGTPLAAAGHATRAGLL +ADVRVLVRPELRGRGLGAYAAAVAAGAAWDEGLVPQARVPAAQDGALRLALGVGFVPTGR +LTRVELTRAG +>PROKKA_01670 +MRPDHPAVGVLALGLARRLGLPDTALLPGDAPAAGAEPRRIEVARQGVAEAEVLALPWAT +VVAGPAWFTRACRGVPAEALGVESALLRTAVRAAAGEAVRSRGEFTLYAAEEPPPVDPSR +TVAVSDDPAHVHAVVAQAPADDVAEAGVPSWESSVALVPDDGAGRAIEAAVAAAGHRVTG +GVLASLGTLTPPRLRGRGLGRYAVAVAMDRAALEGLLPFAEVPAGHTAAHHVAIAVGLEA +AGTRTVLALD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001414.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001414.fa new file mode 100644 index 0000000000000000000000000000000000000000..e3502582244bfbc5334e77b253270d36a4ab8466 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001414.fa @@ -0,0 +1,40 @@ +>PROKKA_01742 +MTTSRSPLLDLAVAEPQGPAGGAVEGRGPDAGVAAHYGRPLPEQRALARGRALVDLSHRA +VLSVSGPDRLSWLHTLGTQHVETLPPGTSTEILFLDVQGRIEHAAHLLEDGTAAWLVTDR +EDGPGLAAWLTSMRFSHDVTLRDHTGAVAVVGATAPVPGWEDRTVWLDPWPRVGAGGWAY +TADPDPATHPGADWSWREYLVTRADLEATVRALGTGVLAGWSLAGTTAAEALRIEAGRPR +RALDVDDRAIPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLLLDGSGHALP +EHGAPVILRPAEDTPEARAAARPVGTVTAAAQHHEAGAVALALLKRTVPVDAELLVREDA +PGEDGVAEGGWIAASQEPLVSPDAGQVVGRPRGVGRLR +>PROKKA_01449 +MTTSRSPLLDLAVAEPQGPAGGAVEGRGPDAGVAAHYGRPLPEQRALARGRALVDLSHRA +VLSVSGPDRLSWLHTLGTQHVETLPPGTSTEILFLDVQGRIEHAAHLLEDGTAAWLVTDR +EDGPGLAAWLTSMRFSHDVTLRDHTGAVAVVGATAPVPGWEDRTVWLDPWPRVGAGGWAY +TADPDPATHPGADWSWREYLVTRADLEATVRALGTGVLAGWSLAGTTAAEALRIEAGRPR +RALDVDDRAIPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLLLDGSGHALP +EHGAPVILRPAEDTPEARAAARPVGTVTAAAQHHEAGAVALALLKRTVPVDAELLVREDA +PGEDGVAEGGWIAASQEPLVSPDAGQVVGRPRGVGRLR +>PROKKA_01135 +MTGAEPAQRSPLLDLASAEPHGPAGGAVEGVGPDAGVAAHYGRPLPEQRALARGRALVDL +SHRAVLSVSGPDRLTWLHTLGTQHVADLPAGTSTEILFLDAQGRIEHAAHLLEDGTAAWL +VTDREDGPGLAAWLASMRFSHQVTLRDHTGAVAVVGSTAPVPGWEDRTVWVDPWPHVGVG +GWAYTADPRPESHPGADWSWREHLVTRADLEATVRTLGTGPLEGWSLAGTTAAEALRIEA +GRPRMATDVDERALPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLMLDGSV +HALPPHGAPVILRPAEDTPQARAAARPVGAVTSSAQHHEAGAVALALLKRSVPVDAELLV +CEDLPGDAEAGDAADAAETGWIAAAQEPLVSPAAGQVVGRPRGVGRLR +>PROKKA_01064 +MTEPRPEPAPAVRAARRSPLLAPPPAAPGGPAEGAVEGVGQDAGVAAHYGRPLVEQRALA +RGRALVDLSQKTVVSVSGPDRLSWLHTLSTQHLKDRPAGTSTEALFLDANGRIEIAVHLL +EDGAAAWLIADPAHADVLVTWLRSMVFSHRVTLRDHTGVVAVVGAMAPVPGWEDRTVWLD +PWPRVDVGGWPYSPDPDPAAHPGAGWSWREYLVTRGDLVATVDRLGTGELEGWSLAGALA +AEALRIEAGRPRPAVDADARAIPHELDILRTAVHLEKGCYRGQETVARVYNLGRPPRRLT +QLLLDGSSHALPAAGAAVILRPEPDTADARAAARPVGTVTSAVQHHEAGAVALAVLKRAV +PVAAELLVREEAAGGGEPEWIAASQQALVSPDAGQVVGRPAGLSRRA +>PROKKA_01671 +MTTSRSPLLDLAVAEPQGPAGGAVEGRGPDAGVAAHYGRPLPEQRALARGRALVDLSHRA +VLSVSGPDRLSWLHTLGTQHVETLPPGTSTEILFLDVQGRIEHAAHLLEDGTAAWLVTDR +EDGPGLAAWLTSMRFSHDVTLRDHTGAVAVVGATAPVPGWEDRTVWLDPWPRVGAGGWAY +TADPDPATHPGADWSWREYLITRADLEATVRALGTGVLAGWSLAGTTAAEALRIEAGRPR +RALDVDDRAIPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLLLDGSVHALP +EHGAPVILRPAEDTPEARAAARPVGTVTAAAQHHEAGAVALALLKRTVPVDAELLVREDA +PGEDGAAEGGWIAASQEPLVSPDAGQVVGRPRGVGRLR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001418.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001418.fa new file mode 100644 index 0000000000000000000000000000000000000000..5b98bfc208b6b701e72c00baf79e0b01d404c8de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001418.fa @@ -0,0 +1,35 @@ +>PROKKA_01746 +MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW +WGATRGPDGAIDGAAVLVPEGTAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREETT +SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ +AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD +AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVTLY +ASLGFELFAADAQYRRP +>PROKKA_01453 +MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW +WGATRGPDGAIDGAAVLVPEGTAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREETT +SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ +AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD +AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVTLY +ASLGFELFAADAQYRRP +>PROKKA_01131 +MAENPVPATPTDPAAPRVSEPRPDEVDAVLALADRAQAADGHPPLSDQTRVVLARGRQRW +WGVVREADGSVSGAAVLAPEGGEDSGSVLELVVDPEARRAGRGAALADAAAAAVRERGLE +STTSVWAHGMLPGSDALARRHGLEPVRELRRMRLPHEALADLPQPQLADGVALRGFVPGR +DEQAWLDANAAAFADHPEQGGLTRADLEDRMAEDWFEAEGLLLAVREEDDALLGFHWTKV +EPQAGPGPRVGEVYAVGVTPATQGLGLGRALTLAGLHRMAGQGVDVVDLYVDADNAAAVR +LYESLGFGLFAADAQHRRP +>PROKKA_01059 +MSEQPASPALPPTPGVVSPGTPSDVDAALALADRAHRSDGHPPLNDQTRAVLARDAQRWW +GLTRDEAGAVTGVAVLAPEGEAAGPGVVELAVDPAHRGAGLGAALAEAAADAVRERGEAR +RTSAWAHGALPGALALARRHGLEPVRELRRMRLDPAGLGALPPTRLPEGVTLRGFVPGRD +EDAWLALNAAAFADHPEQGSLTRADLDAREAEDWFEAAGLLLAEDAEGTPVGYHWTKVTP +AEAGAPSEGEVYAVGISPAAQGRGLGRALTLAGLHHMAGRGVDAVDLYVDADNVPAVRLY +ESLGFALAAADVQLRPAR +>PROKKA_01675 +MAEHPTPTTSDADGMPRVVTPRPEEASAVLDLADRAGAADGHPPLSDQTRVLLARGGQLW +WGATRGTDGAIDGAAVLVPEGAAAVLELVVDPTARRTGRGTVLADAAAAAVRDLAREATT +SVWAHGMLPGAVRLARRHGLEPVRELRRMRLSHAALAALPEVRLADGVALRGFVPGQDEQ +AWLDVNAAAFADHPEQGSLTRADLDDRMAEDWFDADGLLLAAREADGRLLGFHWTKVEPD +AGADGPRVGEVYAVGVSPDAQGLGLGRALTLAGLHRMAEQGVDVVDLYVDADNTAAVALY +ASLGFELFAADAQYRRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001420.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001420.fa new file mode 100644 index 0000000000000000000000000000000000000000..a97b6cc312835913351978007422e42d06b1eda2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001420.fa @@ -0,0 +1,15 @@ +>PROKKA_01748 +MENTAAQSQPEKIVHERLTVTRDPDRQRFELRQDGTFIGFLGYDQETVRGADGEDTVVLR +LQHTIIDEQFGRRGYARALVTMVLDRLRAEGDRIVPECSYVEDYLRRYPEYQDMVFHG +>PROKKA_01455 +MENTAAQSQPEKIVHERLTVTRDPDRQRFELRQDGTFIGFLGYDQETVRGADGEDTVVLR +LQHTIIDEQFGRRGYARALVTMVLDRLRAEGDRIVPECSYVEDYLRRYPEYQDMVFHG +>PROKKA_01129 +MENTAAKSQPEKIVHERLKVTRDPDRERFELRQDGTFIGFLGYAQETVPGPDGEDRTVVR +LQHTIIDEAHGRKGYARALVTMVLDRLRAEGDSIVAECSYVEDYLRRYPEYQDMVFNG +>PROKKA_01057 +METTANQHPEKIVHERLQVTRDPDRQRFEMRQDGVFIGFLGYDVEELPAADGGEDETVVR +LQHTIIDEAHGRKGYARALVTIVLDRLRAEGEKISPECSYVQDYLRRYPEYQDMVREV +>PROKKA_01677 +MENTAAQSQPEKIVHERLTVTRDPDRQRFELRQDGTFIGFLGYDQETVRGADGEDTVVLR +LQHTIIDEQFGRRGYARALVTMVLDRLRAEGDRIVPECSYVEDYLRRYPEYQDMVFHG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001421.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001421.fa new file mode 100644 index 0000000000000000000000000000000000000000..9fef71bb11e1e2c01963283e612e7ff2a8ba6ff3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001421.fa @@ -0,0 +1,30 @@ +>PROKKA_01749 +MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS +VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK +VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA +DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP +RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV +>PROKKA_01456 +MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS +VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK +VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA +DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP +RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV +>PROKKA_01128 +MSIPTPYEDLLADVMANGAVKSDRTGTGTRSVFGRQMRFDLSRSFPLITTKRVHFKSVAL +ELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAKVVE +QIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSADLF +LGVPFNIASYALLTVIVAQQTGLAPGEFVWTGGDVHIYANHEEQVREQLSREPYPYPRLW +LRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV +>PROKKA_01053 +MSIPTPYEDLLADVLAHGAVKADRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKSVAL +ELLWFLRGDSNVRWLQERGVTIWDEWADEGGELGPVYGVQWRSWPTPDGGSIDQIAKVVE +QIRTSPDSRRHLVTAWNPAEVDEMALPPCHAMFQFYVAPDVDGAPGVLSCQLYQRSADLF +LGVPFNIASYALLTLMVAQQTGLTPGEFVWTGGDCHIYANHEEQVREQLSREPYPYPTLR +IRRTPESIFDYEYDDFELVDYRHHPAIKAPVAV +>PROKKA_01678 +MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS +VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK +VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA +DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP +RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001424.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001424.fa new file mode 100644 index 0000000000000000000000000000000000000000..57108196c7ef1400238974542a55fa7645969f3c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001424.fa @@ -0,0 +1,40 @@ +>PROKKA_01752 +MRSRAASLEGMTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARVHPVF +FSTSNAGGPAPVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWD +GIWIDAASTLRMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAG +LVEWGTAMTYQAASGGGARHMRELLTQYAELGGAVRAELADPASAILEIDRKVIELQRGG +LDSTQFGVPLGGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGA +MRSHSQALTLKLTQDVPLDEVEQIIAADNEWVQVVPNTKEVTVTDLTPIAATGTLQIPVG +RLRKLNMGPEYLSAFTVGDQLLWGAAEPVRRMLMIATGNL +>PROKKA_01459 +MRSRAASLEGMTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARVHPVF +FSTSNAGGPAPVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWD +GIWIDAASTLRMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAG +LVEWGTAMTYQAASGGGARHMRELLTQYAELGGAVRAELADPASAILEIDRKVIELQRGG +LDSTQFGVPLGGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGA +MRSHSQALTLKLTQDVPLDEVEQIIAADNEWVQVVPNTKEVTVTDLTPIAATGTLQIPVG +RLRKLNMGPEYLSAFTVGDQLLWGAAEPVRRMLMIATGNL +>PROKKA_01125 +MTSAAPPPSPPPDAAAVPTVGLIGWRGMVGSVLMQRMAEEGDFARIRPVFFSTSNAGGPA +PTFEGLPGDAGPLQDAYDLNVLASLPVIVTAQGGDYTKDVYPRLRAAGWDGIWIDAASTL +RMEDTSVIALDPVNRSVIDAALASGVKDFIGGNCTVSCMLMGLGGLFKAGLVEWGTAMTY +QAASGGGARHMRELLTQYADLGGVVRDELADPASAILEIDRKVLELQRDGLDATQFGVPL +GGSLIPWIDSDLGNGVSREEQKAFDETNKVLGLRGEDRIAFDSLCVRIGAMRSHSQALTL +KLTRDVPLDEVEQIIAEDNEWVRLVANTKEASVAELTPIAATGTLQIPVGRLRKLNMGPE +YLSAFTVGDQLLWGAAEPVRRMLMIATGNL +>PROKKA_01050 +MTSAAPAPVSPAAPAAVPTVGIVGWRGMVGSVLMQRMAEEGDFARIHPVFFSTSNAGRPA +PVFEGMDGDAGTLQDAHDVEALKALPIIVTAQGGDYTKAVYPALRAAGWDGIWIDAASTL +RMEDSSVIVLDPVNRSVIDAALASGTKDFIGGNCTVSCMLMGLGGLFREGLVEWGTAMTY +QAASGGGARHMRELLTQYAALGGVVAEELADPSSAILEIDRKVLELQRGGLDASQFGVPL +GGSLIPWIDSDLGNGVSREEQKAYDETNKVLGLTGDDRIPFDSLCVRIGAMRSHSQALTL +KLTRDVPLDEITEIVADGTEWAQVVPNEKEASLRDLTPIAASGTLQIPVGRLRKLNMGPE +YLSAFTVGDQLLWGAAEPIRRMLMIATGNL +>PROKKA_01681 +MTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARIHPVFFSTSNAGGPA +PVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWDGIWIDAASTL +RMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAGLVEWGTAMTY +QAASGGGARHMRELLIQYAELGGAVRAELADPASAILEIDRKVIELQRDGLDSTQFGVPL +GGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGAMRSHSQALTL +KLTRDVPLDEVEQIIAADNEWVQVVPNTKEATVTDLTPIAATGTLQIPVGRLRKLNMGPE +YLSAFTVGDQLLWGAAEPVRRMLMIATGNL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001425.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001425.fa new file mode 100644 index 0000000000000000000000000000000000000000..9965d9a05ec711535e9523bd113d6f0d2f32afde --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001425.fa @@ -0,0 +1,40 @@ +>PROKKA_01753 +MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP +GTVVRLAFEGIHVLDGPLPGEGETPPAGDGARSADHEGEAVVVRIAAGHPWDDAVAWTVA +HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY +RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL +AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG +TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN +RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL +>PROKKA_01460 +MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP +GTVVRLAFEGIHVLDGPLPGEGETPPAGDGARSADHEGEAVVVRIAAGHPWDDAVAWTVA +HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY +RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL +AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG +TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN +RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL +>PROKKA_01124 +MSERLAEHTTTRVGGPARAWETARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP +GTVVRLAFEGIEVRAGDEAHGGDADDQDPAAGGDRAGEAVVVRVAAGHPWDDAVAWTVEH +GLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVSLRAWDREAGQVVELGAEELEFDYR +DSIIKRSMLETGAPSPRWIVLSIDLRLRRASGAAEPTAPVRYGQLASALDVAEGTHAPLA +VVRREVLALRAAKGMVSDPQDPDTWSTGSYFTNPIVPAAVRASLPEGAPAFAAGRAADGT +ELVKLSAAWLIDHAGFAKGFGLPDVAPREGGPDGRGADGAGLAGGRASVSTKHTLAMTNR +GDASTEDVLTIARTVRDGVKARFGVDLHPEPMIIGTSL +>PROKKA_01049 +MSERLSDHTTTRVGGPARAWVEARTEAEAVAAVRAADAAGEPLFVLGGGSNTLMADAGFE +GTVVHMGFTGVEVLPAEGAADGAGDVVVRVAAGHVWDEAVAWTVEHGLAGVEALSGIPGS +AGATPVQNVGAYGADVSQVLVSLRAFDRAAGQVVELSAEDLRFGYRDSVIKRSMFEDGSP +SPRWIVLSIDLRLRRAEEGAEPTAPVRYAQLARALEVEEGADVSLAQVREHVLALRASKG +MVSDAADHDTWSTGSYFTNPIVPATVRVTLPEGAPAFAAGTDEDGTPLVKLSAAWLIDHA +GYGKGFGLPDAPRREGDADGSGPDGRGLAGGRAALSTKHTLAVTNRGGASTEDVLTVARA +VRDGVKARFGVDLHHEPMIIGTRL +>PROKKA_01682 +MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADSGFP +GTVVRLAFEGIGVLDGPVPGEGEAPPVGDGARLADHEGEAVVVRVAAGHPWDDAVAWTVA +HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY +RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL +AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG +TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN +RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001426.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001426.fa new file mode 100644 index 0000000000000000000000000000000000000000..2b8b1179c2d4ee110a381b72824094a036f45847 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001426.fa @@ -0,0 +1,20 @@ +>PROKKA_01754 +MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPSFAEHVGLPGVIAHG +MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGRTDDDGAPVPGATLEVVGTVG +AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA +>PROKKA_01461 +MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPSFAEHVGLPGVIAHG +MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGRTDDDGAPVPGATLEVVGTVG +AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA +>PROKKA_01123 +MSTAPRLSELSKGETIGTRTVPLTRADLVAYAGASGDHNPIHWSPSFAERVGLPGVIAHG +MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTGQTGDDGAPVPGATLQVVGKVG +AVDEAAGTVRIDLDVTNPDAEKPRVLTKAQAVVRLAEPAPAAGESA +>PROKKA_01048 +MRAQSARPVLAELAKGQSIGSRTVPLTRAGLVAYAAASGDHNPIHWNQAFAASVGLPGVI +AHGMLTMGAAVQLVTDWAGDPGAVVDYQTRFTAMVPVADTTGQTDDAGAPVPGAVLEVSG +AVGAIDAEAGTVRIDLTVNDPAQAKPRVLTKAQALVRLTRAVETPEETA +>PROKKA_01683 +MSTAPRLSDLARGEVVGTRTVTFTRADLVAYAGASGDRNPIHWSPTFAEHVGLPGVIAHG +MLTMGAAVQLVSDWAGDPGAVVDYQTRFTGMVPVADTTVRTDDDGAPVPGATLEVVGTVG +AVDEAAGTVRIDLNVTNPDAAKPRVLTKAQAVVRLADPAGESA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001428.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001428.fa new file mode 100644 index 0000000000000000000000000000000000000000..8f41e342890f191f69204db118789ffc747fde91 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001428.fa @@ -0,0 +1,15 @@ +>PROKKA_01756 +MSTRRPAHQPTRGTAAPRGFVSPWEHGSRLYRTLVLTGSALFLVGIVLAVVGGTTGRLAV +SGTALGVLGAGVAVHLSAQLVRFRQAARRQGERRPGR +>PROKKA_01463 +MSTRRPAHQPTRGTAAPRGFVSPWEHGSRLYRTLVLTGSALFLVGIVLAVVGGTTGRLAV +SGTALGVLGAGVAVHLSAQLVRFRQAARRQGERRPGR +>PROKKA_01121 +MSSHRPSSQRRPDRGPSTGPQRAGFVSPWENGSALYRALVLTGSALFLVGIVLAVVGATT +SQLTVSWFALGVLGLGVVVHLSAQMVRFRQAARRQGQRPPGR +>PROKKA_01046 +MPTSARRPEPSARSGGFVSPWEHGSRLYRGMVLTGSALFLIGIVLSVVGATAHVLALSWT +ALGVLGAGVLVHLSAQLVRLREAGRRESAARSARRKGRGSGR +>PROKKA_01685 +MSTRRPAHQPTRGTAAPRGFVSPWEHGSRLYRTLVLTGSALFLVGIVLAVVGGTTGRLAV +SGTALGVLGAGVAVHLSAQLVRFRQAARRQGERRPGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001430.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001430.fa new file mode 100644 index 0000000000000000000000000000000000000000..219af5364e391a2ca5a040369ffd0ff56c9f41b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001430.fa @@ -0,0 +1,26 @@ +>PROKKA_01760 +MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER +DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG +MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA +NGLLIILAVVMLLGAALVWLPPVRSRVRR +>PROKKA_01467 +MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER +DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG +MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA +NGLLIILAVVMLLGAALVWLPPVRSRVRR +>PROKKA_01117 +MPQNSEDRPLARGLGRAAGRAARSFQESQRADDARLRAERARLAAEDEERLSRRREDRER +GLAERDAAESDAGLVHPLLRIARMYWLALTVVLAVVAGAFVWNGMRARESGEPVVDPLTG +IESVGVLGGATGQFTMGVTVALFAAAALWGWIGLLRRRRSAIGTLTFIALLLAAPAFLRA +NGLLIVLAVIMLVGAALLWLPPVRSRLRR +>PROKKA_01042 +MADNSAENSSDRIARAAGRAARAFREGQDAERIRREQARAEAPRTADADGSRATGLRERA +VRAAAQAAERAEPLKERVGHAAGEAGRSFKENQAQDAARLRGVREQVRADDDAARAERQA +ERERALDARDETEAGRVHPLLRLTRLWWLAVSLLLLGLATAFVYNGVRADRDGGEVIDPV +TGLQSIGPLGGATGQYTVGGVLAALALVTLWGWVGLLRRRRASLGTLTTVAVLLAIPAVL +RPNPLFIVLGAAMAIGAVLLWLPPVRSRVRR +>PROKKA_01689 +MPQNSEDRPLARGLGRAAGRATQSFRENQRADDARLRAERARLTAEDEERLERRRADRER +DLAARDAAESDAGLVHPLLKVARLYWLAVTVVLVGIAGAFIWNGARAQDSGEPVIDPLTG +MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA +NGLLIILAVVMLLGAALVWLPPVRSRVRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001431.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001431.fa new file mode 100644 index 0000000000000000000000000000000000000000..e622c9810440f86aa2fdf52cfe74dc0c1e2a32dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001431.fa @@ -0,0 +1,40 @@ +>PROKKA_01761 +MTLTAFVNAHVVPVAAEPFDGALLVEDGRITALGPDVEAPDGAEVVDCEGRWVLPGFVDA +HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG +NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA +FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF +GYDLVLDHGTEAHPLAGQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI +ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL +WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED +>PROKKA_01468 +MTLTAFVNAHVVPVAAEPFDGALLVEDGRITALGPDVEAPDGAEVVDCEGRWVLPGFVDA +HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG +NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA +FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF +GYDLVLDHGTEAHPLAGQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI +ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL +WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED +>PROKKA_01116 +MTVTAFVNAHVVPVESAPFDGALIVEDGRITALGPDVAAPEGADVVDCEGKWLLPGFVDA +HVHLGMHAEGEVGTTSDVNEMTDPVMAGVRAIDAVDPNEPGWRDALAGGVTTVNVNPGSG +NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA +FLKAQGYLARQEEAEREGKPFTKDPHMEALGQVLRREIPWRQHCHRTDDIATALRIADEF +GYELVLDHGTEAHPVADLLAERGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI +ITDHPVIPIDFLVYQAALSVKEGLDPETALRAITLNPAKVLGLDDRIGSLAVGKDADLVL +WSGDPLDVMQRALRVWIGGRCVMEYDLATARPVVASARPVED +>PROKKA_01041 +MSITAFTNVHVVPVESDPFDGVLLAEDGRISALGPDVEIPAGADVVDCGGRWLLPGFVDA +HVHLGMHAEGEVGATADVNEMTDPVMAGVRALDAVDPNEPGWRDALAGGITTVNVNPGSG +NPIGGQAVAMHTHGRTVDEMVLRAPSGVKSALGENPKTVYKEQGRTPSTRLGTALVIRRA +FMEAQGYMARRTEAEADGKPFTKDPHMEALALVLERRIPWRQHCHRTDDVATALRIADEF +GYDLVLDHGTEAHPLADVLAERGVPVLIGPLFTTKSKPELRGRSLRNPGRLARAGVEISI +ITDHPVVPIDFLVYQAALAVKEGLDRDTALRAITLNPAKVLGLADRIGSLAPGKDADLVL +WSGDPLDVMQRALRVWIGGRPVMEYDAAAARPVVASARPAED +>PROKKA_01690 +MTLTAFVNAHVVPVAAEPFDGTLLVEDGRITALGPDVEAPDGAEVVDCEGRWLLPGFVDA +HVHLGMHAEGEVGATADVNEMTDPVMAGVRAIDAVDPNEPGWKDALAGGVTTVNVNPGSG +NPIGGQAVALHTHGRTVDEMVLRSPSGVKSALGENPKNVYKEKGRTPSTRLGTALVIREA +FLRAQGYMARRAEAEREDKPFTRDPHLDALALVLERTIPWRQHCHRTDDVATALRLADEF +GYDLVLDHGTEAHPLADQLAARGVPVLIGPLFTTKSKPELRGRSMRNPGRLARAGVEISI +ITDHPVVPIDFLVYQAALSVKEGLDRETALRAITLHPARVLGLDDRIGSLEVGKDADLVL +WSGDPLDVMQRALRVWIGGRQVMEYDLATARPVVASARPVED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001432.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001432.fa new file mode 100644 index 0000000000000000000000000000000000000000..024dc3387ff9ac8eee594b11b8855038e0af5a55 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001432.fa @@ -0,0 +1,40 @@ +>PROKKA_01762 +MTEQNVHEDPHATTPDTGAEDAAAHPQGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA +PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM +GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAAAGPVMV +WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG +GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA +VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF +QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL +>PROKKA_01469 +MTEQNVHEDPHATTPDTGAEDAAAHPRGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA +PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM +GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAAAGPVMV +WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG +GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA +VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF +QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL +>PROKKA_01115 +MTTHEQRPAGFGTRAVHAGQDLDEVYGAVVPPVHLSSTYAPVRVGELRRGYDYGRGTNPT +RDALQTQLAALEAGVGEDGTPNALALTFASGLAAETALIMGAAEPGTTIVMGNDVYGGSY +RLISKVLAKWGIRHAVVDMGDTAKVAAAVESAAAQGPVMVWLETPSNPLMKVSDIAAIAE +VAHGHDALLVVDNTFATPYLQTPLALGADVVVHSTTKYIGGHSDVIGGALVIKDPELGAQ +VQFQQFAAGAVNGPWDAYLTTRGLKTLGVRMDRHQANAQAVAEWLAGRPEVTQVLYPGLP +DHPDHELAARQMRGFGGMVSFRLTGGAAAARTVAESTRLFQLAESLGGIESLMNYPAEMT +HASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALEALAG +>PROKKA_01040 +MTEQNAHEQPHDTAPTGPEATEGPAEGFGTRAVHAGQHLDEVYGAVVPPLHISSTYAPTA +IGELRRGYDYGRGTNPTRDALQEQLAALEAGVDDAGTPKATGLTFASGLAAETALIMGAG +QPGMTIVMGNDVYGGSYRLISRVLKPWGVDHAVVDMGEPEQVAAAVEQAAASGPVMVWLE +TPSNPMMKISDVAAVAEAAHGRGAQLVVDNTFATPYLQNPIALGADVVVHSTTKYIGGHS +DVIGGALVIPDAELAEKVKFQQFAAGAVNGPVDAYLTTRGLKTLGVRMDRHQANAQALAE +WLTEQSAVSQVLYPGLPDHPGHELAKRQMRGFGGMVSVRFHGGAAAAKKVAESTRLFQLA +ESLGGIESLMNYPAEMTHASVAGTELAVPDDLVRLSVGIEDASDLIADLEQAIAGLAG +>PROKKA_01691 +MTEQNVHEDPHATTPDTGAEDAAAHPRGGGFGTRAVHAGQHLDEVFGAVVPPIHLSSTYA +PTAVGELRRGYDYGRGTNPTRDALQEQLAALEAGVDESGAPRATGLTFASGLAAETALIM +GAGRPGMTIVLGNDVYGGSYRLISRVLAPWGVEHVVVDMGDAEQVAAAVERAAATGPVMV +WLETPSNPMMKISDVAAVAEAAHAHGALLVVDNTFATPYLQSPIALGADVVVHSTTKYIG +GHSDVIGGALVIPDAALAEQVKFQQFAAGAVNGPMDAYLTTRGLKTLGVRMDRHQANAQA +VAEWLTGRAEVSQVLYPGLPDHPGHELAQRQMRGFGGMVSLRLSGGAAAARRVAESTRLF +QLAESLGGIESLMNYPAEMTHASVAGTELAVPDDLLRLSVGIEDAEDLVADLERALGSL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001434.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001434.fa new file mode 100644 index 0000000000000000000000000000000000000000..1e48d40afabfc6a603cada60c053e49fca33daeb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001434.fa @@ -0,0 +1,35 @@ +>PROKKA_01764 +MIAPDAERCVRVPVPVDVALTLRPLQRGAADPTVRATPQGVWLTLRSPAPDAASGGPGRP +TSLLVSGVRETAGGGTAVTARAWGAGARTAVADVERLLGLHDDGWAAFDALLRPDSGAPA +LPRHVREARRTRAGLRLPAAGALSRQLLTAVLEQKITHDQARHGWRTLVRLAARIDGDGP +APGPVPPGMLPPPTPAAVLRIPSWDWHARAWVQPSQSRTVLEVARRAASIDRLGDAVAPG +DTAGVAALARRLESVPGIGPWTTAEALQRSHGAADLVSVGDYHLAQYVGQVLTGRRTDDA +GMLRLLAPWAGHRQRVVRMIGLSGERKQAFGPKLAPADHRAH +>PROKKA_01471 +MTAPDAERRVRVPVPVDVALTLRPLQRGAADPTVRATPQGVWLTLRSPAPDVASGGPGRP +TSLLVSGVREAAGGGTAVTARAWGAGASAAVAGVERLLGLHDDGWDAFDALLRPDSGAPA +LPPHVREARRMRAGLRLPAAGALSRQLLTAVLEQKVTHDQARHGWRTLVRLAARIDDDGP +APGPVPPGMLPPPTPAAVLRIPSWDWHARAWVQPSQSRTMLEVARRAASIDRLGDAVTPG +DTAGVAALARRLESVPGIGPWTTAEALQRSHGAADLVSVGDYHLAQYVGQVLTGRRTDDA +GMLRLLAPWAGHRQRVVRMIGLSGERKQGFGPKLAPADHRAH +>PROKKA_01113 +MSAPDAVRRVRVPVPVDVPLTLRPLQRGAADPTVRAVPEGVWLTLRVPDQGAPAGSPGRP +TSLLVSGAREAAGPGTVVTARAWGPGARAAVASVERLLGVDDAGWDAFDALLHRDSSAPA +LPRHVREARRTRAGLRLPAAGALSGQLITVVLEQKVTHDQARHGWRTLVRLAARIDDDGP +APGPVPSGMLPPPSPAAVLRIPSWDWHARAWVQPAQSHTVLEVARRAASIDRLGAAVAPG +DTAGIAALARRLESLPGIGPWTTAEALQRSHGAADLVAVGDYHLAQFVGQVLTGRRTDDA +GMLRLLEPWAGHRQRVVRMIGISGARKQAFGPKLAPADHRAY +>PROKKA_01038 +MVPPLSVPPDAVVRLAPGVPVDVAATLRPLQRGAADPTVRAAPTGVWLTRRERVDGATLP +ATLLVSPQVRGEVTARAWGPGAAAALAGLPALLGLHDTGWDAFDALLAPDPRRPSLPHAL +REARRTREGLRLPAAGHLSTQLMTVVLEQKVTHDQARHGWRTLVRLAHGIDDATPPGPAP +AGMLLPPTPRAVLAIPSWDWHARAWVQPAQSRTVLEVARRASAVDRLGAAVAPGDVAGTA +ALAARLQAIPGVGPWSAAEALQRSHGSADLVSVGDFHLAHLVGQVLAGRRTDDAGMLRLL +QPWEGHRQRVVRMIGASGASKERFGPRLAPADHRAY +>PROKKA_01693 +MTAPDAERRVRVPVPVDVALTLRPLQRGAADPTVRATPQGVWLTLRSPAPDAASGGPGRP +TSLLVSGVREAAGGGTAVTARAWGAGASAAVAGVERLLGLHDDGWGAFDALLRADSGAPA +LPRHVREARRTRTGLRLPAAGALSRQLLTVVLEQKVTHDQARHGWRTLVRLAARIDDDGP +APGPVPPGMLPPPTPAAVLRIPSWDWHARAWVQPSQSRTMLEVARRAASIDRLGDAVAPG +DTAGVAALARRLESVPGIGPWTTAEALQRSHGAADLVSVGDYHLAQYVGQVLTGRRTDDA +GMLRLLAPWAGHRQRVVRMIGLSGERKQAFGPKLAPADHRAH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001437.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001437.fa new file mode 100644 index 0000000000000000000000000000000000000000..3070ad3f66d006d81d303e3bbe429cf8d124ff4a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001437.fa @@ -0,0 +1,20 @@ +>PROKKA_01769 +MLYLIDPRGAVWSADTTIGRARARARVDGRPVDDLKFAKAAMLLTFDDHVDLALRHGVAA +PRGLLLDHGFVAQVLAPANLKAQRANQDAIAEQLAVVERRTEDVGSLRSHRHAAAYEGAD +QSLERRIKKAEEAARETLQAAPDEDLVRHWTRLGGAVPATLQAGRDR +>PROKKA_01476 +MLYLIDPRGAVWSADTTIGRARARARVDGRPVDDLKFTKAAMLLTFEDHVDLALRHGIAA +PRGLLLDHGFVAQVLAPANLKAQRANQDAIAEQLAVVERRTEDVGSLRSHRHAAAYEGAD +QDLERRIKKAEEAARETLQAAPDEDLVRHWTRLGGAVPATLQADRDR +>PROKKA_01108 +MLYLIDPRGAVWSADATIGQARARARVDGRPIDDLKFARAAMLLTLDDYVDLALRHGVEA +PRGILLDHGFVAQALAPANLKAQRANQDAMAEQLLPVERRTEDAGSLRGHRHDAAYEGAH +QDLDRRIKKAEETARETLQKTPDEDLIRHWRRLGGDVPATIEADRKD +>PROKKA_01034 +MLYLIDPRGAVWQSDVTLGRALARQKVDGRPVDDVPLKKAVLPIDEADVLDLGLRHGVAA +PRGILLDGGWVTQVLQPSQLKRQRANQDATADQLEPVELRTETDSLRSSRHAAVVEGAHR +DLDTRIEKAEKAAREALQAAPRRELVTHWRGMGGGLPATIQADLADAD +>PROKKA_01698 +MLYLIDPRGAVWSADTTIGRARARARVDGRPVDDLKFTKAAMLLTFEDHVDLALRHGIAA +PRGLLLDHGFVAQVLAPANLKAQRANQDAIAEQLAVVERRTEDVGSLRSHRHAAAYEGAD +QDLERRIKKAEEAARETLQAAPDEDLVRHWTRLGGAVPATLQADRDR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001440.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001440.fa new file mode 100644 index 0000000000000000000000000000000000000000..eb0ebbf93a0cc2e8968f3fdf0947264098ef27d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001440.fa @@ -0,0 +1,20 @@ +>PROKKA_01773 +MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL +REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW +RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDGEGLDR +>PROKKA_01480 +MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL +REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW +RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDDEGPDR +>PROKKA_01104 +MPAKPPAPVHLPAFQRLVPDLLGDAWAEDDGLSPADVEARLGQSPAAGQLGAGFMVPAAL +REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDAEETVVWGLPVDNLALPDPLVW +RRSSGAEAEEGDWQDEGGTFSEFITDLLAWTFEDPEDDDGRDER +>PROKKA_01029 +MPAKPPAPVYLPGFQRLVPDLLGDTWAKDDGLAPADVEARLAESPAAEQLGTGFMVPAAL +REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDEGETVVWGLPVDNLALPDPLVW +RRDTGADAEEGDWQDEGGTFSEFITDLLVWTFEDPEDDAAEDAR +>PROKKA_01702 +MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL +REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW +RRSAGADAPEGEWQDEGGTFSEFLTDLLAWAFEDPEDDDEGPDR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001441.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001441.fa new file mode 100644 index 0000000000000000000000000000000000000000..aeb9cff25687583ef320e9ff1d88ef299d6e27e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001441.fa @@ -0,0 +1,20 @@ +>PROKKA_01774 +MTAPAPVSHAPDDYVCPFCGLVASDVSDPGNRCELGDTVYQDEDLLVLIAVDGFGDHEGH +AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPDGVSTRQHNEPAGNQHVWHY +HLHVFPRFEGDMLYRQLRHPVAPEVRAGKARELAAALDPAPTRLD +>PROKKA_01481 +MTAPAPVSHAPDGYVCPFCGLVAGDVSDPGNRCELGDTVYQDEDLIVLIAVDGFGDHEGH +AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPDGVSTRQHNEPAGNQHVWHY +HLHVFPRFEGDMLYRQLRHPVAPEVRAGKARELAAALDPAPTRLD +>PROKKA_01103 +MSGPRLRSHAPEGYVCPFCGLVAGDVSDPGNRCELADTVYQDEDLLVLIAVDGFGDHEGH +AMVCPAGHYENLYELPPRVLQRIALMAREVALAMKRAWSPDGVSTRQHNEPAGNQHVWHY +HLHVFPRFEGDLLYRQLRHPVSPEVRALKARELAAELDPAPTFLD +>PROKKA_01028 +MSAQPLSHAPEGYVCPFCGLVAGDVSDPGNRCELEDTVYQDEDVLVLIAVDGFGEHDGHA +MVCPSGHYENLYDLPPRVLQRIALMAQQVALAMKRAWGPDGVSTRQHNEPAGNQHVWHYH +LHVFPRYEDDLLYRQLRHPVAPEVRAARARELAAALDPAPTLLD +>PROKKA_01703 +MTAPAPVSHAPDGYVCPFCGLVAGDVSDPGNRCELGDTVYQDEDLLVLIAVDGFGDHEGH +AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPEGVSTRQHNEPAGNQHVWHY +HLHVFPRFEGDMLYRQLRHPVAPEVRALKARELAAALDPVPTRLD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001442.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001442.fa new file mode 100644 index 0000000000000000000000000000000000000000..3eade8ae04512ddf0ee0ded5ed51d7ee60e9f9d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001442.fa @@ -0,0 +1,36 @@ +>PROKKA_01775 +MTTADPGFALPSGFEPLAEHGRVLEVVLTALEQVEEQLDTALGFDDLFSDTAAHHLLAAG +GKRVRPVLTVLASLLGDPALASGEVADVDAPARQAAVVMELTHLATLYHDDVMDEAPVRR +GAPAAHRLWGNSAAILAGDLIFARASQLMAELGPRPVQIQADTFERLVQGQLWETRGPAE +GADPIEHYYAVLSGKTGSLIAAAGMLGALLGGADEAAVQVMRAYGEKVGLAFQLADDLID +LTGDAERIGKVPGTDLRERVPTLTTLLLARAAQGEGPEAEDARRVRALVDGPLDTDEQLA +AAVAALTGHPAIDEAWAITRGWAEQAKQALDPLPDSAVKAALEAFADYVVGRSA +>PROKKA_01482 +MTTADPGFALPSGFEPLAEHGRVLEVVLTALEQVEEQLDSALGFDDLFSDTAAHHLLAAG +GKRVRPVLTVLASLLGDPALASGEVADVDAPARQAAVVMELTHLATLYHDDVMDEAPVRR +GAPAAHRLWGNSAAILAGDLIFARASQLMAELGPRPVQIQADTFERLVQGQLWETRGPAE +GADPIEHYYAVLSGKTGSLIAAAGMLGALLGGADEAAVQVMRAYGEKVGLAFQLADDLID +LTGNAERIGKVPGTDLRERVPTLTTLLLARAAQGEGPEAEDARRVRALVDGPLDTDEQLA +AAVAALTGHPAIDEAWAITRGWAEQAKQALDPLPDSAVKAALEAFADYVVGRSA +>PROKKA_01102 +MSTADPGFALPSGFEPLAEHGRVLEVVLTGLEQVEEQLDRAVSFEDPFSDTAAHHLLAAG +GKRVRPVLTVLASLLGDPALASGEVADVNAQVRQAAVVMELTHLATLYHDDVMDEAPVRR +GAPAAHRLWGNSAAILAGDLIFARASQLMSELGMRPVRVQADTFERLVQGQLWETQGPAE +GADPVEHYYRVLAGKTGSLIAAAGMLGALLGGADEEAVQVMSAYGEKVGLAFQLADDLID +LTGTAEQIGKTPGTDLRERVPTLTTLLLDRAAAGEGPDAQEARRVRALVDGPLDTDEQLA +AAVAALTAHPAIDEAWAVTRAWVDDAKQALAPLPDSVVKTSLEGFADYVVERSAWPGARP +RAVHRRAAVRAPLGGADLSPGRSGPGRARRRAPGP +>PROKKA_01026 +MTTSAAGFALPSGFDPLAEHGRVLEAVLTALERVEEQLTASLEFDDVFSQTATRHLASAG +GKRVRPVLTVLASLLGDAGLAEGQVGEVGPETRQAAVVMELTHLATLYHDDVMDEAPVRR +GAPAAHRLWGNSQAILAGDLIFARASQLMAELGPRPVRIQAETFERLVQGQLWETRGPDE +GQDLLEHYYRVLRGKTGSLIAAAGVLGAYLGGADETAVQVMADYGEKVGLAFQLADDLID +LTSSAEELGKTPGTDLREHVPTLSTILVARAAAGEGPEADDARRVLALVDGPLDTDEQLA +AAVAALTAHPAFAEAGALTRRWAEEAKAALAPLPESVVTEALAAFADYVVSRAS +>PROKKA_01704 +MTTADPGFALPSGFEPLAEHGRVLEVVLTALEQVEEQLDTALGFDDLFSDTAAHHLMAAG +GKRVRPVLTVLASLLGDPALASGEVADVDAPARQAAVVMELTHLATLYHDDVMDEAPVRR +GAPAAHRLWGNSAAILAGDLIFARASQLMAELGPRPVQIQADTFERLVQGQLWETRGPAE +GADPIEHYYAVLSGKTGSLIAAAGMLGALLGGADEAAVQVMRAYGEKVGLAFQLADDLID +LTGDAERIGKVPGTDLRERVPTLTTLLLARAAQGEGPEAEDARRVRALVDGPLDTDEQLA +AAVAALTGHPAIDEAWAITRDWAEQAKQALAPLPDSAVKTALEAFADYVVGRSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001444.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001444.fa new file mode 100644 index 0000000000000000000000000000000000000000..b137d705dfc813c498b0cf2fb543d39c27feb4e9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001444.fa @@ -0,0 +1,60 @@ +>PROKKA_01777 +MTSVDSLSVARAVATALIDAGMRDAVVCPGSRSAPLAYALAALEHAGQVRLHVRVDERSA +GFLAHGLSLASGRPVGVLTTSGTAVGNLVPALMESFHAGTRVIALTADRPPELHGTGANQ +TTDQRDVFGTHVRHAASLGCDAADGVDTEQHLRHVRATVRRALLAAEGVVAETDSDDGAP +GPVTMAEAPAGPVHLNLHFRDPLVPSPEEAAAMGAAAAAPHTPAPAVAPTGASPAAAASA +YRAPGAVLSGLPELDVARLDQRRTVVLACHGAGPVAAAFALSLGLPLLAEPSSNARFSAN +AIAAYPLLLGAAGGRDADAHPLAARIQRVVLFGRPTLTRTVNALLARPDVATALHAPEPA +PWFEPGRRRETPVETLEELAAFAGQGEPGWLAAWQHASMRAQAAVEDVLVTTDAGDRLSP +QTVAHVSAAMVRGPLVLGSSSVIRDVDLTWRPPSAPDAEVYANRGLAGIDGTVSTAAGVA +LARGRRTVALLGDLTALHEAGGLLVGPTETEPDLDLVVLNDNGGAIFASLEHGAVAEAPG +MADPVERLFGTPHGVDLAALAAAYGVPHTRVTDRVDLVRALSDPVRGRRLLEVRCDRADR +PRVAAALAAAVRATFPPACPVPDPAPDAGPAPAPPTAELAAEEAPQ +>PROKKA_01484 +MTSVDSLSVARAVATALIDAGMRDAVVCPGSRSAPLAYALAALERAGEVRLHVRVDERSA +GFLAHGLSLASGRPVGVLTTSGTAVGNLLPALMESIHAGTRVIALTADRPPELHGTGANQ +TTDQRGVFGTHVRHAASLGCDAADGVDAEQHLRHVRATVRRALLAAEGVVAEAGSDDGAP +GPVTMAEAPAGPVHLNLHFRDPLVPSPEEAAAMGAAAAPHTPAPAVAPTGASPAAAASAY +RAPGAVLSGLPELDVARLDQRRTVVLACHGAGPVAAAFALSLGLPLLAEPSSNARFSANA +IAAYPLLLGAAGGRDADAHPLAARIERVVLFGRPTLTRTVNALLARPDVATALHAPEPAP +WFEPGRRRETPVETLEELAAFAGQGEPGWLAAWQHASMRAQAAVEDALVTTDAGDRLSPQ +TVAHVSAAMVRGPLVLGSSSVIRDVDLTWRPPSAPDAEVYANRGLAGIDGTVSTAAGVAL +ARGRRTVALLGDLTALHEAGGLLVGPTETEPDLDLVVVNDDGGAIFASLEHGAVAEAPGM +ADPVERLFGTPHGVDLAALAAAYGLPHTRVTDRVDLVRALSDPVRGRRLLEVRCDRADRP +RVAAALAAAVRATFPPACPVPDPAPDAGPAPAPPTAELAAEEAPQ +>PROKKA_01100 +MTSVDSLSVARAVADALIEAGMRDAVVCPGSRSAPLAYALAERERAGAVRLHVRVDERSA +GFLAHGLSLASGRPVGVLTTSGTAVGNLLPALMESFHAGTRVIALTADRPTELHGTGANQ +TTSQEGVFALHVRHAASIGCDAPAGRDADAHLRAVGAVVHRALLAADGVVADGPGHDDGG +HVPEPGPVTVGEAPAGPVHLNLQFRAPLVPAPDEAAAMGSARQSAPQSPADPASEAAVHS +AYRAPGALLSGFPELDVARLTQRRTVVLACHGAGPVAAAFALALGLPLLAEPSSNARFSV +DAIAAYPLLLGSAGGRGPDSHPLAGRIERVVLFGRPTLTRPVTALLAREDVETVLFAPEP +APWFEPGRRRERPIETLEELADFAGHGEAGWLSAWQRASMRAQAAVEDVLVAEDLRHGLS +PQSVAQVGAAVTRGPLVLGSSSVIRDVDLTWRPPTAPDAEVYANRGLAGIDGTVSTAAGV +ALARGMRTVALLGDLTALHDVGGLLVGPTEVEPDLELVVVNDDGGAIFAGLEHGAVAAVP +GLAAPVERLFATPHGVDVAALAAAYGIPHVAVSDRVGLIHCLADPVRGRRIVEVRCSRAD +RPRVAAALAEAVRATFPAAADSAPADTDPAPADPAAEEAPQ +>PROKKA_01024 +MSSVDSTTLARTVAAALLEGGMREAVVCPGSRSAPLVYALAEAERRGRIRLHVRVDERSA +AFLAHGISLATGRPVGVLTTSGTAVGNLLPALMEAFHAGTRLVALTADRPAEMHGTGANQ +TTRQDGLFALHTRGAASISADLAPGEGAEEHLGRVAATVRRLLVRAEGLVVDPAAARPDL +AEAPAGPVHLNLPFRAPLVPDAGQLAAMAAPAAPGDDADRPAEPAPWRAPGSDLTARVDL +DVSRRPERRTVVLACHGAGPVAAAFAMALGLPLLAEPSSNARFTVNAVAAYPLLLGPAGG +APGSDQGHPLAECIERVVLFGRPTLTRTVTALLDRPDVEAVLYSPEPAPWFEPGRRPERV +VTDLGELADFAGQGAAGWVPAWQRASHRAQNAVEDALVRADRRHGLSPQSVAHVVPAVTR +GPLVLGSSSLIRDVDLTWRPPTAPDAGVFANRGLAGIDGTIATAAGVALGTGRRTVALIG +DLTALHDAGGLLVGDGEPEPDLDVVVVNDAGGAIFAGLEHGQVAGHAGMADVVERFFGTP +HRVDLAALAAAYGVPHVLVEDRVELVHVLGAPERGRRLVEVRVHRADRPAVAAAIARAVA +EAVAADPVPACTGAAAPEEES +>PROKKA_01706 +MTSVDSLSVARAVATALIDAGMRDAVVCPGSRSAPLAYALAALERAGEVRLHVRVDERSA +GFLAHGLSLASGRPVGVLTTSGTAVGNLLPALMESIHAGTRVIALTADRPPELHGTGANQ +TTDQRGVFGTHVRHAASLGCDAADGVDAEQHLRHVRATVRRALLAAEGVVAEAGSDDGAP +GPVTMAEAPAGPVHLNLHFRDPLVPSPEEAAAMGAAAAPHTPAPAVAPTGASPAPAASTY +RAPGAVLSGLPELDVARLDQRRTVVLACHGAGPVAAAFALSLGLPLLAEPSSNARFSANA +IAAYPLLLGAAGGRDADAHPLAARIERVVLFGRPTLTRTVNALLARPDVATALHAPEPAP +WFEPGRRRETPVETLEELAAFAGQGEPGWLAAWQHASMRAQAAVEDVLVSTDAGGRLSPQ +TVAHVSAAMVRGPLVLGSSSVIRDVDLTWRPPSAPDAEVYANRGLAGIDGTVSTAAGVAL +ARGRRTVALLGDLTALHEAGGLLVGPTETEPDLDLVVVNDDGGAIFASLEHGAVAEAPGM +ADPVERLFGTPHGVDLAALAAAYGLPHTRVTDRVDLVRALSDPVRGRRLLEVRCDRADRP +RVAAALAAAVRATFPPACPVPDPAPDAGPAPAPPTAELAAEEAPQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001445.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001445.fa new file mode 100644 index 0000000000000000000000000000000000000000..e4339366ffda450ef840376b14e2eceff7e0af0c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001445.fa @@ -0,0 +1,31 @@ +>PROKKA_01781 +MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP +DVTSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLAGSNLTTQLLKAALPRPE +HADGVPWSGGNSLPSGHMTLATGAAVAALLLVPARWRPLTTVLGAVVSSCTGAVAYTEAW +HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA +LTLDTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD +>PROKKA_01488 +MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP +DVTSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLVGSNLTTQLLKAALPRPE +HADGVPWSGGNSLPSGHMTLAMGAAVAALLLVPARWRPLTTVLGAVVSACTGAVAYTEAW +HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA +LTLGTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD +>PROKKA_01097 +MVAMPRTARPPLRVPSWPWWAALAACVAGVVLLYAALVWSSAGQVLEYQVFRAVEERYAD +TVPDLASRVVRLLPLTLAAGVALASLGALAVPRWRRRGLLALAALIGANLTTQLLKAVLP +RPEHAAGVPFSGGNSLPSGHMTLAAGAAVAALLLVPARWRPVTAVLGTAVSALTGAVAYT +EAWHRPSDMAAAALVAAGWGLLAVPLALHEDGPRPAPRGARAAEIGMWTVGAVGMAAGLV +LLWLTLEAPAAAGASPHPAAEPAGILLSAAPVVLCWGALATAFRRSRTA +>PROKKA_01020 +MVGMTVTPPPGSPADAAARPVASSRRPRGSRWAWLLGLAAAAGVVALVHAVFVGTSGGQL +LEYQVFHAVEDRWGTRSTGPAQRILTVLPVVLAGAATLAALACLIPRRTRRRGVVALVAL +AGANVGTQALKESLGRPSFANHVPWAGGNSLPSGHTTLAASAAVAALLLVPARWRPAVAV +VGAGATALTGSAAYLEAWHRPSDMAAAFGVAAFWAVLVAPWRRAADHRPRHASRAALAVE +RMLWTLGVAGVLVGLGLAVATLGSPAVSADPHPLAAPAGALLSGTPALVLCAALLTGLRR +AEQH +>PROKKA_01710 +MPPTARAPRRLPSWTWWLALAACVAGVVLVYAALVWSSAGQVLEYQVFRAVEERYADTVP +DVSSQVVRILPLALAVGMALASLGALAVARWRRRGLLALLVLAGSNLTTQLLKAALPRPE +HADGVPWSGGNSLPSGHMTLATGAAVAALLLVPARWRPLTTVLGAVVSSCTGAVAYTEAW +HRPSDMAAAALVSAAWGLLAVPFARYDGAPRPAPRGARGVEATLWSLGVAGLAAGLTLLA +LTLDTPATSGAGPHPAAEPAGILLSASPAVLLWGALGTAFRRGRAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001449.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001449.fa new file mode 100644 index 0000000000000000000000000000000000000000..ebfa89963d7b6bba75617d5952a5ebda634c5e69 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001449.fa @@ -0,0 +1,20 @@ +>PROKKA_01785 +MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD +PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDTADLRR +VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD +>PROKKA_01492 +MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD +PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDTADLRR +VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD +>PROKKA_01093 +MPTEALDRVDRAIVRALTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD +PVKVGFGASAHVTLKLRQHNWRELRATLLAIPEVWHVSLVGGNVDVILLVRARDTADLRR +VIFDELQTLPGVVDTQTYMVFDDHASGQTLPPEDPAA +>PROKKA_01016 +MSTSSPLDRVDRAIVRELSQDGRLSVAALAERVHVSRAHCYSRLNRLQNSGVITGFSARV +DPVKTGFTASAHVMLKLRQHDWRELRAALLAIPEVWHVSLVGGNMDVVLLVRARDTADLR +HVIFEKLQSLPAVVDTQTYMIFDDHASGQTMPPEEGADAPRTPTAFG +>PROKKA_01714 +MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD +PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDPADLRR +VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001450.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001450.fa new file mode 100644 index 0000000000000000000000000000000000000000..89ad3100fdd4c22a97090ae325f69b9c2deb4e70 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001450.fa @@ -0,0 +1,49 @@ +>PROKKA_01787 +MASRTASPPPSPAPSPAAPRGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI +LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG +LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPESLKSGIVVGIGLFIALIGLVNAGFV +RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVVATILAN +VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL +LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVAVGGAASGSAHQI +FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ +IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF +VAYFGLGVVRAALGLN +>PROKKA_01494 +MASRTASPPPSPAPSPAAARGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI +LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG +LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPEALKSGIVVGIGLFIALIGLVNAGFV +RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVAATILAN +VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL +LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVTVGGGASGSAHQI +FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ +IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF +VAYFGLGVVRAALGLN +>PROKKA_01089 +MGQEFRGGLATFLAMSYIVVLNPLILSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWA +RHPFAVAAGLGVSAFVSITIATTPGLTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPE +ALKSGIVVGIGLFIALIGLVNAGFVRRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLL +TAVLVIRKVRGAILIGIVAATILANVLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTA +PDLHLLGSVDLFGAFTSVGGLMASLLVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPD +LNRVLAADALAVAVGGGASGSAHQIFVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLI +HLVPFEAVAPALVVVGFMMCQHVVQIDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVA +YAVIRTGQGRGREVHPLLWFVALAFVAYFGLGVVRASLGLN +>PROKKA_01015 +MSSRTTGATPPGTAPSNPASPAGPRSGLDRFFGISALGSSVGQEVRGGIATFLAMSYIVV +LNPLILSGPDSTGAVLGIPRVAAATALVAAVATLAMGLWARHPFALASGLGVNAFLAITV +ATTPGLTWPDVMGLVVIAGLVMVVLVATGFRTAVFNAVPEALKTAIVVGIGLFIALIGLV +NAGFVRRLPDAAGTTVPVGLGTGGELAGWPVLVFIVGLLVTAILVIRNVRGAILVGIVTA +TVLANILEAVFHIGPSVGADGSHNPTGWALVAPSLPEWAAPDLSLLGSARPFGAFEAVGG +LMGALLVFAILLSVFFDAMGSTVGLAREAGSMDEHGNVPRLNRVLMVDALAVTGGGAASA +SAGQIYVESGTGIGEGARTGLASVVTGLMFVATIFLTPLIHLVPFEAVAPALVVVGFMMC +SQVVRIDWTDWGAALPAFLTFILMPFTYSIANGIGAGMIAYAVIRTGQGRAREVHPLLWV +VAAAFVLYFGMGVFRGILGLA +>PROKKA_01716 +MASRTASPPPSPAPSPAAPRGALDRYFRITERGSSVGQEFRGGLATFLAMSYIVVLNPLI +LSGPDSAGNTLGIPAVAAVTALVAGVMTIVMGVWARHPFAVAAGLGVSAFVSITIATTPG +LTWPQLMGLVTLAGLVMLLLVVTGFRRAVFDAVPEALKSGIVVGIGLFIALIGLVNAGFV +RRLPDAADTTVPVGLGTGGELEGWPVLVFVVGLLLTAVLVIRKVRGAILIGIVAATILAN +VLEAVFHIGPSVDADGNAVPTGWSLIAPSLPEWTAPDLHLLGSVDLFGAFTSVGGLMASL +LVFAILLSVFFDAMGVSVGLAREAGTVNPDGSIPDLNRVLAADALAVTVGGGASGSAHQI +FVESGTGIGEGARTGLASVFTGLFFLAAVFLSPLIHLVPFEAVAPALVVVGFMMCQHVVQ +IDWSDPGAAFPAFLTFILMPFTYSIVNGIGAGVVAYAVIRTGQGRGREVHPLLWFVALAF +VAYFGLGVVRAALGLN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001452.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001452.fa new file mode 100644 index 0000000000000000000000000000000000000000..46d3afa8b5477a64ddfa97ba38d402bd11af6633 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001452.fa @@ -0,0 +1,35 @@ +>PROKKA_01799 +MSTPQPDAARPDRDRLPEQVSDLFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT +VRIAFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ +RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV +VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVAM +GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY +MTDEAVEGRDAFLQKRDPDWSAFPYHF +>PROKKA_01496 +MSTPQPDAARPDRDRLPEQVSDVFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT +VRIAFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ +RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV +VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVAM +GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY +MTDEAVEGRDAFLQKRDPDWSAFPYHF +>PROKKA_01074 +MTETTPAAARDRLPEKVSDLFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPTVRI +AFDRPEVRNAFRPGTVDELYRALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQRIR +GRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHVVAD +LTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEEMVALGAV +NEAVDHERLEEVALEYAADINAQSPQALRMLKFAFNLADDGMAGQQVFAGEATRMAYMTD +EAVEGRDAFLQKRDPDWSAFPYHF +>PROKKA_01010 +MPAVRFSNDSIPGGIHVTNENAVVATTVLSMTESTPHHDRDRLPEKVSDVFDPTRWRVVE +GFEFEDMTYHRQVERDADGRWVRDLPTVRIAFDRPEVRNAFRPGTVDELYRALDHARMTP +DVGTVLLTGNGPSPKDGGHAFCSGGDQRIRGRDGYRYAEGETAETIDPARAGRLHILEVQ +RLMRNSPKVVIAVVNGWAAGGGHSLHVVADLTLASRQHGKFKQTDATVGSFDAGYGSALL +AREVGQKRAREIFFTAREYSAEEMVAMGAVNEAVDHERLEEVALEYAADINRQSPQAIRM +LKFAFNLPDDGMAGQQVFAGEATRMAYMTDEAVEGRDAFLQKRDPDWSAFSYYF +>PROKKA_01720 +MSTPQPDAARPDRDRLPEQVSDIFDPTRWRVVEGFDFEDLTYHRQVERDADGRWVRDLPT +VRIAFDRPEVRNAFRPGTVDELYHALDHARMTPDVGTVLLTGNGPSPKDGGHAFCSGGDQ +RIRGRDGYRYAEGETAETIDPARAGRLHILEVQRLMRTSPKAIIAVVNGWAAGGGHSLHV +VADLTLASREHGKFKQTDATVGSFDAGYGSALLARQVGQKRAREIFFTAREYSAEKMVAM +GAVNEAVDHERLEEVALEYAADINRQSPQALRMLKFAFNLPDDGMAGQQVFAGEATRMAY +MTDEAVEGRDAFLQKRDPDWSAFPYHF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001453.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001453.fa new file mode 100644 index 0000000000000000000000000000000000000000..db69d8e3bf2f8df45eacc5cbb96116ea702dfe08 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001453.fa @@ -0,0 +1,50 @@ +>PROKKA_01800 +MLALLDDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLALFQ +SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLNLDLPTAIG +VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITVLAARPWSSSPRDPAP +VTDGKLRFTAAVATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG +TEKNIDAAVQAFGRRTGADPARVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL +RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSDLDWISLGTGMALGY +LLGMVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQFGLMIFL +GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTYGALAGIT +GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFLL +>PROKKA_01497 +MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLALFQ +SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLNLDLPTAIG +VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP +VTDGKLHFTAAAATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG +TEKNIDAAVQAFGRRTDADPAQVMNPLQTAMVIVTARALADRRLGTLSLRERFGTDVARL +RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSNLDWISLGTGMALGY +LLGLVTIPLPGGASFSLGPAAGCILVGLTLGAIGRTGPTVWEPSTEIALTLRQLGLMLFL +GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLITAARLLGQSVDRTFGALAGIT +GQPAILDYALSRSTDVRVTEGYAQLFALIMVVKIATVPFML +>PROKKA_01073 +MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLVLFQ +SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLNLDLPTAIG +VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP +VTDGKLRFTAAAATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG +TEKNIDAAVQAFGRRTDADPAQVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL +RRDDVESLPTPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSDLDWISLGTGMALGY +LLGLVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQLGLMLFL +GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTFGALAGIT +GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFML +>PROKKA_01009 +MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGHRLALFQ +SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLHLDLPTAIG +VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP +VTDGKLRFTAAAATSALAVREIPGISEGLVRVVALRHGGVARIAGSADRIEPGDEVVLDG +TEKNIDAAVQAFGRRTDADPARVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL +RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSNLDWISLGTGMALGY +LLGMVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQFGLMLFL +GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTFGALAGIT +GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFML +>PROKKA_01721 +MLALLNDQPILVLMATVALGAAVGTIPLGKIRLGASGALFVGLLVGAVLPDVGDRLALFQ +SFGLALFAYLIGLGAGKVFFRDLRRNLPLMLAAVVVVILTAFTVHPLAALLHLDLPTAIG +VWTGSLTATPAMALANQLTGGQAPAVGYGLSYLVGVVGTIIAITLLAARPWSSSPRDPAP +VTDGKLRFTAAAATSALAVRDIPGISEGLVRVVALRHGGMARIAGSADRIEPGDEVVLDG +TEKNIDEAVQAFGRRTDADPARVMNPLQTSMVIVTARALADRRLGTLSLRERFGTDVARL +RRDDVESLATPQTELKVGDRVLIVTTAPRMEAVRDFFGNSTRGLSDLDWISLGTGMALGY +LLGMVTIPLPGGASFSLGPAAGCILVGLALGAIGRTGPTVWEPSTEIALTLRQFGLMLFL +GVVGLAAGPAFIETVFTRVGGLAILMSAVLTALTAALLIAAARLLGQSVDRTYGALAGIT +GQPAILDYALSRSTDARVTEGYAQLFALIMVVKIATVPFML diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001455.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001455.fa new file mode 100644 index 0000000000000000000000000000000000000000..db9014b7b8ab4e49ea93ee49ae4618db1384f76f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001455.fa @@ -0,0 +1,30 @@ +>PROKKA_01802 +MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN +DYSDGIRGTDDERVGPFRLTVSGLVPAARVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV +GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG +LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL +LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGIVYAITFTLGALL +>PROKKA_01499 +MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGRFHLGAALLALVVSLALQVGVNYAN +DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFASFGLAGLAGLGLILLSGHWWFLLV +GVACVVAAWYYTGGKKPYGYLGLGEVFVFVFFGLVAVLGTTYTQAGQVSGLAWAGAIGCG +LISTALLMANNIRDIPTDRAVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPWL +LLVPLGGLLAIRPVRTVLRAQDRRALIPVLRATGVIGIVYALTFTLGVLL +>PROKKA_01071 +MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN +DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV +GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSRLAWAGAIGCG +LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL +LLVPIGGLLAIRPIRTVLRADDRRTLIPVLRATGVIGIVYALTFTLGVLL +>PROKKA_01007 +MAATLSQWVAAARLRTLPMAVAPVIVGSAAAHALDQFRPGRALLALVVSLALQIGVNYAN +DYSDGIRGTDDARVGPFRLTVSGLVPAKTVKHAAFACFGVAAVAGLALVALSGTWWLLIV +GVASIVAAWYYTGGKKPYGYMGLGEVFVFVFFGLVAVLGTTYTQALAVNGLAWAGAVGCG +LISTALLMANNIRDIPTDREVGKMTLAARIGDGPARASYVAMLAVAVVLPLLFTGAHPWL +WLVLAAGAVAVKPCLTVLHAHERAALIPVLKATGIVGVVYAAAFALGVAL +>PROKKA_01723 +MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN +DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV +GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG +LISTALLMVNNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL +LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGLVYAITFTLGVLL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001457.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001457.fa new file mode 100644 index 0000000000000000000000000000000000000000..204b2bcd7dd3cf1065c7a3777c197a0a0a49f051 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001457.fa @@ -0,0 +1,20 @@ +>PROKKA_01804 +MGRFIIPAAIILAGLTLYALFEALLTPAREVRSLPKAAWVAVIVLVPLVGPLLWLLLGRA +RPAGAGGRPAPRPTGAPDDDEAFLRSLRVQRRQVAREQDLDRREAELRAREEELRRRREQ +GDDDADPDGDGPRA +>PROKKA_01501 +MGRYIIPAAIVLVGLTLYALFEALMTPAHEVRSLPKWGWVAVVVLLPLVGPLLWLVLGRA +RVARGTARPAPRGPGAPDDDEAFLRSLRVQRRQAEREQELDRRDAELKAREEELRRRRER +GEEPDADDPDAPTP +>PROKKA_01069 +MGRYIIPAAIVLVGLTLYALFEALMTPAHEVRSLPKWGWVAVVVLLPLVGPLLWLVLGRA +RVARGTARPAPRGPGAPDDDEAFLRSLRVQRCQAEREQELDRRDAELKAREEELRRRRER +GEEPDADDPDAPTP +>PROKKA_01005 +MARILVPTAILLVALTLFALFDALLTPAGRHRGMPKWAWIPTVLLLPLAGPLLWLFLGRP +VPLFSGRTAAPASRPASPDDDDEFLRTLRVQRAQTERARNLDRREAELRAREEELRRRRE +RGEDDATGEPDADA +>PROKKA_01725 +MGRFIIPAAIILAGLTLYALFEALLTPAREVRSLPKAAWVAVIVLVPLVGPLLWLLLGRA +RPAGAGGRTAPRPSGAPDDDEAFLRSLRVQRRQDAREQDLDRREAELRAREEELRRRREQ +GDDDADPDGDGPRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001458.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001458.fa new file mode 100644 index 0000000000000000000000000000000000000000..e4df2f7a5ef04c58abae257f930cf4331ca7652c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001458.fa @@ -0,0 +1,30 @@ +>PROKKA_01807 +MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG +RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL +QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY +CLGLGLPFVLMALGMERGMRAVGFFTRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ +LWFANEWEMPL +>PROKKA_01504 +MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG +RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL +QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY +CLGLGLPFVLMALGMERGMRALGFFLRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ +LWFANEWEMPL +>PROKKA_01067 +MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG +RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL +QQERRVHFKPAAGLAGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY +CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ +LWFANEWEMPL +>PROKKA_01002 +MQDNRFAEIALDGSLLAAAPVAFLAGLISFLSPCVLPLVPGYLGYVSGLGGAALDGARRG +RVALGAALFVLGFTVVFMVMNILFAQVAFRILRDLSWVMQLLGVLVILMGVVFMGGLRWF +QTERKVHVKPAAGLTGAPLLGMTFGLGWAPCIGPTLAAVFALSYTQDSSSVARAALLAFV +YCLGLGLPFVLISFGVERGMRALGFFRRHRRGVMVFGGAVLILLGAVMVTGLWTQWMVQL +QTWFQNEWVMPL +>PROKKA_01728 +MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG +RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL +QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY +CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ +LWFANEWEMPL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001459.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001459.fa new file mode 100644 index 0000000000000000000000000000000000000000..cd0a6f25467ab69c97ea61d3bc3297c2252f5182 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001459.fa @@ -0,0 +1,29 @@ +>PROKKA_01810 +MSGTSPTDPHGSQNPYGTDPYGAAPQGPTPGSPDPAGASPYGQNPYGAPPAAPYGAPGQA +GMPQAPSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLLAAFAITQPEGQ +VAIQQELDRSVEQMNLPADQAEQMRTMMDGMLPALATTAAVFGVLAFLVYLWVAFAIRGG +SRAARIVGTVLASLSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRPDATEYMRLKTW +QRFARR +>PROKKA_01507 +MSGTSPTDPHGSQNPYGTDPYGAAPQGPTPGSPGPAGASPYGQNPYGAPPAAPYGAPGQA +GMPQAPSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLLAAFALTQPEGQ +AAIQQELDRSVEQMDLPADQAEQMRAMMDGMLPALATTAAVFGVVAFLVYLWVAFAIRGG +SRAARIVGTVLAALSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRPDATEYMRLKAW +QRFARR +>PROKKA_01064 +MSGTSPTDPQRGQNPYGQEAPGPSPYGENPYGAHPYGQAPYGQGGPAQGQPGQGHPNPGH +PAPSYADQGYPAQGGWPGQQAPGPLTAPRRPGAITASFWLILAGGLVLLASTLLAAFAMT +LPESRAMLEQQMRETYEQMGLPADQLAQMEQMTDQLLPVMSVVAAAFGVVAFLVYLLIAL +KIRKGSRAARTVGTVLAALSVLMIVTNLMMGAFNPFDLLWVGLGVAGIVMAFRPEASEYM +RLKAWERAGTR +>PROKKA_00999 +MSGTENSNPYGRPAGQSGPQWPDAAAQAPYGQAPDASAQAPYGAPPQGWGAPQQWGGQPG +WPAAAPVPARRPGPINAAFWLIVSAGVVFLASTVLSALVATSDAGRRELEAAMTKVWGDY +GMTPEQIREYQDMLPPMMPVMAGVMVAVGVLALLVYLLIASKIRGGSRAARTVGTVLAVL +SVLMVLAPLASGQFSPLDLLWCLLGVAGIATAYRKEATEFMRLRAWERAARR +>PROKKA_01731 +MSGTSPTDPHGSQNPYGADPYGAVPQGSTPGSPDPAGASPYGQNPYGAPPATPYGAPGQA +GMPQAPSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLLAAFALTQPEGQ +AAIQQELDRSVEQMDLPADQAEQMRAMMDGMLPALATTAAVFGVLAFLVYLWVAFAIRGG +SRAARIVGTVLAALSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRPDATEYMRLKAW +QRFARR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001460.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001460.fa new file mode 100644 index 0000000000000000000000000000000000000000..4837dfb5c32a86d9c66ba6d945fc5c841bd86c12 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001460.fa @@ -0,0 +1,15 @@ +>PROKKA_01811 +MTADLPAATARVQLLVKPGCHLCAEAEATVVQVCDARGEAWEAVDGAAHPDLLERFVDEV +PVLFVDGVQRDFWRVDPARLGRLLDAPRA +>PROKKA_01508 +MTADLPAATARVQLLVKPGCHLCAEAEATVAQVCDARGEAWEAVDGAAHPALLERFADEV +PVLFVDGVQRDFWRVDPARLGRLLDAPRA +>PROKKA_01063 +MSTLLPASAARVQLLVKPGCHLCEDAAATVAQVCGARGEAWEAVDGAAHPDLLERFVDEV +PVLFVDGVQRDFWRVDPARLGRLLDAPRP +>PROKKA_00998 +MAAMMTPPASAARVQLLVKPGCHLCAEAEAVVAEVCDARGTAWERVDGPAHPDLLETYAE +EVPVLFVDGVQRDFWRVDAQRLGRLLDGPAA +>PROKKA_01732 +MTADLPAATARVQLLVKPGCHLCAEAEAAVAQVCDARGEAWEAVDGAAHPALLERFADEV +PVLFVDGVQRDFWRVDPARLGRLLDAPRV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001463.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001463.fa new file mode 100644 index 0000000000000000000000000000000000000000..0ac0a1185d4149505feb31917aa539dc59f01f99 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001463.fa @@ -0,0 +1,48 @@ +>PROKKA_01814 +MAGPRPTPHARRHGGVRRPGGLPRPGQASTLESSTDLRTVLRRSGRAVSSVVGGSPARAA +LSAFALMALVFTGLLALPWAAADGHATPLHDAMFTAVSAFSVTGLTTVNTAAHWSPAGQV +IILVAIQIGGLGILSIASLLTLAVSRHLGLRSKLATQQAGMTSGSLGEVGQLLRVVVVTV +LTAEAALALVLVPRFAAISGSWLTGLWHGVFYSVSAFNNAGFTLHVDGLPEIMHDPVIIT +VLGVGVFLGALGFPVVMVLLEKGWRFREWNLHTKLTVEVTLALLVLGAVALFFFEAGNPA +TQAGMGFWQRVGHSLFGSVMTRSGGFAIDDTNAHRPESLLLMDALMFVGGGSASTAGGIK +VTTLAIMFLAIVAEARGDREVTAHGRTIAPESLRVAIAVLALGATLVLVATLALVHITDE +SLQRPLFEVISAFGTCGLSVGVSAESPPAGKYVLTAMMFAGRVGTITFAAALALRQRRVL +YRYPVERPVIG +>PROKKA_01511 +MAGPRPTPHARRHGGVRRPGGLPRPGQASTLESSTDLRTVLRRSGRAVSSVVGGSPARAA +LSAFALMALVFTGLLALPWAAADGHATPLHDAMFTAVSAFSVTGLTTVNTAVHWSPAGQV +IILVAIQIGGLGILSMASLLTLAVSRHLGLRSKLATQQAGMTSGSLGEVGQLLRVVVLTV +LTAEAALALFLVPRFAAISGSWLTGLWHGVFYSVSAFNNAGFSLHVDGLPEIMHDPVIIT +VLGVGVFFGALGFPVVMVLLEKGWRFRQWNLHTKLTVEVTLALLVLGAVALFFFEAGNPA +TQAGMGFWQRVGHSLFGSVMTRSGGFAIDDTNAHRPESLLLMDALMFVGGGSASTAGGIK +VTTLAIMFLAIVAEARGDREVTAHGRTIAPESLRVAIAVLALGATLVLVATLALVHITDE +SLQRPLFEVISAFGTCGLSVGVSAESPPAGKYVLTAMMFAGRVGTITFAAALALRQRRVL +YRYPVERPVIG +>PROKKA_01060 +MSTLESSSELRTALRRSSRAVSSVVSGSPARAALSAFLLVSLVFTALLSLPWASADGRPT +ALHDAMFTAVSAVSVTGLTTLNTAEHWSVAGQVIILVAIQIGGLGILSMASLLTLAVSRH +LGLRSKLATQEAGMTTGNVGEVGRLLRVVVVTVLTCEAALAVFLVPRFAAESGSWLTGLW +HGVFYSVSAFNNAGFSLHVDGLSAVAHDPVILTVIAVGVFAGALGFPVVMVLLDKGWRYR +AWNLHTKLTVEVTLALLVLGAVLLFFFEAGNPGTNGDLGVVERIWRSLFGSVMTRSGGFA +IDDTNAHRPESLLLMDALMFVGGGSASTAGGIKVTTLAVMFLAILAEARGDREVTAHGRT +IAPETLRVAISVLALGATLVLVATLALVNIMDESLQRPLFEVISAFATCGLSVGVSAEAP +PAGKYLLAAMMFAGRVGTITFAAALALRQRRVLYRYPVERPILG +>PROKKA_00995 +MPSGALSPARRVVTAVTGVVAGSPARAALSAFALGALLFTGLLMLPAAATDGRVTPLHDA +MFTAVSAFSVTGLTTLDTAEHWTPLGQVILLAAMQIGGLGILSMASLLTLAVSRHLGLRT +KLATQESGMTTGNMGEVGHLLKVVVLTVLTCEGALAVILVPRFAALSDSWATGLWQGVFY +SVSAFNNAGFTIHEGGTAAFMHDPVILTVIAVGVFAGALGFPVVMVLVDKGWRFRSWNLH +TKLTVEVTLVLLVVGAVALFFFEAGNPATHGDMVVGQRIGHSFFGSVMTRSGGFAIDDTN +SHRPESLLLMDALMFVGGGSASTAGGIKVTTLAVMFLAIVAEARGDKEVTVHGRTIAPET +LRVAISVLALGATLVLLATLALVSIVDQPLQRPLFEVVSAFGTCGLSVGVSAEAPPAGKY +LLTAMMFAGRVGTITFAAALALRQRRVLYRYPVERPILG +>PROKKA_01735 +MAGPRPTPHARRHGGVRRPGGLPRPGQASTLESSTDLRTALRRSGRAVSSVVGGSPARAA +LSAFALMALVFTGLLALPWAAADGHATPLHDAMFTAVSAFSVTGLTTVNTAEHWSPAGQV +VILVAIQIGGLGILSMASLLTLAVSRHLGLRSKLATQQAGMTSGSLGEVGQLLRVVVVTV +LTAEAALALVLVPRFAAISGSWLTGLWHGVFYSVSAFNNAGFTLHVDGLPEIMHDPVVIT +VLGVGVFLGALGFPVVMVLLEKGWRFREWNLHTKLTVEVTLALLVLGAVALFFFEAGNPA +TQAGMGFWQRVGHSLFGSVMTRSGGFAIDDTNAHQPESLLLMDALMFVGGGSASTAGGIK +VTTLAIMFLAIVAEARGDREVTAHGRTIAPESLRVAIAVLALGATLVLVATLALVHITDE +SLQRPLFEVISAFGTCGLSVGVSAESPPAGKYVLTAMMFAGRVGTITFAAALALRQRRVL +YRYPVERPVIG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001466.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001466.fa new file mode 100644 index 0000000000000000000000000000000000000000..605fb59e8007b08462ea64371eeb9a15abc5d202 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001466.fa @@ -0,0 +1,31 @@ +>PROKKA_01817 +MADATAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA +RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ +GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGREAKMYLPHWNPLPEPYEHICWDFSH +AAIARADSLAAVRELGPRLRHVHLTDGNDSGKDDHLVPGEGTQRVAETLRHLAAEGLAGA +VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTDHHDDDGVPRPTTKETDRP +>PROKKA_01514 +MPDSTAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA +RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ +GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGRKAKMYLPHWNPLPEPYEHICWDFSH +AAIARADSLAAVRELGPRLRHVHLTDGDDSGKDDHLVPGEGTQPVAETLRHLATAGLAGT +VCVEVGTRGVEYAGQREEMLAASLAFAREHLAAGGTDHHHDGGVLRPTTKEMDRP +>PROKKA_01053 +MAGSTAHLAPAPRFGSDIPVTLSSSSVFPLGTQDVFATAQDLGYDGVEVMVTHNAWSQDA +DRLKRLSARHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAPVVVAHPPFRWQ +GTYASGFAEGIHEIMADTGVVIAVENMYPWRAHGREATMYLPHWDPMPEPYEHVCWDFSH +AAIAREDSLEALRRLGSRVRHIHLTDGNDSGKDDHLVPGEGTQKVAESVRHLAADGFAGT +VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTKDDDGAPGA +>PROKKA_00991 +MTGPSGAGSRPWDPHGRHLEPPLVSTAHLAPAPRFGAEIPVTLSSSSVFPLGTQDVFATA +ADLGYDGVEVMVTHNATSQDARALARLSERTGMRIDSIHAPTLLFTQQVWGSAWSKIVRS +VELARAVGAVTVVAHPPFRWQGSYASQFARRTAEIMEATGVVIAVENMYPWRAHGRDLTM +YLPHWDPVPEPYEHVTWDFSHAAIAREDSLANIRGLGGRLRHVHLTDGVDGTKDAHLVPG +EGTQNVAESLRFLGREGLAGTVCVEVGTRGVEYAGQREEKLSASLAFAREHLGQNDQSGR +HES +>PROKKA_01738 +MPDSTAHLAPAARFGADIPVTLSSSSVFPLGTQDVFATAEDLGYDGVEVMVTHNAWSQDA +RRLTRLSERHGMPIDSIHAPTLLFTQQVWGSAWSKIRRSVELAQAVGAATVVAHPPFRWQ +GTYAVRFAEGIHELMAETGVVIAVENMYPWRAYGREAKMYLPHWNPLPEPYEHICWDFSH +AAIARADSLAAVRELGPRLRHVHLTDGNDSGKDDHLVPGEGTQRVAETLRHLAAEGLAGA +VCVEVGTRGVEYAGQREEKLAASLAFAREHLAAGGTDHHDDDGVPRPTTKETDRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001471.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001471.fa new file mode 100644 index 0000000000000000000000000000000000000000..bedf3ac239016923a25c7dbca96b15eddb55a1f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001471.fa @@ -0,0 +1,30 @@ +>PROKKA_01822 +MRDGRGLARTGLTPYPSDMTEHLDPALVDIWFAAWSRSRGYRTSQEAGRRAALRTPRPAH +MIPGGSGRATVDVPATWEHVVVNPSRAELEDLREAVRDQEQILLTVFGDAGEDPKAMGLK +AQAEPERFMTMDMDPELQDVEPPLLPEGYEARVDQPMEGSRRLRILAVGASTAPEGEEEL +AALGWVTEEDGTAVYDRIWTSPNHRRRGLGSLVMRYLTSEVMSEGEISRGLLVASPDGQK +LYRHLAWTDLGPVSIWGRGLAEDNPTAEHTGTMGA +>PROKKA_01519 +MTEHLDPALVDIWFAAWSRSRGYRTSQEAGRRAALRTPRPACMIPGGSGRATVDVPATWE +HVVVNPSRGELEDLREAVRDQEQILLTVFGDAGEDPKAMGLKAQAEPERFMTMDMDPELQ +DVEPPLLPEGYEARVDQPMEGSRRLRILAVGASTVPEGEEELAALGWVTEEGGTAVYDRI +WTSPNHRRRGLGSLVMRYLTSEVMSEGEISRGLLVASPDGQKLYRHLAWTDLGPVSIWGR +GLAEDNPAAEHTGTMGA +>PROKKA_01047 +MSEHLDTALVDTWFAAWSRSRGYRTSPEAGRRAALRTRRPARMIPGGSGRATVDVPATWE +YVVVDPTREQLEELREALRDEEQILLTVFGDAGADPKAMGLTPQAEPERFMSMDMDPEVQ +DVEPPLLPDGYEARVDQPMEGSVRVRIMAVGASTAPEGEEELAALGWVTREDGTAVYDRI +WTSPNHRRRGLGSLVMRYLTSEVMSDGEISLGLLVASPDGRKLYEHLAWTDLGPVSIWGR +GLAADTPTAEHTGTMGA +>PROKKA_00986 +MTQSIDDTLVGTWFAAWSRSRGYETRIEDGMRSALRKKRSAQRIPGGAGRAAMDIPTTWE +HVLVSPDADALAPALASLEEQPDRLVTVFGETDQDLTSAGLHSAVLPERFMSMELDREVQ +DVEPPLLPEGYEAHVDEPRPGSRRVRFYAAGALSGVPEGEEELAALGWVTFEGETAVFDR +IWTSPDHRRRGLGSLVMRHLTSEALGADDELERGLLVASPDGQKLYGHLGWTDLGPVRIW +TRADGEAPGAEHTGTMAR +>PROKKA_01743 +MRDGRGLARTGLTPYPSDMTEHLDPALVDIWFAAWSRSRGYRTSQEAGRRAALRTPRPAH +MIPGGSGRATVDVPATWEHVVVNPSRAELEDLREAVRDQEQILLTVFGDAGEDPKAMGLK +AQAEPERFMTMDMDPELQDVEPPLLPEGYEARVDQPMEGSRRLRILAVGASTAPEGEEEL +AALGWVTEEDGTAVYDRIWTSPNHRRRGLGSLVMRYLTSEVMSEGEISRGLLVASPDGQK +LYRHLAWTDLGPVSIWGRGLAEDNPTAEHTGTMGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001475.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001475.fa new file mode 100644 index 0000000000000000000000000000000000000000..1e1f314b92f866cc3e7eb986db66fa4f9ff10039 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001475.fa @@ -0,0 +1,15 @@ +>PROKKA_01826 +MTHRSHSAQPAVTRPSGRNRLARVVDAAGEETGAITAEYGILTLAAVGFAGVLAVVLTSP +DVQSLLVDLVSGALQRD +>PROKKA_01523 +MTHRSHSAQPAVTRPSERDRLARVVDAAGEETGAITAEYGILTLAAVGFAGVLAVVLTSP +DVQSLLVDLVTGALQRD +>PROKKA_01043 +MTQLSHTVHDALATAAERHHLARVADAAADETGAITAEYGILTLAAVGFAGVLAVVLTSP +DVQSLLVELVSGALQRD +>PROKKA_00982 +MTHNSTALTETLVPLVGPQRAAALATWAEDETGAQTAEYGILTLAAVGFAGVLAVVLTSP +EVRELLVDLVSQALQRG +>PROKKA_01747 +MTHRSHSAQPAVTRPSGRNRLARVVDAAGEETGAITAEYGILTLAAVGFAGVLAVVLTSP +DVQSLLVDLVSGALQRD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001479.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001479.fa new file mode 100644 index 0000000000000000000000000000000000000000..ff14bfc2507e635587593f0cd85f4c59de8a293a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001479.fa @@ -0,0 +1,30 @@ +>PROKKA_01831 +METEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV +RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP +ARLEDLVALPGVGRKTEFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA +LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK +PGREELLELLRAGRTRRELRALGHGLEA +>PROKKA_01528 +MEPEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV +RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP +ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA +LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK +PGREELLELLRAGRTRRELRALGHGLEA +>PROKKA_01037 +MDAEQADTPTGESRLALVRRARRIDRELAATYPYAVAELDFETPFELLVATVLSAQTTDV +RVNAATPALFARFPDAAAMAGASEAELQGLVRSTGFYRNKASAILRLSQELVERHGGEVP +GRLEDLVALPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTQDTDPVKVEHAVAE +LFPRRDWTMLSHRLIFHGRRICHARRPACGACPIARWCPSYGEGETDPEKARALLSYELK +PGREELLALMRAGLSRRELRARGHGLDA +>PROKKA_00977 +MAPADTTTPTGETPLALTRRARRIDRALAEAYPYAVAELDFETPFELLVATVLSAQTTDV +RVNAVTPALFARFPDAVAMAGADEVELQELVRPTGFYKNKASAVLRLSRELVERFDGEVP +DRLEDLVTLPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTEETDPVKVEHAVAA +LFPPRDWTMLSHHLVFHGRRVCHARKPACGACPIARWCPSYGAGETEPEAARALLSYELK +PGREELLARMRAGATRRQLRDEGWTLEA +>PROKKA_01752 +METESTGTPTGETRPALVRRARRINRILAETYPYAVAELDFETPFELLVATVLSAQTTDV +RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP +ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA +LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGAGETDPERARALLAYELK +PGREELLELLRAGRTRRELRALGHGLEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001481.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001481.fa new file mode 100644 index 0000000000000000000000000000000000000000..f773e1d0810f03cde423e70787bfd8be4018bb04 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001481.fa @@ -0,0 +1,20 @@ +>PROKKA_01833 +MAFSTRSTGETMRATGPSAAAPSAAPVAGGAAGVVSTSLPVVAVDGSLPTPPYRQIVDAV +LAGVTSGSLARGDRLPPVRALAAELGVAPGTVARAYKELEAHGTIRTRGRAGTFVAASAD +ARADAAHQAVRRCLDTLLERLGYTPDEAVELVRRDAAARA +>PROKKA_01530 +MAVSTRSTGETMRAPGPSAAAPSAAPVAGGAAGVVSASLPVVAVDGSLSAPPYRQIVDAV +LAGVASGSLARGDRLPPVRALAAELGVAPGTVARAYKELEAHGTIRTRGRAGTFVAASAD +ARADAAHQAVRRCLDTLLERLGYTPDEAVELVRRDAAARA +>PROKKA_01035 +MTATPSGAAPSPASAEGGAARVVSASLPVVAVDAALSAPPYRQITDAVLAGVASGCLARG +DRLPPVRALASELGVAPGTVARAYKELEARGTILTRGRAGTFVAASADARADAAHQAVRR +CLDTLLDRLGYTADEAVELVRRDAAARA +>PROKKA_01055 +MNGVEPTLELDLRSPVPPFEQIRAGISAFVDAGVLAPGDRLPSVRALAADLGVAPNTVVR +AYRELESAGVVRTARGKGTVVADRPRGALTADDDGTARTLEAAVHSALAAGWDRERVQRV +VEAALVSPPAPVDRKDTP +>PROKKA_01754 +MAVSTRGTGESMRLPGPFAAAPVADGAAGVVSASLPVVAVDASLPAPPYRQIVDAVLAGV +ASGSLARGDRLPPVRVLAAELGVAPGTVARAYKELEAHGTIRTRGRAGTFVAASADARAD +AAHQAVRRCLDTLLERLGYTPDEAVELVRRDAAARA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001482.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001482.fa new file mode 100644 index 0000000000000000000000000000000000000000..459fcdf98d167f5221ef808ecd92fe20bfdda606 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001482.fa @@ -0,0 +1,14 @@ +>PROKKA_01834 +MSTAAIVMMSLAILLVWGGLAVSAIHLLRHPDDSSGDLAIEDDLAPAVWEREDGLLDAQH +R +>PROKKA_01531 +MSTAAIVMMSLAILLVWGGLAVSAIHLLRHPDDSSGDLAIEDELAPAVWEREDGRLDAQH +R +>PROKKA_01034 +MSTAAIVMMSLAILLVWGGLALSAVHLLRHPDDSSGDLALGDRLAPAAWEREDELGREDV +RLGARRG +>PROKKA_00975 +MHTPALIMMVIAMLTVWGGLVLSAVHLLKHPDETSGTLADAVDVDHTL +>PROKKA_01755 +MSTAAIVMMSLAILLVWGGLAVSAIHLLRHPDDSSGDLAIEDELAPAVREREDGRLDARH +R diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001484.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001484.fa new file mode 100644 index 0000000000000000000000000000000000000000..f9cf132a1f44337392803358dadfb4e53a6daf66 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001484.fa @@ -0,0 +1,26 @@ +>PROKKA_01837 +MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR +TASDGRENLVAVLGPGEIFGEMALFNPAPRNATATAVSATRLAGLRHENLRRAIASSPDV +SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE +LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR +>PROKKA_01534 +MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR +TASDGRENLVAVLGPGEIFGEMALFNPAPRNATATAVSATRLAGLRHENLRRAIASSPDV +SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE +LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR +>PROKKA_01031 +MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR +TASDGRENLVAVLGPGEIFGEMALFNPAPRSATATAVSATRLAGLRHENLRRAIGSSPDV +SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE +LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR +>PROKKA_00972 +MGHNGTDIPGAPRPRLAVSQKGRARMDLEVLRKAPLFTNLDDEVFSILTSELTEVELSRG +ASAFHEGDQGDQLYVIMSGKIKLGRTASDGRENLVAVLGPGEIFGEMALFNPAPRSATAT +AVSAARLAGLRHENLRRAIASSPDVSLQLLQALAQRLSKTNESLADLVFSDVPGRVAKAL +LDLADRFGRPAADGLLVAHDLTQEELAQLVGASRETVNKALAEFVQRGWIRLENRAVVIL +DLQRLRQRSR +>PROKKA_01758 +MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR +TASDGRENLVAVLGPGEIFGEMALFNPAPRNATATAVSATRLAGLRHENLRRAIASSPDV +SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE +LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001486.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001486.fa new file mode 100644 index 0000000000000000000000000000000000000000..f20092b08c2f96c331b013705ac7bea5526252a6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001486.fa @@ -0,0 +1,20 @@ +>PROKKA_01839 +MTEQSSAPTWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP +ATGKVGAEVTPERAQELARACAVNAVAAVHELVGDLDRVAQVVKVVGFVASDPAFTGQPG +VVNGASDVLAEIFGEAGRHARSAVGVAVLPMDAPVEVEITVRVR +>PROKKA_01536 +MTAQSSAPAWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP +ATGKVGAEVTPERAQELARVCAVNAVAAVHELLGDLDRVAQVVKVVGFVASDPAFTGQPG +VVNGASDVLAEIFGEVGRHARSAVGVAVLPMDAPVEVEITVRVR +>PROKKA_01029 +MAEKAQAPTWGEGAVADRLAELGLERPAVAAPVGSYVPAIRDGDLVLTSGQLPFVAGSLP +ATGKVGAEVSAERAQELARVCAVNAVAAVHELIGDLDRVAQVVKVVGFVASDPSFTGQPG +VLNGASDVLAEIFGEAGRHARSAVGVAVLPLDAPVEVEITVRVR +>PROKKA_00970 +MAGQNAWGGGPAAERLAALGIERPAVAAPVGSYVPAVRDGDLVLTSGQLPFVAGALPRTG +KVGAEVTLEQAQELARTAAVNAVAAVHELVGDLEAVVQVVKVVGFVASAPDFTAQPAVVN +GASDVLAEIFGEAGRHARSAVGVAVLPLDSPVEVEITVRVR +>PROKKA_01760 +MTAQSSAPAWGDGAVAARLAELGIDRPAVAAPVGSYVPALRDGDLVLTSGQLPFVAGALP +ATGKVGAEVTPERAQELARVCAVNAVAAVHELLGDLDRVAQVVKVVGFVASDPAFTGQPG +VVNGASDVLAEIFGEVGRHARSAVGVAVLPMDAPVEVEITVRVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001488.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001488.fa new file mode 100644 index 0000000000000000000000000000000000000000..41bfcd3c631f5301441467bfcd65d207ab1c90aa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001488.fa @@ -0,0 +1,70 @@ +>PROKKA_01841 +MASRTTRFPAPSSALGRLLAFVGLSAVAGLLVAALLLPVAGLAGVAAASGREMLDELPDE +LPTEPVSVPSRILSEDGEEIAVFYEENRTPVPLDEISEHMQHAIVAIEDERFYDHDGVDA +RGLIRATVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGSKNIADKVKEIKL +AVAVEKQMSKDEILEGYLNIVLFSGRAYGVEAASQYVFGKSAADLESWEAATLAGMVQSP +TRFNPARNPEEATERRNLVLNAMKDNGYLSQEEYDHAVAQPMEVVMESRPSGCLYAKFGT +YFCDYVERQILADPTFGPDVQSRQALLDRGGLTIRTTIDSTLQKETEKNLRASVPNNESL +GAGHALTSVEAGTGNIRTMAQNTEYAIQDELGHTSLNFNVDKQWGGGQGFQAGSTLKPFV +ALTWLRNGNRLVDSVDASRNVYPTGTRFAASCRPGGYTTIGGTWQFKNVIPGMLRQVRVD +EGLFWSVNTPTVATAYQLDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSVAPLSL +AGAYAAIAANGLYCEPRAILEVTDTVGNQYDVADPQCDQVIDPDHVRELMPVLRHIAGFN +IAEEGAGYEFGGKTGTNDNVSSTWFVGFTSELATAVWTGRYNNLKSMTGETVNGEVRNPF +YSTSINGPSWLEYNQLAKEKFPPGELPEWDGPQSEDPGEAGEHPDGRQFHIDDLDRGGPL +PEAVPGF +>PROKKA_01538 +MASRTTRFPAPSSAPGRLLAFVGLSALAGLLVAALLLPVAGLAGVAAASGREMLDELPDE +LPAEPVSVPSRILSEDGEEIAVFYEENRTPVPLDKISKHMQHAIVAIEDERFYDHDGVDA +RGLIRATVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGSKNIADKVKEIKL +AVAVEKQMSKDEILEGYLNIVLFSGRAYGVEAASQYVFGKSAADLESWEAATLAGMVQSP +TRFNPARNPEEATERRNLVLNAMKDNGYLSQEEYDHAVAQPMEVVMESRPSGCLYAKFGT +YFCDYVERQILADPTFGPDVQSRQALLDRGGLTIRTTIDSTLQKETEKNLRASVPNNESL +GAGHALTSVEAGTGNIRTMAQNTEYAIQDELGHTSLNFNVDKQWGGGQGFQAGSTLKPFV +ALTWLRNGNRLVDSVDASRNVYPTGTRFAASCRPGGYTTIGGTWQFKNVIPGMLRQVRVD +EGLFWSVNTPTVATAYQLDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSVAPLSL +AGAYAAIAANGLYCEPRAILEVTDTVGNQYDVADPQCDQVIDPDHVRELMPVLRHIAGFN +IAEEGAGYEFGGKTGTNDNVSSTWFVGFTSKLATAVWTGRYNNLKSMTGETVNGEVRNPF +YSTSINGPSWLEYNQLAKEKFPPGELPEWDGPQSEDPGEAGEHPDGRQFHIDDLDRGGPL +PEAVPGF +>PROKKA_01027 +MASRTSRRLPEPSSALGRLLAFLGLSALAGLLVAALLLPLAGLTGVAAASGREMLDELPD +ELPAEPVSVPSRMISEDGEEIAVFYEEDRIPVPLDQISEHMRNAIVAVEDERFYEHDGVD +ARGLIRATVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGTKNVSDKVKEIK +LAVAVEEQMTKDEILEGYLNIVLFSGRAYGVEAASRYVFGKSAAELESWEAATLAGMVQS +PTRFNPARNPEEATERRNLVLGAMKKNGYLTEEEHAEAVAQPMEVVMESRPSGCLYSKFG +SYFCDYVERQILADPAFGPDPQSRQALLDRGGLTIRTTIDSELQKAAEENLRKSVPNNES +LGAGHALTSVQAGTGNIVTMAQNTEYAIQDELGHTSLNFNVDREWGGGQGFQAGSTLKPF +VALTWLRNGNRMVDSVDASRNVYPTGTRFEASCRPGGYTTIGGTWQFKNVIPGMLRQVRV +DEGLFWSVNTPTVATAYQMDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSIAPLS +LAGAYAAIAADGLYCEPRAILEVTDTVGNQYDVAGPQCDQVVDPKHIAELMPVLRHIGAF +NIAEEGAGYEFGGKTGTNDNVSSTWFTGFTTELATAVWTGRYNNMKSMTGETVNGEVRNP +FYSTSINGPSWLEYNQLAKEKYPPGELPDWDGPQSEDPGAEGEHPDGTAFRIDDLDRGGP +QPQAVPGN +>PROKKA_00968 +MASRSSRLPARSSALGRLLSFLGLSALAGLLVAGLMMPAAGATGIVFASGRDMLDELPDQ +LPAEPVSMPSKIYSADGELIATFFQENRQPVPLDQISPYMRNAIVAIEDERFYQHDGVDA +KGLVRAMVNNVSSSSTQGASTLTQQFVNNMLINSQQVRGDSRLTLSGTKQASDKVKEIKL +AVAVEKQMSKDQILEGYLNLVLFQGRAYGIEAASQYVFGKPAKDLELWEAATLAGMVQSP +TRFNPARNPEGTTARRNTVLKAMLKNGYISQEEHDHAVAQPLTYTMKGQSTGCLSAAFGA +YFCDYVERQILADPTFGPDTASRQALLDRGGLTIRTTIDSNLQKKAEELTRRVIPNNESL +GAGHSLISLRPGSGDIVTMAQNTEYSIQDELGKTTLNLNVDAKWGGGTGFAAGSTFKPFI +GLTWLRNGGKLIDSVDGSKDRYPPDARFQASCLPGGYTTAGGGTQGWQLNNVIDGMKKRD +RIDEGIFWSVNTPTVALAYQMDLCDIVNTLTQVGIVTARDGAPLSPAEPSFVLGKDDVSP +MTMAGAYATLAANGKYCKPRAITEVTDTTGNQYTVPAPECRQVLDPAQVAEVTPLLRHIA +AHNIAPDGTGYEFAGKTGTNNNMSSTWFIGYTTELATAVWAGRYTSQKTMRGETINGVVQ +KEFYGATVNGGTWLEWNDMAKRTFVPGELPEFDGPQSEDPALEGDHPDGRFYRPEDIDRN +GGTPTSSLGPAAGETAFSSAENAAKFESGVLTR +>PROKKA_01762 +MASRTTRFPAPSSALGRLLAFVGLSAVAGLLVAALLLPVAGLAGVAAASGREMLDELPDE +LPTEPVSVPSRILSEDGEEIAVFYEENRTPVPLDEISEHMQHAIVAIEDERFYDHDGVDA +RGLIRAAVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGSKNIADKVKEIKL +AVAVEEQMSKDEILEGYLNIVLFSGRAYGVEAASQYVFGKSAADLESWEAATLAGMVQSP +TRFNPARNPEEATERRNLVLNAMKDNGYLSQEEYDHAVAQPMEVVMESRPSGCLYAKFGA +YFCDYVERQILADPTFGPDVQSRQALLDRGGLTIRTTIDSTLQKETEKNLRASVPNNESL +GAGHALTSVEAGTGNIRTMAQNTEYAIQDELGHTSLNFNVDKQWGGGQGFQAGSTLKPFV +ALTWLRNGNRLVDSVDASRNVYPTGTRFAASCRPGGYTTIGGTWQFKNVIPNMLRQVRVD +EGLFWSVNTPTVATAYQLDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSVAPLSL +AGAYAAIAANGLYCEPRAILEVTDTAGNQYDVADPQCDQVIDPDHVRELMPVLRHIGGFN +IAEEGAGYEFGGKTGTNDNVSSTWFVGFTSKLATAVWTGRYNNLKSMTGETVNGEVRNPF +YSTSINGPSWLEYNQLAKEKFPPGELPEWDGPQSEDPGEAGEHPDGRQFTIDDLDRGGPQ +PQAVPGF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001492.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001492.fa new file mode 100644 index 0000000000000000000000000000000000000000..45f489ccf9d602b7acea36f17236e8a2c8e7ce27 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001492.fa @@ -0,0 +1,15 @@ +>PROKKA_01848 +MPPLHHGQPGDDRDPRDPRHRPGAGLGPGLRTAWTFVGVMFTCALIVFWTLRGLGVQRGD +LSLPAALGVLALAAVAAAVITRYVRRR +>PROKKA_01544 +MPPLHHGQPGDDRDPRDPRHRPGAGLGPGLRTAWTFVGVMFTCALIVFWTLRGLGVQRGD +LSLPAALGVLALAAVAAAVITRYVRPR +>PROKKA_01020 +MGPRMNSAWLFVGVMFTCALIGFWTLRGLGFARGDLSLPAALGVLAVAAVAAAVITRFVR +RR +>PROKKA_00962 +MTLPPLHHGRDDDADRPAASGPGGRGLGGPAGPGAGLRRTYTFVGVLFACALIGFLSLRL +LGVERGSMTLPAALGVLAVAAVAAAVITRVVGRR +>PROKKA_01768 +MPPLHHGQPGDDGDPRDPRHRPGAGLGPGLRSVWMFVGVMFTCALIVFWTLRGFGVQRGD +LSLPAALGVLALAAVAAAVITRYVRRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001493.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001493.fa new file mode 100644 index 0000000000000000000000000000000000000000..8f6b87cbe6e3e866ac5546043c290fb0a2288dfd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001493.fa @@ -0,0 +1,25 @@ +>PROKKA_01849 +MSVRVMLVDDHPVVRAGVRAVVEAHPDLTVVAEAADGAEAIGVLEAGEPAVDVVLMDLQM +GAGMDGVTATRAVRERWPGVQVLILTTFDTEADILAAVNAGAAGYLLKDAPSEEIASAVR +QAAAGRKALAPQVAATLMGRMSGGSEVLSEREIQLLELIARGATNKVAAKELFISEATVK +THLVHIFQKLGVDNRTRAVDEARRRRIIR +>PROKKA_01545 +MSARVMLVDDHPVVRAGVRAVVEAHPDLTVVAEAADGAEAIGVLEAGEPAVDVVLMDLQM +GAGMDGVTATRAVRERWPGVQVLILTTFDTEADILAAVNAGAAGYLLKDAPSEEIASAVR +QAAAGRKALAPQVAATLMGRMSGGSEVLSEREIELLELIARGATNKVAAKELFISEATVK +THLVHIFQKLGVDNRTRAVDEARRRRIIR +>PROKKA_01019 +MTVHVMLVDDHPVVRAGVRAVVEAHPDLRVVAEAADGAEALRILEAASGPVDVVLMDLQM +GEGMDGVSATRAVRERRPDVQVLILTTFDTEADILAAVDAGAAGYLLKDAPSEEIARAVR +QAAAGQKALAPQVAATLMGRMAGGADVLSAREIELLELIARGATNKAAAKELFISEATVK +THLVHVFQKLGVDNRTRAVDEARRRRIIR +>PROKKA_00961 +MSVRVMLVDDHPVVRAGVRAVLEADPELTVVAEAGDGAAALDVLQARPGEVDAVLMDLQM +GEGMDGVSATRRLRAAHPGIPVLILTTFDTEADILAALDAGAAGYLLKDAPAEQIADAVH +RAVAGRPALTPDVAERLLGRTTGATAASALSAREIELLELIARGDTNREAARALFLSEAT +VKTHLVHIFQKLGVDTRTQAVHEARARRIIR +>PROKKA_01769 +MSVRVMLVDDHPVVRAGVRAVVEAHPDLSVVAEAADGAEAIGVLEAGEPAVDVVLMDLQM +GAGMDGVTATRAVRERWPGVQVLILTTFDTEADILAAVNAGAAGYLLKDAPSEEIASAVR +QAAAGRKALAPQVAATLMGRMSGGSEVLSEREIQLLELIARGATNKVAAKELFISEATVK +THLVHIFQKLGVDNRTRAVDEARRRRIIR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001495.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001495.fa new file mode 100644 index 0000000000000000000000000000000000000000..c07c3a0d37c3032e6177b160d0e4aeb28d1ff504 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001495.fa @@ -0,0 +1,40 @@ +>PROKKA_01851 +MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAAIDRLGEQGVQRLVF +GGAAGQEPTASFTQSEFTVAQRDAWAATDGVASVEPLGVSQGRAIGLEHPVDTDPQGRAD +VSGEPTTGVATTAFIGLTPGGSDAPAGVELGQIVLSQDVADSLHAQAGDAVAVSGFVYTV +ADVVPTEYYSHSPVTWLALEDWNAISHTADDAVLGTAGLVRFDAGADVDAVAAAGDDAAG +TVAETVKGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG +GSNGWVLKDSLAQAAFVLVGGVAVGTGLAAVIGAFAGRAVPFELSWATTAVPAAGVLVLG +MLAAVIAVYRVTRIDPLVALGGN +>PROKKA_01547 +MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAAIDRLGEQGVQRLVF +DGAAGQEPTASFTQSEFTVAQRDAWAATDGVASVEPLGVSQGRAIGLEHPVDTDPPGRAD +VSGEPTTGVATTAFIGLTPGGSDAPAGVEPGQIVLSQDVADSLHAQEGDAVAVSGFVYTV +ADVVPTEYYSHSPVTWLALEDWNAISHTADDAVLGTAGLVRFDADTDVDAVAAAGDDAAG +TVAETVKGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG +GSNGWVLKDSLAQAAFVLVGGVAVGTGLAAAIGAFAGRAVPFELSWATTAVPAAGVLVLG +MLAAVVAVFRVTRIDPLVALGGN +>PROKKA_01017 +MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAALDRLEEQGVQRLVF +GGAAGQEATASFTQSKFTAEQRDAWAATDGVASVEPLGVSQGRAVGLAHGVETDEAGRAD +VADVPTTGVASTAFLGLVPGGADAPAALAPGEVVLSSDVADSLGAQAGDAVAVSGFVFTV +AEVVPNEFYSHSPVTWLALEDWRAISHTADDAVLGTAGLVRFAAGADPDAVAAAGDAAAG +TVSETVRGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG +GTDGWVLKDALTQAAFVLLGGVLVGTALAAGIGVLAARGVPFELSWATTLVPAAGILVLG +MLAAVAAVFRVTRIDPLVALGGN +>PROKKA_00959 +MFLALRDLRFATGRFSLMGAVVALITVLLVMLSGLTAGLGHQNTAALDDLGARGTDRIVF +GGTAGQDPTASFTSSEVTAAQLDSWCAADGVARVEPVGVAQGRLTGVAGHVDTDAAGRPA +ETPEVAGVGSASFVGLDPAAPQAPAGLEDGELVLSQALAEALEVEEGGQVESSGRVYTVA +SVAADSWYSHTPVAWTTLTDWRALSHTEDADVAGTAGLVTLVDGADADAVASAADDAAHT +VATDVKGAYAALPAYSSEHGSLTMMQGFLYGISALVVVAFLSIWTIQRTREIAVLKALGA +STGWVLRDSLLQGGIVLAVGVGLGTALAAGAGWFAAQAVPFVLSPATTVLPALGVLALGL +AGSALAVARVTRIDPLIALGGN +>PROKKA_01771 +MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAAIDRLGEQGVQRLVF +GGAAGQEPTASFTQSEFSVAQRDAWAATDGVASVEPLGVSQGRAIGLEHPVDTDPQGRAD +VSGEPTTGVATTTFIGLTPGGSDAPAGVEPGQIVLSQDVADSLHAQEGDAVAVSGFVYTV +ADVVPTEYYSHSPVTWLALEDWNAISHTADDAVLGTAGLVRFDAGADVDAVAAAGDDAAG +TVAETVKGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG +GSNGWVLKDSLAQAAFVLVGGVAVGTGLAAVVGAFAGRAVPFELSWATTAVPAAGVLVLG +MLAAVVAVYRVTRIDPLVALGGN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001497.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001497.fa new file mode 100644 index 0000000000000000000000000000000000000000..2733cedaf6f293aa876c5f56dd50fe48ddb1332a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001497.fa @@ -0,0 +1,20 @@ +>PROKKA_01854 +MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRATAVRFALEELATRVPGN +SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV +RADLGAHLPLVRP +>PROKKA_01550 +MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN +SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTSWDEATAAGGVRASGV +RADLGAHLPLVRP +>PROKKA_01014 +MTTGSVPRRRIPVPEGHAALTSWARTHAQDPAAAAALPRSTRATAVRFALEELATRVPGN +AVEVRVPPFGVAQAIPGPRHTRGTPPNVVEMDAVTWLSLATGLLGWADAVGTGAVRASGT +RADLGAHLPLIRP +>PROKKA_00956 +MTTGSVPKRRVPVVEGHAALTAWARAHAEDPAAAAALPRSTRATAVRFALEELATRAPGN +SVEVRVPPFGVAQCIPGPRHTRGTPPNVVETDPVTWLSLATGLTRWNDAVASGAVRASGV +RADLAGHLPLVRP +>PROKKA_01774 +MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN +SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV +RADLGAHLPLVRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001500.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001500.fa new file mode 100644 index 0000000000000000000000000000000000000000..75febb07f7b8f719898f48870940b0598afa2ca2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001500.fa @@ -0,0 +1,40 @@ +>PROKKA_01857 +MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL +LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG +KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAADEYDVAGAATGVVEADMVLGA +ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR +ACLDLVQRLNGHEGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL +VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA +AGLNFVQGAKGVDGGAVLMRGQYAA +>PROKKA_01553 +MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL +LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG +KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAVDEYDVAGAATGVVEADMVLGA +ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR +ACLDLVQRLNGHEGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL +VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA +AGLDFVHGAKGVDGGAVLMRGQYAA +>PROKKA_01007 +MTENQNTAHDAPITYASAGVDVEAGDRAVELMKDAVKATHSPEVMGGIGGFAGMWDASAL +LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGATPLFMTDYIACG +KVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLGVDEYDVAGAATGVVDADMVLGA +DRVQTGDVLIGMASSGIHSNGYSLVRRVVNAAGWSLDREVSELGRTLGEELLEPTRIYAR +SCLDLVQRLNGHDGGSGLPVRAFSHVTGGGLAANLARVLPQGLMATVERETWSLPPVFRL +LAEAGRVPQPDLERTLNLGVGMVAVVDPEIAAKSISVLVDAGIDAWEMGTIGHVTDEAAG +AGLDFVQGAKGVDGGAVLMRGAYAA +>PROKKA_00951 +MTDAPRTETQTADALDAPLTYAAAGVDVEAGDRAVELMKDAVKATHTAEVLGGVGGFAGM +WDASALTGYRKPLLATSTDGVGTKVAIAQALDRHDTIGQDLVGMVVDDIVVVGAKPLFMT +DYIACGKVVPERVADIVRGVAEGCRLAGTALVGGETAEHPGLLAVDEYDVAGAATGVVEA +DRVLGAERVRSGDVVIGMASSGIHSNGYSLVRRVINAAGWQLDRDVDELGRTLGEELLEP +TRIYTRACLDLMDSLNGTEGGADLSLRGFSHVTGGGLAANLARVLPQGMMATVDRGTWAL +PPVFRLVGELGRVPLADLERTLNLGVGMVAVVAADAADRAVAAIEAAGIPAWVMGGIDEV +TEQAQAAGEDYVQGAKGVDGGAVLMTGTYAD +>PROKKA_01777 +MTPNQTPSSAAPITYASAGVDVEAGDRAVELMKDAVKATHTPEVMGGIGGFAGMWDASAL +LQYRKPLLTTSTDGVGTKVAIAQAMDKHDTIGQDLVGMVVDDIVVVGAQPLFMTDYIACG +RVVPERIADIVRGVAEGCRLADTALVGGETAEHPGLLAAEEYDVAGAATGVVEADMVLGA +ERVQSGDVVIGMASSGIHSNGYSLVRRVVNAAGWSLDREVTELGCTLGEELLVPTRIYSR +ACLDLVQRLNGHDGGSDLPVRAFSHVTGGGLAANLARVLPQGLMATVERDTWSLPPVFRL +VGELGRVPQSDLERTLNLGVGMVAVVDPEVAATSISVLVDAGIDAWEMGTIGALTDDAAA +AGLDFVQGAKGVDGGAVLMRGQYAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001502.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001502.fa new file mode 100644 index 0000000000000000000000000000000000000000..b44f5dc5036ef5f11ed68d09110bd3c9f836387e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001502.fa @@ -0,0 +1,35 @@ +>PROKKA_01859 +MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEESRPLVITGAGVSTDS +GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA +AEGRIAGVLTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE +AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPPA +RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR +APVADALAWLDARL +>PROKKA_01555 +MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEESRPLVITGAGVSTDS +GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA +AEGRIAGILTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE +AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPAA +RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR +APVADALAWLDARL +>PROKKA_01004 +MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLLEETRPLVITGAGVSTDS +GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNAAHRILAGWA +VRGLVSGILTQNVDGLHAQAAAEAGAPEDRLIELHGDLARVVCLHCGATESRRDLDVRLE +AANLGYLERVSIDPEAVNPDGDVTLDRHWVDEFAMVGCLRCGSVELKPDVVYFGESVPVA +RREAAEAMADDGGAVLAVGTSLAVMSGYRFVLRAERAGKDTGLINLGSTRADPKASWRWR +APVADALAWLDSRL +>PROKKA_00947 +MTPVRHPSQDGHQAALRSIARVVGETAPLQDPETASRGLLRMLEAGRPLVITGAGVSTDS +GIPDYRGPNGTLHRHRPMTYQEFRDDPAARHRYWARSFVGWRHMDEAAPNAAHHVLADWV +RRDVVAGIVTQNVDGLHAQAFAAAGAAPSRLIALHGDLARVVCLQCGAMEDRTSLDARLA +AANPGYLEAVTVDPDAVNPDGDVTLDQRWVDAFTMVGCRVCGSVQLKPDVVYFGENVPPA +RRDAARALAEEADSVLAVGTSLAVMSGFRFVLDAERAGKEVGVITLGPTRADPKAQWRWR +TRVAEALAWLDARL +>PROKKA_01779 +MTPARHPALDGHQAALRSIARVVDETAPLQDPETASRGLLRLMEEFRPLVITGAGVSTDS +GIPDYRGPNGSLHRHRPMTYQEFRDDPAARHRYWARSFVGWRRMDQARPNEAHRILARWA +AEGRIAGILTQNVDGLHAEAGRAAGMPEDRLIELHGDLARVACLNCGATESRRDLDLRLE +AANPGYLERVAIDPDAVNPDGDVSLDQHWVEEFTMVGCRVCGSVKLKPDVVYFGESVPAA +RRAAAEAMADDGGTVLAVGTSLAVMSGYRFVLRAERAGHETGLINLGPTRADAKARWRWR +APVADALAWLDARL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001503.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001503.fa new file mode 100644 index 0000000000000000000000000000000000000000..e0bd5636698ac1d50fbfe56e79fafe8768c65f6b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001503.fa @@ -0,0 +1,15 @@ +>PROKKA_01860 +MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRGPEQDQEPEYEDPYADLYAED +EDDDARAR +>PROKKA_01556 +MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRGPEQDQEPEYEDPYADLYAED +EDDDARAR +>PROKKA_01003 +MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRAPEPELDQKPEYEDPYADLYT +DDDEDDDARAR +>PROKKA_00946 +MGRGRQKAKATKQAREMKYMSLGTDLSALERELTGGRTDAPAVEPEVDYEDPYADLYADD +DEDDDSRVR +>PROKKA_01780 +MGRGRQKAKATKQAREMKYFSPGTDLSALERELTGGRTRSPEPDQEPEYEDPYEDLYAED +EDDDARAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001506.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001506.fa new file mode 100644 index 0000000000000000000000000000000000000000..140595bb6aaf4e8b9856091161e34292315947a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001506.fa @@ -0,0 +1,40 @@ +>PROKKA_01863 +MAGSTAAPRRLRTYTRPRVSLLYVLRRTLHRLFELQVWDVAAAMTFFGALSLLPTVIALL +SVVSLLGVEEETVDAAAHLAAEIWPSLTPDVVREWILTLGSAGPGTGAVVLGAVGTVVSA +SGAVGAFHRAMHRIHDTREGRPFLHFRLVVFVETLALMLGAVLITILVVVGGDLSLRLGQ +AVGLPEETVQTWNVVKWPVILVVIALIVTLAYRLGPNVRQPRYRPLSLGAVAVVVLLFGA +TVALGWITDRFGQFAVVGRINSAIGVLALAWVACIVLLAGAAFDAEVLRARQLAVGIDAS +VEIQLATRHTAVLEASERYEARNRRLARLVADAVRAGEDLTIEATPLLSEEGRLLAVESG +RRDPEDVSSGSPFHADPVSHDGARLEPTPRPDD +>PROKKA_01559 +MAGSTAAPRRLRTYTRPRVSLLYVLRRTLHRLFELQVWDVAAAMTFFGALSLLPTVVALL +SVVSLLGVEEETVDAAAHLAAEIWPSLTPDVVREWILTLGSAGPGTGAVVLGAVGTVVSA +SGAVGAFHRAMHRIHDTREGRPFLHFRLVVFVETLALMLGAVLITILVVVGGDLSQRLGQ +AVGLPEETVQTWNVVKWPVILVVIALIVTLAYRLGPNVRQPRYRPLSLGAVAVVVLLFGA +TVALGWITDRFGQFAVVGRINSAIGVLALAWVACIVLLAGAAFDAEVLRARQLAVGIDAS +VEIQLATRHTAVLEDFERYEARIRRLARLVAEAVRAGESLTIEATPLLSEEGRLLAVESG +GRGPEDVSSGSPFHADPVSDDGARLEPTPRPDD +>PROKKA_00997 +MSGSTAAPRRLRTYARPRVSLLYVLRRTTHRLLELQVWDVAAAMTFFAALSLLPTVVALV +SLVSLLGVQEETVDAAAQLATEIWPSLTPDTVREWILTLGSAGTGTAAVVLGILGAVVSA +SGAVGAFHRAMHRIHDTREGRPFLQFRLVLLVETLALMVGIVLVVILVVLGGDLSLRIGQ +AVGLPEETVLTWNVVKWPVILVVIALTVTLAYRLGPNVVPPRYRPLSAGAVSVVVLLFAA +TLALGWITDRFGQFAVVGRINSAIGVLVLAWIACIVLLAGAALDAEMLRGRQLAVGVDAA +SEIQLATRHTVVLEAAERHEDRSRRLARLVAEAVREDEDLSIDATPLLSQEGRMFAIGSA +RRTAAEVSSGRPFHAAPVLDDGARLEPTSRPDD +>PROKKA_00936 +MPSSPVPDASTGGRAPRTYARPRASLLYVLERTWTRLVGMQVWDVAAAMTFFAVLSLLPT +LVALVSLVSLLGVEARTVETAARLATEVWPSLDAAEVSAWILNAGRTATGTPGLVLGAAG +AVVSASGAVGAFHRAMHRIYDTREGRPFLVYRLVVLLETLALIVGAALVMSLMVLGGDLS +ERLGRLLGVGRGAVAVWNASTWPMILVLLALIVSVAYRRGPNVRPPCHRPFSLGAVGAVA +LLFAAALALGWIVARFGGLALVGRLNSALGVLGLAWAACIVLVAGAAFDAEMLRARQLAV +GVESADELQLATRDTWVLRQVERQEARHLRVGRLVAEAVRTEEPVTTPATRLLAEAGSLF +AVDAAGRSASDLTSGRPFHAVPPADRAGV +>PROKKA_01783 +MAGSTAAPRRLRTYTRPRVSLLYVLRRTLHRLFELQVWDVAAAMTFFGALSLLPTVIALL +SVVSLLGVEEETVDAAAHLAAEIWPSLTPDVVREWILTLGSAGPGTGAVVLGAVGTVVSA +SGAVGAFHRAMHRIHDTREGRPFLHFRLVVFVETLALMLGAVLITILVVVGGDLSLRLGQ +AVGLPEETVQTWNVVKWPVILVVIALIVTLAYRLGPNVRQPRYRPLSLGAVAVVVLLFGA +TVALGWITDRFGQFAVVGRINSAIGVLALAWVACIVLLAGAAFDAEVLRARQLAVGIDAS +VEIQLATRHTAVLEASERYEARNRRLARLVADAVRAGEDLTIEATPLLSEEGRLLAVESG +RRDPEDVSSGSPFHADPVSDDGARLEPTSRPDD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001507.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001507.fa new file mode 100644 index 0000000000000000000000000000000000000000..0160d0455015fc1c807142f3236dc77445692a57 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001507.fa @@ -0,0 +1,27 @@ +>PROKKA_01864 +MGALALVGCAGGGGEASSSSADASKSAPTGAGSDLTDEQEERVEALEDVLLTPETAPGGV +FTGMETQAGGGEPISTSLSLTGVTPTGACADLIEQINTQQAPGLGGALAQYEVDPAAVTG +LAGSQAGAFGMVAVTDDGTDLLAPFGKLADTCGTFGDPDGVEAAFTKVPGVPDAAHIALG +NSGMDTALFTMTVGGVTDGDELVYLGMVGLDEEIAAETLRAQVEAFEARER +>PROKKA_01560 +MGAHALVGCAGGGGEASSSASADASESGPTGAGSDLTDEQEERVEALEDVLLTPQTAPDG +VFTGMETQAGGGEPISTSLSLTGVTPTGACADLIEQINTQQAPGLGGALAQYEVDPAAVT +GLAGSQAGAFGMVAVTEDGTDLLEPFGELADTCGTFGDPDGVEAAFTTVPGVPDAVHISL +GNSGMDTALFTMIVGGVTDGDELVYLGMVGLDEEIAAETLRAQVEAFEKRER +>PROKKA_00996 +MEALEDVLLTPQTAPDGVFTDMETQAGGGGEPISTSLSLTGVTPTGACADLIEQINTQQA +PGLGGALAQYEVDPDAVTGLAGSQAGAFGMVAVTEGGTDLLAPFGELADTCGTFGDPDGV +EAAFTKVPGVPDAAHIALGNSGMDTALFTMTVGGVTDGDELVYLGMVGLDEEIAAETLRA +QVEAFEKRER +>PROKKA_00935 +MSRTATSRPRLRALLPLTATAALLASGCAAPGPAASSSATPSSSASSAAAESSSSPTVST +GPASSSDASSSAAAASSSADASATTSSSSAADLAASSPAAGGASVENPLEPLLLLATAAP +QEVFSSRTVQSGADQPLTMSLTLTGVTPTGRCQELVDEINATHEPMDVASLATYQVNPAS +PAVVDQETGAFTMIGTSTAPADLMAPYGELVSACGTLEGEQGQKAEFTAVPGVPDAATVT +MTTPGQSRKLVMTVGGASEGRDHVYMLMLGLDADVSQQVLADQVAAFQER +>PROKKA_01784 +MLRPAAPARPAVALSLLAVGALALVGCGGGGGEASSSSADASESAPTGAGSDLTDEQEER +VEALEDVLLTPETAPGGVFTGMETQAGGGEPISTSLSLTGVTPTGACADLIEQINTQQAP +GLGGALAQYEVDPAAVTGLAGSQAGAFGMVAVTDDGTDLLAPFGKLADTCGTFGDPDGVQ +AAFTKVPGVPDAVHIALGNSGMDTALFTMTVGGVTDGDELVYLGMVGLDEEIAAETLRAQ +VEAFEARER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001508.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001508.fa new file mode 100644 index 0000000000000000000000000000000000000000..24dfd016ad5465d3014f2a80a2fb1fe41b314123 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001508.fa @@ -0,0 +1,30 @@ +>PROKKA_01865 +MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV +PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI +TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV +QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL +GSAVNRALQELRNDGTVAELQERWFGQAQEDYR +>PROKKA_01561 +MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDI +PYPPFEFEEKGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI +TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV +QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL +GSAVNRALQELRNDGTVAELQERWFGQAQEDYR +>PROKKA_00995 +MGLTASAALLTGCAVLGGDSGVAGVVSDDDLSTTYNLVQPGVLTVCSDIPYPPFEFELDG +ELTGYDIQLVHAIAEELELGVNVIDSSFEAIESGASLTGCDLNASSISITEQRQRAMAFT +LPYLDDDLVLVAATDSGITDVESAKGRRVGVQAATTGDAYAKENGLNPIEFEDGGMQVQA +LQAGTVDALLGNQSVILYSLKDDERFEVVENLPTGEQLGMAVAPQNAQLGSAVNRALQQL +RNDGTVAELQERWFGLAQEDYR +>PROKKA_00933 +MPRTPSRALGAVGAGLSAALLSGCAVIGGDAGTTGPLAEDDLRATYRLHEPGVLTVCADV +PYPPFEFEQDGQLTGYDIDLTRKLAETMDLQLKVVDTSFEAIESGASLTGCDLNASAISI +TEPRQHVMAFTLPYLDDDLVLVARKDSGITDVASAQGKRVGVQTATTGEEYAQSQGLDTV +QFEDGGMQVQALQAGTVDALLGNQSVLLYSLKDDPRFGVVESLPTGEQLGMGVAPDNALL +GSAVNRALQTLRNDGTVAELQQKWFGTAQKDYQ +>PROKKA_01785 +MTRIHSRLLGTVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV +PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI +TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV +QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVELLPTGEQLGMAVGPQKAQL +GSAVNRALQELRNDGTVAELQERWFGQAQEDYR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001509.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001509.fa new file mode 100644 index 0000000000000000000000000000000000000000..a478907acf31847637ca1fcdd47ceebf523a5931 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001509.fa @@ -0,0 +1,30 @@ +>PROKKA_01866 +MSTQAPVSPAPAMKPGRARRRRRLSLIIQAAVFVLALVVLAVLIDWGALAENVLNFPAVA +PMFPNVILVGLGNTLFYTVTSFVVGLLGGIVLALMRLSSFGPYRWLATAYVEFFRGVPAL +LVFLAFGYGVPFAFGVSWPIPVVVMVALGMVSAAYIAETLRAGLQAVPRGQMEAARSLGM +PTWRAMVTIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD +AGMTPILVAGLFYLVITVPLSLLARRFETRSTKKGH +>PROKKA_01562 +MSTQAPVSPAPAMKPGRARRRRRLSLIIQAAVFVLALVVLAVLIDWGALAENVLNFPAVA +PMFPNVILVGLGNTLFYTVTSFVVGLLGGIVLALMRLSSFGPYRWLATAYVEFFRGVPAL +LVFLAFGYGVPFAFGVSWPIPVVVMVALGMVSAAYIAETLRAGLQAVPRGQMEAARSLGM +PTWRAMVTIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD +AGMTPILVAGLFYLVITVPLSLLARRFEARSTKKGH +>PROKKA_00994 +MFVLAIVVLALLIDWGTIGENVLNFPAVAPLFPNIILVGLGNTLFYTATSFVVGLLGGIA +LALMRMSAFAPYRWLATAYVEFFRGVPALLVFLAFGYGVPFAFGVSWPIPVVVMTALGMV +AAAYIAETLRAGLQAFPPGQMEAARSLGMPAWQAMITIVIPQAFRIVLPPLTNEVILLTK +DSSLVYVLGLAAHEYELTKFGRDGISALDAGMTPILVAGLFYLVITVPLSLLARRFEARS +TKKGH +>PROKKA_00932 +MSTQASPAPRTAAAPSRAGRRRTLSVAVQAAVFVLAIVVVALLADWQAIAENVLNFSAAG +PMFPNVILVGLGNTIFYTVTAFVVGLLGGMLLALMRMSSFAPYRWLATAYVEFFRGIPAL +LVFLAFGYGVPFAFGVSWPIPVVVMIALGMVSAAYIAETLRAGLQAVPKGQMEAARSLGM +PHWRAMLTIVIPQAFRVVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGIAALD +AGMTPILVAGLCYLVITIPLSLLARRFEARSSRKAH +>PROKKA_01786 +MSTQAPVSPAPAMKPGRARRRRRLSLIIQAAVFVLALVVLAVLIDWGTLTENVLNFPAVA +PMFPNVILVGLGNTLFYTVTSFVVGLLGGIVLALMRLSSFGPYRWLATAYVEFFRGVPAL +LVFLAFGYGVPFAFGVSWPIPVVVMVALGMVSAAYIAETLRAGLQAVPRGQMEAARSLGM +PTWRAMVTIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD +AGMTPILVAGLFYLVITVPLSLLARRFETRSTKKGH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001511.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001511.fa new file mode 100644 index 0000000000000000000000000000000000000000..5e42974f1eb61475c6d44931c3fa20a3c387cd85 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001511.fa @@ -0,0 +1,25 @@ +>PROKKA_01868 +MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMGARGLPALANLSPEQFKKFLVTT +EIGVGSALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTGVAKDIFL +VGSGLAIAADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV +AALREARDELKKLRKKA +>PROKKA_01564 +MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMGARGLPALANLSPEQFKKFLVTT +EVGVGAALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTGVAKDIFL +VGSGLAITADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV +AALREARDELKKLRKKA +>PROKKA_00992 +MSIVQIPLRLASGAFILNSGLNKRNISEEQAAGMRDMGAQGVPYLAKLTPAQFKNFIVAT +EVGTGAALLAPFVPGWLAGSALTAFSGGLMSMYLNTPAMTEKDGVRPSQEGTGVAKDVFL +VGSGLAIAADSVANRSGKRRKAAKKRAARIGNARDAKVQAIRDAQDEKVAAIHAARDEQV +AALREAREELKKLRQKA +>PROKKA_00930 +MSIIQIPLRLTSGAFILNSGLGKRKLGEEQAAYLQNMAAKGVPSLAKLSPSQFKNFITAT +EIGTGAALLAPFVPGWLAGSALTAFSGGLMSMYLNTPEMTEADGVRPSQDGTAVAKDVFL +LGAGLAVTADSVVNRPGKRKKAAKKRAARISDARDAKVDAIRAAQDEKVAAIHEAREQQV +AALREARQELAKLRKKA +>PROKKA_01788 +MSIVQIPLRLASGAFILNSGLNKRGISAEQAQGLRDMSARGLPALANLSPEQFKKFLVTT +EIGVGSALLAPFVPGWLAGSALTAFSGGLFSMYLNTPEMTEADGVRPSQEGTAVAKDIFL +VGSGLAIAADSVANRPGKRRKAAKKRAARIEGARDAKVQAIRDAQDEKVAAIHAAREEQV +AALREARDELKKLRKKA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001514.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001514.fa new file mode 100644 index 0000000000000000000000000000000000000000..c01c788079a1645d4db18436ed79c963ef98efb5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001514.fa @@ -0,0 +1,35 @@ +>PROKKA_01871 +MTEHLPRPCPDAPGPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV +WDRQAERVLVDVPRGRGATSVDGQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD +WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH +KKRHHKRRLVSPAFADRVARVLTPGGVLRLATDWSGYAVQMREVLEAHPEFENLFPGRAA +GEDSPLTRVRREGRETEVGAQPLPAGWESAAEEERPLRAGLGEARAGAAAADPVDHDGGW +APRFEGRPITSFEAKSQRAGRLVFDLAYRRR +>PROKKA_01567 +MTEHLPRPCPDAPGPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV +WDRQAERVLVDVPRGRGATSVDGQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD +WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH +KKRHHKRRLVSPAFADRVARVLTPGGVLRLATDWSGYAVQMREVLEAHPGFENLFPGRAA +GEDSPLTRVRREGRETEVGAQPLPAGWESAAEEERPLRAGLGEARAGAAAADPVDHEGGW +APRFEGRPITSFEAKSQRAGRLVFDLAYRRR +>PROKKA_00989 +MTEQPPAPDAPSRGTPANDGRDGVLAPHERAHEHDHNRDKDPALMRREPVSFVRRGARLN +SGRQAVWDRQAQRVLVDVPRERGATSVARDARLDWDAAFGRRAPLLVDIGSGLGESTAQA +AADRPDWNVLAVEVYVPGLAALMTRVEQSGLENVRAVEANAPELMDHLLAPGSVSEVWVF +FPDPWHKKRHHKRRLVSPAFADRVARVLAPGGVLRLATDWSGYAVRMREVMEAHPEFENL +HPGRAAGEKSPLTRVRREGREAEVGAQPLPAGWESAAEDERPLRAGLGEALEAAVAEDPV +DHEGGWAPRFEGRPVTSFEAKSRRAGRLVFDLAYARR +>PROKKA_00926 +MTGGPENAHERDHDREKDPELIRREPVSFVRRGARMTTGRQAVWDRMAETVLVDVPRHRA +ATSVAPDAHLDWDAAFGRHAPLLVDIGSGLGESTAQGAADHPDWNVLSVEVYLPGLAALM +AQVESRGLENVRAVEANAPELLDHLLPAGSAQEVWVFFPDPWHKKRHHKRRLVNAAFADR +VARVLAPGGVLRLATDWSGYAVQMREVMESHPDFVNLHPGRAAGEESPLTRVRREGRELE +VGAQPLPAGFDPARPASELPERAGLGEAVEASLAEDPVDHDGGWAPRFEGRPLTQFEGKA +LRAGRLVFDLAYARR +>PROKKA_01791 +MTEHLPRPRPDAPDPDAVPPPAERVHAHDHNRDKDPALVRREPVSFVRRGARLNAGRQAV +WDRQAERVLVDVPRGRGATSVDAQARLDWAGVFGREAPLLVDIGSGLGESTAQAAADRPD +WNVLAVEVYVPGLAALMTRVEQQGLENVRAVEANAPELLDALLTPGSVSEVWVFFPDPWH +KKRHHKRRLVSPAFADRVARVLAPGGVLRLATDWSGYAVQMREVLEAHPEFENLFPGRAA +GEDSPLTRVRREGRETEVGAQPLPAGWERAAEEERPLRAGLGEARAGAAAADPVDHEGGW +APRFEGRPITSFEAKSQRAGRLVFDLAYRRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001515.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001515.fa new file mode 100644 index 0000000000000000000000000000000000000000..f3940c39aa3ad163dddeaa00a6161af78047a05a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001515.fa @@ -0,0 +1,35 @@ +>PROKKA_01872 +MQERLRADMARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLEGPDGPRAVVA +AGDPATATHLTWLVSGMGIRPQTALWGTAREAAHLAAAQRAAGAPRPVVIGWLGYPAPTP +WRVVLDGPGRRGGAMLAADVRAWWEFLRHGPGEDDDVAPALRARGTAVHGAVEAHSYGSL +VAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGTVGLPAALAARSAHLGLRSGRTFR +ALAPGDLLARVGRAVGRRRDWTDAAVLPVAPRPGLAGAAVRGHRTARWSPTAPEDAPRGY +RDAGSVTLAATARVTAGLPLSPVPDGADPAGPVAPA +>PROKKA_01568 +MQERLRADMARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLEGPDGPRAVVA +AGDPATATHLTWLVSGMGIRPQTAMWGTAREAAHLAAAQRAAGAPRPVVIGWLGYPAPTP +WRVVLDGPGRRGGAMLAADVWAWWEFLRHGPGEDDDATLALRARGTAVHGAVEAHSYGSL +VAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGAVGLPAALATRAAHLGLRSGRTFR +ALAPGDLLARVGRAVGRRRDWTDAAALPVAPRPGLAGAAVRGHHTARWSPTASEDAPRGY +RDAGSVTLAATARVTAGLPLSPAPDGADPAGPVAPV +>PROKKA_00988 +MARRDGLGRQARSALDGIVHALKPEGMDPHLPARHLLDYVLDGPDGPRAVVAAGDPATAT +HLTWLVSGMGIRPHTAMWGTAREAAQLAAAQRAAGAPRPAVLAWLGYAAPTPWRILLDGP +GRRGGERLADDVAAWWDFARTGAGETEDRAGEPDDDRPSLRARGTALHGAVEAHSYGSLV +AAHALRLLAERGLQPDDVEVLDDTDGGADADAGAQDTARPAERPVEALVVSGAVGLPAAF +AARAGRLGLPPGRVFRAQAPGDVLARVGRALGRRRDWTDAVLLPVTPRPGLEGGAVHGHR +TARWSPAAGTDAPRGYRDPGTVTLAATARVTAGLPLPPEPA +>PROKKA_00925 +MDLPEQARAAAARLDADRARARDGRLSARQLAALDGAEHALRRDSMDAAIPERVLVDWDL +DAPDGPVAAVAVGELERPTHLTWQVSGMGIAASTAAWGSAREAGQLLLAQRAAGAPRPCV +VAWLGYPAPPWWRTLDDGLARRGGARLAEAVRETRPGPSHGAGTAVHTAIEAHSYGTLVA +THALEGLAAGDPPLTVDALALSGALGLPRRLAGRLEALGLAAGRVFEARAPGDRLAWLGR +TLAGRAPWPEAVALPVAADPAAGLAGVRGHNTARWRPEDGDDGAPRGYRDPGSVTLAALA +RVTAGLPVAGGGPRSGQRRA +>PROKKA_01792 +MAARSRVRERLRADMARRDGLGRRARSALDGIVHALKPEGMDPHLPARHLLDYVLDGPDG +PRAVVAAGDPATATHLTWLVSGMGIRPQTAMWGTAREAAHLAAAQRAAGAPRPVVIAWLG +YPAPTPWRVVLDGPGRRGGAMLAADVRAWWEFMRHGPGEDDAAAPALRARGTAVHGAMEA +HSYGSLVAAHALRLLADRGLQPDDAEAPWPAERPVEALVVSGAVGLPAALAARAAHLGLR +SGRVFRALAPGDLLARVGRAVGRRRDWTDAAVLPVAPRPGLAGAGVRGHHTARWSPTAPG +DAPRGYRDAGSVTLAATARVTAGLPLPPVPDGADPAGPVAPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001516.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001516.fa new file mode 100644 index 0000000000000000000000000000000000000000..cb3e43e46b1341959e72bbc6deafa343c700d67f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001516.fa @@ -0,0 +1,25 @@ +>PROKKA_01873 +MSARDGAARADRGREGGPDRHAPVFVISVAAEMADMHPQTLRQYDRLGLVVPARQDGRHR +RYSLADVERLQTVQTLSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA +RVFTVGSGGDVSARYADRMAVRRHAAARAGADTAGEACPSGLRRLPSGVAGLRRVPTWQS +EQD +>PROKKA_01569 +MSARDGAARADRGREGGPDRHAPVFVISVAAEMADMHPQTLRQYDRLGLVVPARQDGRHR +RYSLADVERLQTVQTLSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA +RVFTVGSGGDVSARYADRMAVRRHAAARAGADTAGEACPSGLRRLPSGVAGLRRVPTWQS +EQD +>PROKKA_00987 +MSARDGAARADRGRERGLDRNAPVFVVSVAAEMADMHPQTLRQYDRLGLVVPARQGGRHR +RYSLADVERLQTVQALSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA +RVFTVGSGGDVSARYADRMAARRQAAARTEADAAGQASPGVLRMLPSGGARPRRVLTWQP +EQD +>PROKKA_00924 +MVSGVAGEHPTGAGRLRGTAGRPGRHDPVFVISVAAEMAGMHPQTLRQYDRLGLVVPQRQ +GGRHRRYSAADVEHLRAVQRLSREGVSLEGIRRILDLQREVERLQDTVVELASQVDRLHS +ASALARVFSVGLAGDVSARYAAPAAHRAAEAVQGQRRPGEGATRSAARGGLLRALPAGRA +AAPRGLTRLPAPRD +>PROKKA_01793 +MSARDGAARADRGREPGLDRNAPVFVISVAAEMADMHPQTLRQYDRLGLVVPARQGGRQR +RYSLADVERLQTVQALSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA +RVFTVGSGGDVSARYADRMAARRQAAARTEADAAGQASPGVLRMLPSGGARPRRVLTWQP +EQD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001517.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001517.fa new file mode 100644 index 0000000000000000000000000000000000000000..aee4bb534638a8c0ee2caec49ab27814e1ab32aa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001517.fa @@ -0,0 +1,32 @@ +>PROKKA_01874 +MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARMYHPDQNPGDEAAEKKFKEISEAYA +VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRATQSEPDLSDL +FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG +ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF +PEAALGATIEVPTLERPVKVKVPAGSQCGRVLRLKGRGVERGKTTGDLLVELRVTVPTTL +NDDARAAVEALQSATAGDDPRRELARKAAW +>PROKKA_01570 +MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA +VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSEPDLSDL +FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG +ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF +PEAALGATIEVPTLDRSVKVKVPAGSQCGRVLRLKGRGVERGTTTGDLLVELRVTVPTTL +NDDARAAVEALQSATAGDYPRRELARKAAW +>PROKKA_00986 +MSLRAADGETIEVKIPKGIRDGQKVRARGKGAPGAAGRGDLLVTVHVREHEFFRRDGDDL +RITVPVTFPEAALGATIEVPTLERPVKMKVPAGSQSGRVLRLKGRGVERGTTKGDLLVEL +HVTVPTELNDDARAAVEALQSALAGDDPRRELARKAAW +>PROKKA_00923 +MASQDWLEKDFYQVLGVSKDASESDIKKAYRTLARKHHPDQNPGDAAAEQRFKEISEAYD +VLSDPKDRQEYDAIRSMGGGARFGAPGGFGGAGGGAGAGGFEDVFGGMFGGGGGSRTFRT +GGAQGGPDLSDLLGAFTGGGAGGFGGGQGFGGGGFGQPAPTKGADRTATTTISFRGAVEG +TTVSLRAADGETVDVRIPKGVKDGQKVRARGKGSPGTAGRGDLIVTVQVREHPFFQRDGD +DLRITVPVTFAEAALGATVEVPTLDRPVKVKVPAGSQSGRVLRLKGRGVAGAKHTGDLLV +ELQVAVPAELSAEARGAVEAYAAATAGDDVREGLAGKAQW +>PROKKA_01794 +MASQDWMDKDFYATLGVSKDASESDVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA +VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSGPDLSDL +FSGMFGGAAGQTGGFGDAGYPRPRPTKGADRTATTTISFRGSIQGTTVSLRAPDGETIEV +KIPKGIRDGQKVRARGKGSPGAAGRGDLLVTVHVREHEFFHRDGDDLRITVPVTFPEAAL +GATIEVPTLERPVKVKVPAGSQSGRVLRLKGRGVERGTTTGDLLVELHVTVPTELDDDAR +AAIEALQSALAGDDPRRELARKAAW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001519.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001519.fa new file mode 100644 index 0000000000000000000000000000000000000000..d6471a17a97ec2162b2804a00593a09522a428e0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001519.fa @@ -0,0 +1,60 @@ +>PROKKA_01876 +MSRAVGIDLGTTNSVVAALEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN +NPERTFASVKRHMGTDWTAEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA +YFNDAERQATKEAGEIAGLNVTRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL +LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE +AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI +KEAGVKVSDIDHVILVGGSTRMPAVSDLVKELTGGKEPNKGVNPDEVVAIGAAVQAGVLA +GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG +EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG +GSSLSKEDIDRMVKDAEAHADEDRKRREAADRRNQAEQSAYSVERLLQDNADKLPEDVKT +EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG +DDEDIVDAEVVDEDDEKKA +>PROKKA_01572 +MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN +NPERTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA +YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL +LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE +AAEQAKKELSSATSTSISLQYLSVTPEGPVHLDEHLSRAKFEDLTKDLLERTRKPFEDVI +KEAGVKVSDIDHVILVGGSTRMPAVSDLVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA +GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG +EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG +GSSLSQEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVERLLQDNGDKLPEDVKT +EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG +DDEDIVDAEVVDEDDEKKA +>PROKKA_00983 +MSRAVGIDLGTTNSVVAALEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN +NPERTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA +YFNDAERQATKEAGEIAGLNVTRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL +LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE +AAEQAKKELSSATSTSISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI +KEAGVKVSDIDHVVLVGGSTRMPAVSDLVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA +GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG +EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG +GSSLSKEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVDKLLQDNADKLPEDVKT +EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG +DDEDIVDAEVVDEDDEKKA +>PROKKA_00921 +MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGEVLVGEVAKRQAVN +NPDRTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA +YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL +LEVAKDEDDFATIQVRATSGDNRLGGDDWDQRIVDWLLQQAKSKGADLSNDKIALQRLKE +AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFNDVI +KEAGVKVSDIDHVVLVGGSTRMPAVSELVKELTGGKEPNKGVNPDEVVAIGASVQAGVLA +GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG +EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG +GSSLSKEDIDRMVKDAESHAEEDKARREAAERRNQAEQSAYSVDKLLADNADKLPEDVTT +EVQADVDALKAALEKQDNDDEVKAAFEKLQASQVKIGEALYAQQSAEGAQPDAESGSAQA +DEDIVDAEVVEDEDEKKN +>PROKKA_01796 +MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN +NPERTFASIKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA +YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL +LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE +AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI +KEAGVKVSDIDHVILVGGSTRMPAVSELVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA +GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG +EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG +GSSLSQEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVEKLLQDNGDKLPEDVKT +EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG +DDEDIVDAEVVDEDDEKKA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001520.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001520.fa new file mode 100644 index 0000000000000000000000000000000000000000..67b87d7941fa353e722a63a9971e2c1de0d237e0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001520.fa @@ -0,0 +1,21 @@ +>PROKKA_01880 +MTRPALIGLDGRSGSGKTVLAAALAARIAPFARVEVIEIESMYRGWDGLAAAVDDDGPYP +GVVRALRERGTATWTTWDWHRAAPGPPRRTAPADVVVCEGVGALSTAARPLLDLAVWLEL +ETPARRTRALARDGETFAPHWDRWAAQEEDYLARHAPRAAADLILRLPSA +>PROKKA_01576 +MTRPALIGLDGRSGSGKTVLAAALAARIAPFARVEVIEIESMYRGWDGLAAAVDDDGPYP +GVVRALRERGTATWTTWDWHRAAPGPPRRTAPADVVVCEGVGALSTAARPLLDLAVWLEL +ETPARRTRALARDGETFAPHWDRWAAQEEDYLARHAPRAAADLILRLPSA +>PROKKA_00979 +MSGPGPGRPVLIGVDGRSGAGKTVLADALAARLAPFARVAVLRIESMYPGWDGLAAAVDE +GGPYPAALRALHADGTAAWRAWDWHRGAPGEPTAIGPADVVVCEGVGALSVAARPLLDLA +VWLELETPARRSRALARDGETYAPHWERWAAHEEAYLARHGPRAAADLVVRLPSA +>PROKKA_00919 +MNASTEPGTARPGGPVSAPRPALIGLDGRSGAGKTTLAAALAARLAPHARVDVLHIEEMY +PGWDGLAAATADDGPYVRAVAALAAGRPAGWRAWDWHAGAPGEARALDPDALDVVVCEGV +GALCPGARPLLDLAVWVDAPEDVRRTAALARDGDAYAPHWERWARQEEAYLAAADPAGAA +DLRLST +>PROKKA_01800 +MTRPALIGLDGRSGSGKTVLAAALAARIAPFARVEVIEIESMYQGWDGLAAAVGDDGPYP +AVVRALRERGTATWTTWDWHRAAPGPPRRTAPADVVVCEGVGALSTAARPLLDLAVWLEL +ETPARRTRALARDGETFAPHWDRWAAQEEDYLARHAPRAAADLVLRLPSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001522.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001522.fa new file mode 100644 index 0000000000000000000000000000000000000000..b6c1969529e4adea4773edcb1e88899186de7be6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001522.fa @@ -0,0 +1,35 @@ +>PROKKA_01882 +MPAPGPDRPGAGVYPGRMRPTAFSPAAGSPVLVLLETDADGAPAPRLADPAVPHLSVTDQ +GVTRGDGIFETALAVADGLGTLRMRKLGAHLGRLAASAAALQLAAPEAAAWEAAVALGLR +AFTEANDVAPGDRLAVRLTVTRGPDAAPGAVPTPTAWALLSPAPAIQDEERQRGLRVLLL +DRGIDSQAPERSPWLLTGAKTLSYAVNMAALRYARAHGADDVVFTSADGYLLEGPTSTVL +IVRTGEDGVRRLLTPLRQKGILAGTSQAVIFAAAHADGWELGYGPLVPADLQGAEGVWLV +SSVRGVLPVRAVDGVEIPVDHELTGMLQAHLDADGDPGRHVSGDPVPTAG +>PROKKA_01578 +MSPTPFSPSPGEPVLVLLEAGADGARLPRVADPAVPHLRVSDQGVTRGDGLFETALAVAD +EAGVLRMRKLGAHLGRLASSAAALQLPAPSAAAWEAAVERGLQAFAAANDVAAGDRLSVR +LTVTRGPEAAPGAVPEPSAWALLSPAPAVEDEERRTGLRVLLLDRGLDSRAPERSPWLLT +GAKTLSYAVNMAALRHARDHGADDVVFTSADGYLLEGPTSTVLIVRTGEDGVRRLLTPLR +QKGILAGTSQAVIFAAAHADGWELGYGPLVPADLQGAEGVWLVSSVRGVLPVRAVDGVEI +PVDHELTGMLQAHLDADGDPGRHVSGDPVPTAG +>PROKKA_00976 +MLLEVGADGARLPRVADPAVPHLRVSDQGVTRGDGLFETALAVADETGVLRMRKLGAHLG +RLASSAAALQLPAPSAAAWEAAVERGLQAFAAANDVAAGDRLSVRLTVTRGLEAAPGAVP +EPSAWALLSPASAVEDEERRTGLRVLLLDRGLDSRAPERSPWLLTGAKTLSYAVNMAALR +YARAHGADDVVFTSADGYLLEGPTSTVLIVRTGADGTRRLLTPLRQKGILAGTSQAVIFA +AAGAAGWELGYGPLVPADLEGADGVWLVSSVRGVLPVRAVDGVEIPVDHALTLELQAHLD +ADGDPGAHVAGDPAPTAG +>PROKKA_00914 +MPTSNPAPAAHTPAPGEPVLVLLSPDADPRLADPAAPHLSVTDQGVTRGDGLFETALAVA +DETGTFAMRKLAAHLGRLASSADALGIAAPDPEPWRAAIEAGLAGFAAANPVAPGDRLSV +RLTVTRGPEAPAGVEARPTAWALLTPAPRTSDAERAEGVRVLLLERGLDSAAVEGAPWLL +TGAKTLSYAVNMAALRHAKAHGADDVVFTSADGYLLEGPTSTLLLARTGADGTRRIVTPL +RQKGILAGTSQSVIFAAAEAAGWRLGYGPLAPADLDGADGLWLVSSVRGVLPIRAVDGQD +VPVDAELTERLQAWLDADGDPGVHVSGDPVRDED +>PROKKA_01802 +MPAPGPDRPGAGVYPGRMRPTAFSPAAGSPVLVLLETDADGAPAPRLADPAVPHLSVTDQ +GVTRGDGIFETALAVADGLGTLRMRKLGAHLGRLAASAAALQLAAPEAAAWEAAVALGLR +AFTEANDVAPGDRLAVRLTVTRGPDAAPGAVPTPTAWALLSPAPAIQDEERQRGLRVLLL +DRGIDSQAPERSPWLLTGAKTLSYAVNMAALRYARAHGADDVVFTSADGYLLEGPTSTVL +IVRTGEDGVRRLLTPLRQKGILAGTSQAVIFAAAHADGWELGYGPLVPADLQGAEGVWLV +SSVRGVLPVRAVDGVEIPVDHELTGMLQAHLDADGDPGRHVSGDPVPTAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001523.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001523.fa new file mode 100644 index 0000000000000000000000000000000000000000..454749b0e186972138a6b07eee21b0bdd09ab218 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001523.fa @@ -0,0 +1,15 @@ +>PROKKA_01883 +MNTLAQKALSAGITLVGGIVGSRVVAGGWRLVTGHSAPNDAADETLPLIEALSFAFISAG +VAALLKVAGQRGAGAAIRKVSESTAHRVDHEV +>PROKKA_01579 +MNTLVQKALSAGITLVGGIVGSRVVAGGWRLVTGHSAPDDAADETLPLVEALSFAFISAG +VAALLKVAGQRGAGAAIRKVSESTAHRVDHEV +>PROKKA_00975 +MNTLAQKALSTGITLVGGIIGSRVVAGGWKLVTGHDAPDDAADETLPIVEALSFAFISAG +VAAILKVAGQRGAGAALRKVTESTAHRVDNEV +>PROKKA_00913 +MDKVIQKVLATGITVVGGIVASRLVAGGWKLVTGHDAPSDATDETVPLVEALAFTFASAG +IASVLKVAGQRAAAEGVRKVAQKTSSDVDNEV +>PROKKA_01803 +MNTLAQKALSAGITLVGGIVGSRVVAGGWRLVTGHSAPNDAADETLPLIEALSFAFISAG +VAALLKVAGQRGAGAAIRKVSESTAHRVDHEV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001524.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001524.fa new file mode 100644 index 0000000000000000000000000000000000000000..35af2d96f27b8b3fceb883f0aaf4a4ef190c06f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001524.fa @@ -0,0 +1,20 @@ +>PROKKA_01884 +MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLAI +EWRSWVWLPVLLLAWVTQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVVRRAEPPA +DPGPRRAGARPRGRR +>PROKKA_01580 +MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLGI +VWRSWVWLPVLFLAWITQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVGRRAEPPA +DPGPRRAGARPRGRR +>PROKKA_00974 +MTETATFLDWLSAALLVSGAFFTLVAGVGLLLLPDLLARMHASAKPQVLGLMLMLAGLAI +AWESWPWVPVLFLAWVTQMVTAPVASHLVGRTAYRTKHARRELLHRDELAAIARRVEPAP +ELDPRSPESRRRRRR +>PROKKA_00912 +MDAAWTDWLAAALLVGGAFFSLVAGVGMTLLPDLLSRMHASAKPQVLGLLLMACGVAVLW +QAWAWVPVLVLAWVTQMITAPVASHLISRTGYRTKHVRRDLLHRDDLAAQAEPGPREDPD +AR +>PROKKA_01804 +MTDTATLLDWLAAFLLVSGAFFSLVAGVGLFVLPDLLARMHAAAKPQVLGLLLMLAGLAI +EWRSWVWLPVLLLAWVTQMVTAPVASHLVGRTGYRTKHARRELLHRDELAAVVRRAEPPA +DPGPRRAGARPRGRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001527.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001527.fa new file mode 100644 index 0000000000000000000000000000000000000000..7715b8c97de3ee16a78c934a8ea575d5cc68b5be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001527.fa @@ -0,0 +1,55 @@ +>PROKKA_01887 +MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD +TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF +HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGVTYVVVSVLS +SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP +DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA +QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAG +TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG +VSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT +TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD +ARK +>PROKKA_01583 +MSIGSVPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD +TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF +HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGITYVVVSVLS +SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP +DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA +QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTTLFLVTGLIENRAG +TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG +VSLLVSLLTLLVVVRVWTRAFWRRVEDLEHPPAQLVAAYERAVARGERPRPLEPGLVLPT +TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD +ARK +>PROKKA_00971 +MSIGSVPMTDLAPLAVMMPVLGAAVTFMLVRRPRAQVVVTVAALVLTLLLNCLLLAAVWE +GGVASVHVGGWPAPLGITLVVDRLSALMLVVSALITLAVLLYASAQGMVNRDEGGPVSIF +HPTFLILVAGVFNAFLAGDLFNLYVGFEILLTASYVLLTMGGTAQRIRAGITYVVVSVIS +SVVFLIAIAMVYAATGTVNMADLAVKLGELPSDVQMVLHVLLLVGFGIKAAVFPLSFWLP +DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA +QTDIKRILSFILVSHIGYMIFGLGLATQMGLAATVFYVGHHITVQTALFLVTGLIENRAG +TANIDRLGSLAKVSPFISVLFLIPALNLGGIPPFSGFLGKVGLLRGGVEQGTGLSYTLVG +VSLLASLLTLLVVVRVWTRAFWRKVEDVEHPPAQLVAAYERTIDRGLRPRRLEPGLVLPT +AALVVMTLAFTVLAGPLFDLADAAATDMLDRTPYIASVLDEAAAERAAETLSHDPTEVHD +ARH +>PROKKA_00909 +MLGSTPLTDLAPLAVMLPVLGAAITFALVGRARAQVVVTVSALTLTLVLDCLLLADVWTG +GVAVVELAAWPAPVGITMVVDRLSALLLVVSSLITLAVLLYASAQGLINKDEGGPVSIFH +PTFLVLVAGVSNAFLAGDLFNLYVGFEILLTASYVLLTLGGTEARIRAGITYVVVSVISS +VLFLIAIAMIYAATGTVNMADLAVKLGELPHDLQLVLHVMLLAGFGIKAAVFPLSFWLPD +SYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPAEHVNGLLMGVAALTMLVGILGALAQ +SGLKRILSFILVSHIGYMVFGLALATQVGLAATVYYVGHHITVQTALFLVTGLIEQRAGT +ASIDRLGSLAKVSPLLGVLFLVPALNLGGIPPFSGFLGKVGLIRGGVEDGGVLAWVLVGV +SLLVSLLTLLVLVRAYTRAFWRKVEDVEHPTPQLVAAYERVTRRGLRPKPLSRGLVLPTA +GLVAMTLAFTVFAGPLYDLADRAAVDMLERSPYISAVLGPEAADRAAVTLSHDPSEVHDA +GR +>PROKKA_01807 +MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD +TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF +HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGVTYVVVSVLS +SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP +DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA +QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAG +TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG +VSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT +TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD +ARK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001529.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001529.fa new file mode 100644 index 0000000000000000000000000000000000000000..c795407dc25c94995dc5a4ac35dbc0ad73288777 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001529.fa @@ -0,0 +1,95 @@ +>PROKKA_01889 +MLVILTALFVVALAAPVLFRWTGRQGFYLLAAAPAAGFVWLLTQLPHVFALQEALDAGRP +VPASAARLDRAVPWVPYLETELAFRMDVLAAFMSLIVLGVGALVLAYCARYFREHEPRNA +VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT +TFGGLAMLAGLIMLAHFAGSWRISGVLEAAPALMADAGLRGLLEVAVALVLIGALTKSAQ +APFHFWLPGAMAAPTPVSAYLHAAAMVKAGVFLVARLAPEFHGLAMWQVLVIGVGLWTLL +LGGWRALRQTDIKLVLAYGTVSQLGFLMVANGLGTRDAAMAGLAMLLAHAVFKAPLFMVV +GIIDHEAGTRDLRQLSGIGRRHPALAAVAVVAGLSMAGLPPLFGFVAKESVLEGLAAHGV +AHADVWGWTPLVLMTVGSVLTFAYTWRFLWGSFAAKRDEEGAAVPVTRFHTRVTTLELAP +AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPEEAPAYLALWHGWTPILALSAGVWVL +GALLALGRPGVEAFQRRVEFPVDALRTYRKITGALDEVAIWVTGRTQTGSLRRYLGIILA +TAFLLPAAFLLFPVGRSERTLATSFLSADVAWFQTPAQLVVVLMIAVATVFAVRARRRFK +AIMLVSVTGYGAAALFAMRGAPDLAITQVLVETIILVTLILGLRVLPPDWYDRRTGSRRL +GRLAVAVGFALTMMWIAATALAARTAERISLPMPELAYTDGYGTNAVNVTLVDIRAWDTW +GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGDFGADSSLGARELSVVRSFAVD +DRKGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL +ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL +FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAARRRHPRMP +TPSTPSTQEAAR +>PROKKA_01585 +MLVILTALFVVALAAPVIFRWTGRQGFYLLAAAPAAGFVWLLTQLPHVFALQEALDAGRP +VPASAAHLDRAVPWVPYLEIELAFRMDVLAAFMSLIVLGVGALVLAYCARYFREHEPRNA +VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT +TFGGLAMLAGLIMLAHFAGSWRISGVLAAAPGLLADDGGRVLLEVAVGLVLIGALTKSAQ +APFHFWLPGAMAAPTPVSAYLHAAAMVKAGVFLVARLAPAFHELATWQVLVLGLGLWTLL +LGGWRALRQTDVKLVLAYGTVSQLGFLMVANGLGVRDAALAGLAMLLAHALFKAPLFMVV +GIIDHEAGTRDLRELSGIGRRHPALAAVAVAAGLSMAGLPPLFGFVAKESVLEGLAAHGV +AHADVWGWTPLVLMTVGSVLTFAYTWRFLWGSFAAKRDEEGAAVPVTRFHTRVTTLELAP +AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPAEKPAYLALWHGWTPILALSAGIWVL +GALLALGRPGVEAFQRRVEFPVDALRTYRKITGALDEVAIWVTGRTQTGSLRRYLGIILA +TAFLLPAAFLLFPVGRSERTLATSFLSADVAWFQTPAQLVVVLMIAVATVFAVRARRRFK +AIMLVSVTGYGAAALFAMRGAPDLAITQVLVETIILVTLILGLRVLPPDWYDRRTGSRRI +ARMAVAGGFALTMMWIAATALAARTAERISLPMPELAYTDGYGTNAVNVTLVDIRAWDTW +GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGDFGADSSLGARELSVVRSFAVD +DRKGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL +ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL +FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAARRRHPRMP +TPSTPDAPEAAR +>PROKKA_00969 +MLVTLSALFVVALAAPAVFRWTGRQGFYLLAAVPAAGFVWLLTQLPHVFALQEALDAGRP +IPASAAHLDRSVPWVPYLDIELAFRMDVLAAFMSLIVLGVGALVLAYCARYFREHEPRNA +VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT +TFGGLAMLAGLIMLAHVSGSWRISGVLEAAPALMADPGMRGLLEVAVALVLIGALTKSAQ +APFHFWLPAAMAAPTPVSAYLHAAAMVKAGVFLVARLAPEFHDLTSWQVLVLGVGLWTLV +LGGWRALRQTDVKLVLAYGTVSQLGFLMVANGLGTRDAAMAGLAMLLAHAVFKAPLFMIV +GIIDHEAGTRDLRQLSGIGRRHPVLAAVAVAAGLSMAGLPPLFGFVAKESVLASLAAHGA +AHGGVWAWTPLVVMALGSVLTFAYTWRFLWGSFAVKRDEEGAPVPATRFRTRVTTLELAP +AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPAEKPAYLALWHGWTPILALSAGIWVL +GALLALARRPFEALQERTESPLDAARGYRRLTGYVDETAVWVTGRTQTGSLRRYLGIILA +TAFLLPAAFLLFPVGRAERPLATSFLAADLIWFETPAQLLIVAIIAVATVFAVRARRRFK +AIMLVSVTGYGAAALFALRGAPDLAITQVLVETIILVTLILGLRVLPPDWHDRRTGSRRL +GRLAVAVGFALTMMWIAATALAARTAERISLPMPELAYTDGYGANAVNVTLVDIRAWDTW +GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGAFGADSALGSRELSVVRSFAVD +DREGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL +ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL +FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAGRRRHPRMP +TPSTPDAPEAAR +>PROKKA_00907 +MTVLLTALFAVALLAPVLFRRTGRRGFHLLAAAPAAGFVWVLAQLPQVFVLQDALDRGAP +VPASAAHLDTTVEWIPYLDIALSFRLDALSAFMSLIVLGVGALVLSYCASYFREHEPRHA +VFGAELLAFAGAMFGLVTTDDVMVLYTFWEITSVLSFLLIGYSGQRIFARRSAIQALIVT +TFGGLAMLAGLVMLAVQAGSWRVSGILAAAPELMERAPRGLLEAAVALVLVGALSKSAQV +PFHFWLPAAMAAPTPVSAYLHAAAMVKAGVFLVARLAPGFASLASWQVLVLGVGLWTLIL +GGWRALRQTDVKLVIAYGTVSQLGFLMVANGLGTRDAALAGLAMLLAHAVFKAPLFMVVG +IIDHEAGTRDLRRLSGIGRREPALAAVAIVAAASMAGLPPLFGFVAKESVLESLAGHGEH +AGTVWGWTPLVGMALGSVLTFAYTWRFLWGAFATKDGRDSPDGEPVPETRFHSRLTAEDL +LPPGLLALACLVLGLAPGLPEALISAHTAGLAPLDAAEEPAHLALWHGITPILGVSVAIW +VLGAALAVARRPLQRLQARVAFPVEAAAVYQRITGAVDAAAVWVTGRTQTGSLRRYLFII +LATATALPALTMLVPAGEEDRVLATAFLEADLVPFTTPAQLGIAALVCVAAVLAVRARRR +FMAIMLVSVTGYGSAALFALRGAPDLAVTQVLVESIVLITVILGLRVLPPDWHSKTTGRR +RVPRLLLGVGFALVMMWVAATALGARTAERISLDMPRLAYEHGYGANAVNVTLVDLRAWD +TWGEITVLAVAATGVASLVFLEHRDKRRRDLDTVVPGSVGNYGAESALGTRELSVVRSFA +VDDRNDQWLIAGHTMAPERRSIILEVVTRFLFPAMMLLSVYLLLAGHNTPGGGFAGGLLA +GLALALRYLAGGRYELQEASRIPAGTLLGLGLGIATLTGLAPLLFGGQVLQSYKVEFHDL +WLFGDSLKIVSATAFDVGVYLVVVGLSIDVLRSLGAEIDRRGDEWQDARRRAARRRASPR +PARPRPRPVPEGRAPAARAIPAHAARHRSEEDPR +>PROKKA_01809 +MLVILTALFVVALAAPVLFRWTGRQGFYLLAAAPAAGFVWLLTQLPHVFALQEALDAGRP +VPASAARLDRAVPWVPYLEIELAFRMDMLAAFMSLIVLGVGALVLAYCARYFREHEPRNA +VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT +TFGGLAMLAGLIMLAHVSGSWRISGVLEAAPALMADPGMRGLLEVAVALVLIGALTKSAQ +APFHFWLPAAMAAPTPVSAYLHAAAMVKAGVFLVARLAPEFHDLTSWQVLVLGVGLWTLV +LGGWRALRQTDVKLVLAYGTVSQLGFLMVANGLGTRDAAMAGLAMLLAHAVFKAPLFMIV +GIIDHETGTRDLRQLSGIGRRHPVLAAVAVAAGLSMAGLPPLFGFVAKESVLESLAAHGA +AHGGVWGWTPLVLMTVGSVLTFAYTWRFLWGSFAAKRDEEGAAVPVTRFHTRVTTLELAP +AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPEEAPAYLALWHGWTPILALSAGVWVL +GALLALGRPGVEAFQRRVEFPVDALRTYRKITGALDEVAIWVTGRTQTGSLRRYLGIILA +TAFLLPAAFLLFPVGRSERTLATSFLSADVAWFQTPAQLVVVLMIAVATVFAVRARRRFK +AIMLVSVTGYGAAALFAMRGAPDLAITQVLVETIILVTLILGLRVLPPDWYDRRTGSRRL +GRLAVAVGFALTMMWIAATALAARTAERISLPMPELAYTDGYGTNAVNVTLVDIRAWDTW +GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGDFGADSSLGARELSVVRSFAVD +DRKGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL +ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL +FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAARRRHPRMP +TPSTPDAPEAAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001536.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001536.fa new file mode 100644 index 0000000000000000000000000000000000000000..f04f8c8824e704158c5734b1d4b3a0032ed25260 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001536.fa @@ -0,0 +1,70 @@ +>PROKKA_01902 +MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ +LSDPGWITRWGVPVGELVSNVAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA +APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI +SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN +SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG +LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG +PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL +PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL +WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI +LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA +LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL +EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA +RMHGTPATDAPSGAEPAARDSSTGPEEARDVR +>PROKKA_01598 +MSAATAPARGSHPTENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ +LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA +APLPEHPAFTRVMRIAAVGAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI +SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHNGAVN +SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG +LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG +PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL +PPALEGARWITMWRFDWLWVAIIAFLSLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL +WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI +LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLQTHVGHEFMNVHFLLTGFLFA +LVMIGSDPLPRRPPYALRLVLLMATMIFHAFIGVAMTTSTGLMQASWFGNMGRDWGPTAL +EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA +RMHGTPVTDAPSGAEPVARDSSTGPEEARDVR +>PROKKA_00956 +MLVAAAGAGALAVAAWLTGITAVRELSDPGWITRWGVPAGELVSNLAMTMAIAAIIFAAG +ILPPHAAGTERWHRSAAQRRADAQEGPLPEHPAFTRTLRVAAVSAGVWTVAALAVGILSY +SDLAGIPVTAGEGFTAGLVAYVAGISVGQAWFWVTVIAAVVTTLVIAVRSHNGLFWTGIL +AMIGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVWVGGLLVLVAISDTLVGPDGAQGR +ARAPREQGPTPLLHTALSRYSVLAGLGLVTVALSGVVNASIRMDDPAQLTSPYGMLVVIK +FLATLGLGLVGLMHRRWVIPRLDAGPDRPSPAPARRLLWQLIAVEAVVMAAVMGLSAVLS +RTAPPVPEELAPDATPARILTGYELPPELTGARWITEWRLDWLWVAIIAFLALWYLRSVW +RLHRRGDRWPVLRTLSWMVGLAVLLWATSGSPAVYGRVLFSSHMMGHMTLTMISPLFLVL +GAPITLALRALPSRTDGSRGPREWILWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFF +RFSLETHVGHEFMNVHFLLTGFLFALVMVGSDPLPSRPAYPLRLVLLLATMVFHAFIGVA +MTGSAGLIQASWFGNMGRDWGPSALEDQHIGGAVMWGIGEFPTVVMAVMVAVLWYRNDRR +NAERLDRRADRDGDAELHRWNEMYARMHGTPAAPAEPAPAAASPADPTPAASAPRPRRPG +DPRWPLSTAHPPEDPAGPEDRAAPARWPRPPSSGCWR +>PROKKA_00896 +MPTSTAVPPATAQHPLGVPRPVLLGAAVVGVLALVLAAWFAGVTAPRELSDPGALTRWGV +PVGKAVNNAAMAVTIGALIFAAGILPPHAAGTERWHRSPRQRAQDAEEGPRPEHPAFGRV +MAVAAAAAGVWTVAALAVGVLSYSDLAGIPVSAGGSFTDGLLAYTLDISVGRAWFWVTVI +AAVVTTLAIGVRSHTGLFWTGVLAMLGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVW +VGGLLVLALISDTLVGPNGAQGRGASLRRQGPAPLLHTVVSRYSVLAGLGLVTVALSGVV +NASIRMDDPAQLLSPYGTMVLTKAGAVLLLGGIGLLHRRWIIPRLDDDGAAESPPAARRL +LWQLIAVEAVVMAAVVGVSAVLARTAPPVPEELAPDATPARILTGYELPPELTGDRWFTM +WRWDWLWVAIIAFLAVWYVRAAWQLRRRGDRWPVLRTLSWLIGLAVLAWATSGAPAVYGM +VLFSAHMVGHMVLTMIVPLFLVLGAPITLALRALPARTDGTRGPREWILWIVHSPWGAFI +TNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFIFATVMVGADPLPSR +PPYPLRLVLLLATMVFHAFIGVAMTTSTGLLQASWFGSIGRDWGPDALTDQHIGGGIMWG +IGEFPTVLMAVTVAVLWARSDTKTAARLDRRADQDGDAELARWNQMYAAMNHPGADQDPA +RGDRP +>PROKKA_01822 +MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWMLVAAAGAAGLAAAGWLTGVTAARQ +LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA +APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI +SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN +SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG +LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG +PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL +PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL +WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI +LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA +LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL +EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA +RMHGTPATDAPSGAEPAARDSSTGPEEARDVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001537.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001537.fa new file mode 100644 index 0000000000000000000000000000000000000000..a2c000a5f00f84c5f61edc56f8dd4cdbbefedfd9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001537.fa @@ -0,0 +1,45 @@ +>PROKKA_01903 +MPTTDPAVRPDDHHGSGGREGARPAPGGPSRRGLLLGAGAVGGGLLGTALGYGAGHASAS +TAPGASAAPGAGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDTVPFHGPR +QAGVDTPAQAHAVFLALDLREDADRVRIERMLRLLTDDAARLTQGRATIADTEPELAAAP +ARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICGDDRMSVA +HTRRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADTPHLDRVV +WGVGAEQVGVTPWIPDGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTGAPLTGEQEH +DEPDFDAVGPTGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAGSGLIFAAYQ +ADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCAEGGFVGDALFA +>PROKKA_01599 +MPTTDPVVRSDDHHGPDDHHGPDGREGARPTPGGPSRRGLLLGAGAVGGGLLGTALGYGA +GHASASTAPGASAASGTGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDTV +PFHGPRQAGVDTPAQAHAVFLAFDLHEDTDRVRIERMLRLLTDDAARLTQGRATIADTEP +ELAAAPARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICGD +DRMSVAHARRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADTP +HLDRVVWGVGAEQVGVTPWIADGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTGAPL +TGEQEHDEPDFDAVGPAGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAGSGL +IFAAYQADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCAEGGFVGDALFA +>PROKKA_00955 +MGGGLLGTALGYGAGHASAAPAAPAASGAAGAGASPSEVMGDTGIEGEVGRAGWAEPGGQ +SARVAVSSPVGTDTVPFHGPRQAGVDTPAQAHAVFLAFDLLPDTDRLGIERMLRLLTDDA +ARLTQGRATIADTEPELAAAPARLTVTFGFGPELLARVAPDRAPAWLRPLPAFPQIDRLD +PAFGDGDLLLQICGDDRMSVAHARRMLIKAARPFAAERWAQEGFRASRGAHPTGTTMRNL +FGQVDGTANPAAQTPHLDRVVWGVGAEQVGITPWIQDGTSLVVRRIEMLLDTWDELDRPG +KERVIGRTLGTGAPLTGEQEHDEPDFVALGPAGFPVIPDISHLRRARMDVPEYGMLRRGY +NYDDPRGAIESGAGLIFAAYQADVDRQFVPVQERLAESDHLNLWTVPVGSAVFAIPPGCA +EGGFVGDVLFA +>PROKKA_00895 +MPTTDPSRRGVLFGLGAVGGGLLGGAVGYGAGAAQATPAPGGAPSGVDASPSGVMEDTGL +EGEVGRAGWAEPGGEASRVAVSSPVGTDTVPFHGPRQAGVDTPAQTHAMLVALDLLPETD +RAGVRALLRLLSDDAARLTQGRATLADTEPELAAAPARLTVTFGFGPELLARVAPERAPA +WLKPLPAFPTIDALEDRWSGGDLLLQICGDDRISVAHARRMLGKVARPFAEVRWVQEGFR +AARGTHPTGTTMRNLFGQVDGTANPQGGSPALERIVWGAGQEAADLGIAPWIPDGTSLVV +RRIDMLMDTWDELDRPAKEKVIGRTLGTGAPLTGELETDAPDLEAIGPTGFPVIPDTAHL +RRARGPEPEYGMLRRGYNYDDGAGASGTGAGLIFAAFQADVDRQYIPVQERLAASDHLNL +WTRPVGSAVFAIPPGCAEGGFVGDVLFA +>PROKKA_01823 +MPTTDPAVRPDDHHGPDGREGARPAPGGPSRRGLLLGAGAVGGGLLGTALGYGAGHASAS +TAPGASAAPGAGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDTVPFHGPR +QAGVDTPAQAHAVFLAFDLHEDTGRVRIERMLRLLTDDAARLTQGRATIADTEPELAAAP +ARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICGDDRMSVA +HARRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADTPHLDRVV +WGVGAEQVGVTPWITDGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTGAPLTGEQEH +DEPDFDAVGPTGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAGSGLIFAAYQ +ADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCTEGGFVGDALFA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001538.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001538.fa new file mode 100644 index 0000000000000000000000000000000000000000..3f73bcd0829b06658a9c667d8bc051bbacb9c853 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001538.fa @@ -0,0 +1,25 @@ +>PROKKA_01904 +MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATDAAPASDASPA +ASTADGQAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVS +GEDGQMVMQESPDGFTVPAGGSLELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLE +VTSVVRPFTGANESYHGGQSHESEDHADH +>PROKKA_01600 +MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATGASSAASTADG +QAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVSGEDGQM +VMQQSPDGFTVPAGGSFELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLEVTSVVR +PFTGANESYHGGESHESEDHADH +>PROKKA_00954 +MTTPRSARCLSAAAVMAAAALGLTACAGGADDAASSSSSAPTAATSSAPAEGQGAPLTVS +DPWTKATEDGMTGSFGLLENSSDEDLHVVGVSAEVGAKAGLHVMVADEDGQMVMQQSPDG +FTVPAGGSFELAPGGAHVMLMGLTEPIEPGEEVAYELELEDGSTVEVVSVARPYTGANES +YDGGEAEESDEHADH +>PROKKA_00894 +MTMKHPSQTVSRRLSLAALAAAGSLALAACGGASAPASSSSSAAASSATATTPEAAGSAA +SSSATAADSSAAPLTMTDAWTKATDGAMTGSFGTLENTSDAPVHVVAVTSDRTDRVELHE +MAADGKGQMTMQQSPDGFTVPAGGTFELVPGGDHVMFMGLTQPVKAGAEVSYTLKTEDGR +TLEVTSVARPFTGADESYHGGEASSSMSGMGMNSSMPAGSGHADH +>PROKKA_01824 +MTTTSPRAPRRLGAAAVLAVAALGLTACAGDDAGSAPSASDASSVAPATDASPAASTADG +QAAGLTITDPWTKATEEGMTGSFGMLENSSDQDLHIVGVRSELGETVELHEMVSGEDGQM +VMQQSPDGFTVPAGGSFELAPGGNHVMFMGLTDPIEPGEDVTYDLELEDGSTLEVTSVVR +PFTGANESYHGGDSHESEGHADH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001539.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001539.fa new file mode 100644 index 0000000000000000000000000000000000000000..a3cbca4bf48b5e0cf4705abac7ebf15525ecb2d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001539.fa @@ -0,0 +1,23 @@ +>PROKKA_01905 +MHHQTTPVRRAARAATGLTLLPALVVAGAAPAAAHDELIRTAPAVGETATTAPSEVSLTF +SGELIDGEGIQNLLQVRDADGNQWQSAAGTVDGSTFSAPLCEGLPNGDYEVAYRVVYSDG +HSEERSFDFAVDDPAAPAAGTAPQGCGTAVAGASTAASPEAAAGQGDAASAEATAQADAS +DAAQPADTDALPAWVWVAGIAGLAVLVVAFLLMGRRARALGHLDDGR +>PROKKA_01601 +MHHQTTPVRRAARAAAGLALLPALVVAGAAPAAAHDELIRTAPAVDETVTTAPSEVSLTF +SGELIDGEGIQNLLQVRDADGNQWQSAAGTVDGPTFSAPLCEGLPNGDYEVAYRVVYSDG +HSEERSFDFAVDDPAAPAAGTAPQGCGSAVAGASIAASPEATASQGDAASAAATAQADAS +HAAQPADSDALPAWVWVAGIAGLAVLVVAFLLMGRRARALGHLDDGR +>PROKKA_00953 +MAAAPAASDASTPASAGSGAGTGEASEAPAEQGSAEAGESAEAGALPAWVWAVGVAGLLV +LVVALILMGRRARALGHLDDGR +>PROKKA_00893 +MNPTPMHPSTPRRAARAAAALTLLPGLAVAAAAPALAHDELLKAVPADGAALAEAPDAVS +LTFSGDLISGQGIQSIVRVTDAAGNQWQKGDVQVSGPTLTAPLCPDLAQGEYTAAYRVVY +SDGHSEEQSLDFSVTDPSAPAAGTAPSGCGVAAAGTASSTAAPASSAEQTGAEQSGAAST +PAAASSTPAESGASAGVPATVWMLGAAGVAVIAVGLAVMGRKARALGRD +>PROKKA_01825 +MHHQTTPVRRAARAAAGLTLLPALVVAGAAPAAAHDELIRTAPAVGETATTAPSEVSLTF +SGELIDGEGIQNLLQVRDADGNQWQSAAGTVDGPTFSAPLCEGLPNGDYEVAYRVVYSDG +HSEERSFDFAVDDPAAPAAGTAPQGCGTAVAGASTAASPEATAGQGDAASAEATAQADAS +DAAQPADSDALPAWVWVAGIAGLAVLVVAFLLMGRRARALGHLDDGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001540.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001540.fa new file mode 100644 index 0000000000000000000000000000000000000000..179101718f39e6a9637cbd11f596bc7bdb08e802 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001540.fa @@ -0,0 +1,25 @@ +>PROKKA_01906 +MRSAVAAAPWAPSGLEDPRPRVVRGPARLARGWAGALAMTALAALFHTAAEPGHGFPEVG +VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLAAGGPAVAPAAGVDPAH +LGHARPGTGALLAPGEALSSAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV +VAAVCPPPAAHGPLPTPARVRVPVPPALRPATSLALLSSPGRRGPPFALAA +>PROKKA_01602 +MRSAVAAAPWAPSGLEDPRPRVVRGPARLARGWAGALAMTALAALFHTAAEPGHGFPEVG +VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLAAGGHAVAPAAGVDPAH +LGHARPGTGALLASGEALSGAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV +VAAVCPPPAAHGPLPTPARVRVPVPPVLRPATSLVLLSSPGRRGPPFALAA +>PROKKA_00952 +MRSAVDAAPHAFGRPHPAPGRVVRGPARLARGVAGALAMTVLAALFHAAAVPGAGLPDVR +VAAFAAVLAAPVCTALAGRALSLWRTAAAVAVAQGLFQVLYGIAAGGHAVAPAAGVDPAH +LHHAAAAAGPLVSVSAGPAAGHVHAAEPLMLAAHAAAAVLTVLVLRRGEALVLAVAERVL +QAVLPRAASAGPLPLPSPARVPALPAPRPTESLVLLGTPGRRGPPFALAA +>PROKKA_00892 +MGTPTPVPSRAVAGPARVLRGAAGALAMTLLAALFHSAAASTPLPAPALLLFSAVLAAPV +CTLLAGRALSLWRTAAAVAVAQGLFHALYSVAAGGRSVATAAGVAPAHLAHSHVGAARPL +LTVDAASETSAHAAHAGTPGMLLAHLAAAALTVAVLRHGERMLVAAAERVLQAAPVWRLL +VALAAGLLPTPRPVRVPAWRAPSAPAAVVVLASPGRRGPPAFALAA +>PROKKA_01826 +MRSAVAAAPWAPSGLEDAPPRVVRGPARLVRGWAGALAMTALAALFHTAAEPGHGFPEVG +VVAFAAVLAAPLCTALAGRALSLWRTAAAVAIAQGLFHVLYGLATGGHAVAPAAGVDPAH +LGHAHPGAGALLAPGEALSGAPTGHLTDLRMLAAHVIAAVLTVLVLRRGEALVLTIAERV +VAAVCPPPAAHGPLPTPARVRVPVPPALRPATSLALLSSPGRRGPPFALAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001541.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001541.fa new file mode 100644 index 0000000000000000000000000000000000000000..d858d32d216505624bb55472e28745f931181300 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001541.fa @@ -0,0 +1,15 @@ +>PROKKA_01907 +MAMNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWLAVERTERKER +TGRNPRTGEEITIPAGHSVKVTAGSKLKAAASE +>PROKKA_01603 +MAMNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWLAVERTERKER +TGRNPRTGEEITIPAGHSVKVTAGSKLKAAASE +>PROKKA_00951 +MAMNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWMAVERTERKER +TGRNPRTGEEITIPAGYSVKVTAGSKLKAAASE +>PROKKA_00891 +MAMNRKELVAAVAERSGNTQAAVSDVLDALFEAFTAQVKKGEKVSIPGWLAVERTERKER +TGRNPRTGEEITIPAGYSVKVTAGSKLKAAASE +>PROKKA_01827 +MNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWLAVERTERKERTG +RNPRTGEEITIPAGHSVKVTAGSKLKAAASE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001544.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001544.fa new file mode 100644 index 0000000000000000000000000000000000000000..a6e5ca4e39df62606b7bb87a5968beebc5e16d29 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001544.fa @@ -0,0 +1,15 @@ +>PROKKA_01910 +MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID +VRGIDAVVADLIAKGVKL +>PROKKA_01606 +MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVMLTLSAKGIKTID +VRGIDAVVADLIAKGVKL +>PROKKA_00948 +MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID +VRGIDAVVADLIAKGVKL +>PROKKA_00888 +MAAHCQVTGAGPGFGHSISHSHRRNKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID +VRGIDAVVADLISKGVKL +>PROKKA_01830 +MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID +VRGIDAVVADLIAKGVKL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001547.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001547.fa new file mode 100644 index 0000000000000000000000000000000000000000..bd15e7235973e222f6a5ef05f1ff4bacd0df8baa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001547.fa @@ -0,0 +1,30 @@ +>PROKKA_01919 +MTTTTATPGPTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL +ERVRAAAEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI +DAAGTPMLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS +LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED +LAPRIYPGLTGTVARVAVQTVAAHLRHLRED +>PROKKA_01615 +MTTTTATPGPTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL +ERVRAATEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI +DVAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS +LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED +LAPRIYPGLTGTVARVAVQTVAAHLRHLREG +>PROKKA_00941 +MTTTPATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDAAAHL +ERVRAAAEGRRIALILVTHRHADHTGGVDAFHTATGAPVRAADPDWCRGGAAVLTPDERI +DVAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS +LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLAQVSAALAELGEDEAATVTPEQ +LAPRIYPGLEGTVARVAVQTVAAHLRHLREG +>PROKKA_00876 +MTTTPATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVLFADDADAAVVLDPGPAEDAEGHL +ERVRQAAEGRRIELVLVSHRHADHTGGIDAFHAGTGAPVRAADPSHCRGGGLPLTPDEEI +VRAGVRILAWHTPGHTSDSYSFAVPESGPHGAVLTGDTILGAGTTMLDHPDGTLTDYLAS +LARLQAAGPLTVLPAHGPVPAPLDVIARDYIDHREGRLFQLRRALDGMDPARAAMVTPSE +LVGVIYPEVTGQVARVAEQVLAAHLAYLRRG +>PROKKA_01839 +MTTTTATPGLTPAPLVRCVTAQNPSPMTLAGTNTYVVAAPDSDAAVVVDPGPEDDVAAHL +ERVRAAAEGRRIALILVTHRHADHTGGVDAFHAATGAPVRAADPDWCRGGAAVLTPDERI +DAAGTPVLAWHTPGHTSDSYSFAVPDAGAHGAVITGDTILGSGTTMLDHPDGTLTDYLAS +LRRLEAAGPLTVLPAHGPVPEPLDVVARDYRHHREGRLEQIRAALAALPETEAATITPED +LAPRIYPGLTGTVARVAVQTVAAHLRHLREG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001548.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001548.fa new file mode 100644 index 0000000000000000000000000000000000000000..c0bee7e4b3d32d6670cfcb50627c025758c15598 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001548.fa @@ -0,0 +1,20 @@ +>PROKKA_01920 +MTILVGYAPSKAADAALDTALDIARSTGEHVVVVNAGPGGEHRTKSLVTEEQQRGVQARL +DASGVTAEFRQYARGRSTVEEMKDVAAELDPSIVVIGVRRRGGFGRFVMGSVSDELLQEI +DQPVLCVKEYRQYGDHTPEAVSHVAETDPAAHGLPASEPMAERRRLTPVDSGDPTLER +>PROKKA_01616 +MTILVGYAPSKAADAALDTALDIARSTGEHVVVVNAGPGGEHRTKSLVTEEQQRGVQARL +DASGVTAEFRQYARGRSTVEEMKDVAAELGPSIVVIGVRRRGGFGRFVMGSVSDELLQEI +DQPVLCVKEYRQYGDHTPEAVSHVAETDPAAHGLPASEPMAERRRLTPVDSGDPTLER +>PROKKA_00940 +MTILVGYAPSTSADAALDTALDIARSTGERVVVVNAGPGGEHRTKSLVTEEQQRGVQARL +DASGVDAEFRQYARGRSTVQEMKDVAAELDPSIVVIGVRRRGGFGRFVMGSVSDELLQEI +DQPVLCVKEYTQYGDRTPEAVSHVAETDPATRGLPASEPMLEQHPLTPVKDQDPTRRG +>PROKKA_00875 +MTILVAYKPSETAKAALSTALDVARQTGEHVVVVNAGPGGEHRSPSLVTEAQQQEVQRLL +DDSGVSAEFRQYARGRSTADELKSVADELDPSIVVVGLRRRGGFGRFVMGSVSDELLQVI +DQPVLAVKEYRGRTPDAVSSVAETDPATHGMPSAEPGHAPRPFTGEHAADDGR +>PROKKA_01840 +MTILVGYAPSKSADAALDTALDIARSTGEHVVVVNAGPGGEHRTKSLVTEEQQRGVQARL +DASGVTAEFRQYARGRSTVEEMKDVAAELDPSIVVIGVRRRGGFGRFVMGSVSDELLQEI +DQPVLCVKEYRQYGDHTPEAVSHVAETDPATHGLPASEPMAERRRLTPVDPGDPTLER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001549.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001549.fa new file mode 100644 index 0000000000000000000000000000000000000000..ba2385e8ee1d888a504da90225e736b3df01d756 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001549.fa @@ -0,0 +1,45 @@ +>PROKKA_01922 +MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV +RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW +IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL +LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA +EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA +FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV +GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL +AEDERLPAHGAAIRARFA +>PROKKA_01618 +MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVVAPIIEQVRHGGEQTLLDLAERFDGV +RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW +IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL +LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA +EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA +FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEDLVGRIRNAGAVFV +GPHAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL +AEDERLPAHGAAIRARFA +>PROKKA_00938 +MEADRPRGPGPAAAVVVPRRCTPTPAPPTSLEDPVLSVTDLRQIDTAAADLSRIIPRADV +DVASTVPVVAPILEQVRTGGEAALLELAERFDGVRPPALRVPAEALAAALEGLDADVRAA +LEESIRRARLVHAAQLPQDSTVELGEGASVQNHWIPVDRVGLYVPGGRAVYPSSVVMNVV +PAQAAGVGSLAVTSPPQADHGGLPHPTVLAACALLGVDEVYAAGGAQAVAMLAHGVRDER +GGWLCAPVDMVTGPGNVYVAAAKRALQGIIGVDAEAGPSEIAVIADGTARADWVAADLIS +QSEHDPLAASVLITDSEDLVRDVLAAIEAQVPGSFHEEQIRVALTGPQSGVLLVRDLDQA +VEVSDRYATEHLEIQTRDPEAVAARIRNAGAVFVGPHAPVPLGDYSAGSNHVLPTSGTAR +HSSGLSTVTFLRLQQRIRYTETGLKELAEGISVLAEDERLPAHGVAVRARFA +>PROKKA_00873 +MEADRTALDPQEEPVLSVTDLRELDTAAADLSAIVPRAEVDVAYTVPVVAPIIEQVRTGS +EQTLLDLAERFDGVRPPALRVPAEALTAALEGLDPAVRAALEESIARARKVHAAQVPSGS +TVELGEGAVVENRWVPVERVGLYVPGGRAVYPSSVVMNVVPAQAAGVESLVVTSPPQRDH +GGLPHPTVLAACALLGVDEVYAAGGAQAVAMLALGVRADDGDGWLCAPVRMVTGPGNVYV +AAAKRALQGVIGTDAEAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSADL +LRDVLASVEAQVPGSFHEEQIRVALTGPQSGVLLVRDMEQALEVSDLYATEHLEIHTRDA +DALAARVRNAGAVFVGPYSPVPLGDYSAGSNHVLPTSGTARFSSGLNTVTFLRSQQLIRY +GEAGLKALADGISALAEDERLPAHGVAVRARFA +>PROKKA_01842 +MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV +RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW +IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL +LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA +EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA +FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV +GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL +AEDERLPAHGAAIRARFA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001550.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001550.fa new file mode 100644 index 0000000000000000000000000000000000000000..0cae1a9f4cb34b03e05da05f60c9b951e6c525b4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001550.fa @@ -0,0 +1,20 @@ +>PROKKA_01923 +MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI +LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD +RR +>PROKKA_01619 +MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI +LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD +RR +>PROKKA_00937 +MSGSVRVSGAVRVDAWLWAVRVYKTRSAATAAVRGGHVRVNDEPVKAAHTLAVGDRVRVR +KDQRERILEVTGLIGTRVGAPVAVTNYIDHSPPPIPRELLAVPHRERGAGRPTKRDRRKL +DELRGRASDERS +>PROKKA_00872 +MGAVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI +LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRA +STGRG +>PROKKA_01843 +MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI +LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD +RR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001552.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001552.fa new file mode 100644 index 0000000000000000000000000000000000000000..2692d308ad3031875dd69647065a2897cddcc12d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001552.fa @@ -0,0 +1,20 @@ +>PROKKA_01926 +MTLTHEPHTAAWDTDLSLGNLRSGLSAFPTGVVALAGLADDVPEVMVSSSFGVGISWEPA +LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLASREGDRFAGLDVHRSPHDALL +IGGSSLWLETRVHAEVPAGDHTVVLLEVTAFADHTDAAPPAALHRNLFHGLRAL +>PROKKA_01622 +MTLTHEPHTATWDTDLSLGNLRSGLSAFPTGVVALAGLADGVPEVMVSSSFGVGISWEPA +LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLASREGDRFAGLDVHRSPHDALL +IGGSSLWLETRVHAEVPAGDHTVVLLEVTAFADHTDAAPPAALHRNLFHGLRAL +>PROKKA_00935 +MTLTLDDRTRVWDTDLSHHNLRSGLSAFPTGVVAVAGLAEDRREVMVSSSFGVGISWEPA +LVAFSAQNTSRTWPRLRQAASLGISLLAADQTHLCRQLASREGDRFAGLDVHVSPNEALL +IEGAALWLETRLHAEVPAGDHTVVMLEVTGFADHTDEVAPAALHRNLFHGLRAL +>PROKKA_00866 +MTLIHAPHTAAWDTDLSLGNLRSGLSAFPTGVVALAGLADDVPEVMVSSSFGVGISWEPA +LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLAAREGDRFAGLDVHRSPHDALL +IGGSSLWLETRVHAEVPAGDHTVVLLEVTAFADHTDDAPPAALHRNLFHGLRAL +>PROKKA_01845 +MTLTHEPHTAAWDTDLSLGNLRSGLSAFPTGVVALAGLADDVPEVMVSSSFGVGISWEPA +LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLASREGDRFAGLDVHRSPHDALL +IGGSSLWLETRVHAEVPAGDHTVVLLEVTALADHTDAAPPAALHRNLFHGLRAL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001553.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001553.fa new file mode 100644 index 0000000000000000000000000000000000000000..e9a53ad9431d713325e308d60439fa15c98397b3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001553.fa @@ -0,0 +1,15 @@ +>PROKKA_01927 +MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGNGFKELQENDRVEFETQDGPKGLQ +AANVTKL +>PROKKA_01623 +MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGGGFKELQENDRVEFETQDGPKGLQ +AANVTKL +>PROKKA_00934 +MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGSGFKELQENDRVEFETQDGPKGLQ +AANVTKI +>PROKKA_00865 +MAVGTVKWFNSEKGYGFIAPEDGSADVFVHFSAIQGNGFKELQENDRVEFETQQGPKGLQ +AADVTKL +>PROKKA_01846 +MAVGTVKWFNAEKGYGFIAPEDNSADVFVHFSAIQGGGFKELQENDRVEFETQDGPKGLQ +AANVTKL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001554.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001554.fa new file mode 100644 index 0000000000000000000000000000000000000000..bab885144dd7637bbab91415df5d1234fc9f9bbc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001554.fa @@ -0,0 +1,42 @@ +>PROKKA_01928 +MTLPAPAARRPSAALLWVLLAAMGAGPLFTYGVSASSTVVMERLDVTSGQLGTVMTVVFA +AAAVTSLGLGRAADRLSARAQLSIIFGGTAAALVLGAVAPSLPVLYAAAAVAGVTQAISN +PTTNRIIRTVVPPERRIGWVGVKQSGVQAAQLVGGLFFPAASLALGWTGAALGAAVLIGA +LWVLALVAAPPLPGAPPSATGPAGGRRRRDTSPLPATVWFSAAIAFLTGLGMQATNTYLP +LFAVETLGMTLVAGGAAAAVSGVVGVLSRIGWSRRMSSGDRPTTLLTVICLGAVAGVVVF +LAADLLDLPALLWVGAAVHGLTVLGANVVVNAGLLSEVPAERLGRATGANSMGMYAGFAL +GPLLMGVLRDVTGDYRAGFAVVALGYLLALGVVLLLRRHVGRRGAA +>PROKKA_01624 +MTLPAPAARRPSAALLWVLLAAMGAGPLFNYGVSASSTVVMERLDVTSGQLGTVMTVVFA +AAAVTSLGLGRAADRLSARAQLSIIFGGTAAALVLGAVAPSLPVLYAAAAVAGVTQAISN +PTTNRIIRTVVPPERRIGWVGVKQSGVQAAQLVGGLFFPAASLALGWTGAALGAAVLIGA +LWVLALVAAPPLPGAPPPATGPVGGRRRRDTSPLPATVWFFAAIAFLTGLGMQATNTYLP +LFAVETLGMTLVAGGAAAAVSGVVGVLSRIGWSRRMSSGDRPTTLLAVICLGAVAGVAVF +LAADLLDLPALLWVGAAVHGLTVLGANVVINAGLLSEVPAERLGRATGANSMGMYAGFAL +GPLLMGVLRDVTGDYRAGFAVVALGYLLALGVVLLLRRHVGRRGAA +>PROKKA_00931 +MTPPSSAPAAARSGPSTALLWVLLAAMGAGPLFNYGISASSTVIIERLGVTSGQLGTVMT +AVFAAAAVTSLGLGRAADRLSSRAQMSIIFGGTAVALVMGAFAPSLPVLYAAAAVAGVTQ +AISNPTTNRIIRTVVPPERRIGWIGVKQSGVQAAQLFGGLFFPAASLALGWTGAALVVAV +LACVLWGFALWAAPPLPGTAPTADPDAGRASAPDVDRASAPDAGPAAARARRRDGRRRRG +TTALPASVWFFAAIAFLTGLGMQATNMYLPLFAVESLDLTLVAGGAAAAVSGVIGVFSRI +WWSRRMAVGARPTTLLAAICLGALAGVVVLLAADLAHLPALLWVGAAVHGLTVLGANVVT +NAGLMSEVPAESLGRASGANAMGMYAGFALGPLVMGVLRDLTGDYRAGFAAVGLGYILAF +LVVLLLRRHVGRRAADPRAEAA +>PROKKA_00863 +MGDAGAGRRLTGSSGGPAAPGGPTLGAVTASPPSRPADRAPGTLLLWTLLAAMGAGPVFN +YAVSTSSTVIIERLGVTSGQLGTVMTVVFAAAAVTSVGLGRAADRLSSRTQMAIIFFGSA +LALAVGGFAGSLWALYGAAVLAGVTQTISNPTTNRIIRTSVPAERRIGWIGVKQSGVQAS +QLFAGLFFPVAALGLGWTGASLVAAALVGLLGVVALRAAPPLPGAPAAPPTTTPDAGRPR +AGRARAPLPATVWFFAGIAFLTGFGMQATNMYLPLFAVESLDQTLVIGGAAAATSGVIGV +FSRIWWSRRMAAGHRPTTLLAGIALGAVVGVVVFLGADLLHAPALLWVGAAVHGLTVLGT +NVVTNAGLMDAVPAHHLGRASGVNAMGMYAGFACGPLVMGLMRDLTGDFRAGFLAVGVFY +LLALAVVGLLRRHTDRQGAPRAA +>PROKKA_01847 +MTPPAPAARRPSAALLWVLLAAMGAGPLFNYGVSASSTVVMERLDVTSGQLGTVMTVVFA +AAAVTSLGLGRAADRLSARAQLSIIFGGTAAALVLGAAAPSLPVLYAAAAVAGVTQAISN +PTTNRIIRTVVPPERRIGWVGVKQSGVQAAQLVGGLFFPAASLALGWTGAALGAAVLIGA +LWVLALVAAPPLPGAPPPATGPVGGRRRRDTSPLPATVWFFAAIAFLTGLGMQATNTYLP +LFAVETLGMTLVAGGAAAAVSGVVGVLSRIGWSRRMSSGDRPTTLLTVICLGAVAGVVVF +LAADLLDLPVLLWVGAAVHGLTVLGANVVINAGLLSEVPAERLGRATGANSMGMYAGFAL +GPLLMGVLRDVTGDYRAGFAVVAAGYLLALGVVLLLRRHVGRRGAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001555.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001555.fa new file mode 100644 index 0000000000000000000000000000000000000000..41293bf1e61a991351ab27d5183eb4b309fd7440 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001555.fa @@ -0,0 +1,62 @@ +>PROKKA_01929 +MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV +LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG +YEFLLHSTAPVNPPEEPPTVRIGGPDCRRPVDISLMNISSMSFGSLSANAVIAMNKGAGL +GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKAVLPEVKGITI +KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL +SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT +EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ +KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR +MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP +QWRSELLIPGREAAGAPVQGSPISGTGSTLVDARRTESVPLTTSPMPRVSSLGEGESLCT +PGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTRRGTTGRVEGEHRGE +GRVG +>PROKKA_01625 +MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV +LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG +YEFLLHSTAPVNPPEEPPTVRIGGPDCRQPVDISLMNISSMSFGSLSANAVVAMNKGAGL +GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKAVLPEVKGITI +KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL +SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT +EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVRRLIQGADFTMSARAMMMATGCIQAQ +KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR +MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP +EWRSELLIPGREAGGAPVQGSPISGTGSTLVDARQTESVPLTTSPMPRVSSLGEGESLSP +HGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTQRGTTGRVEGEHRGE +GRVG +>PROKKA_00930 +MNNRLLIVATLSLGALVVVLVAAIGNGAWWVLAAIVVGLLILAVRDMTQKRHAILRNFPV +LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSLVYARSKGLDSHKAFGTERDTSEIG +YEFLLHSSAPVNAPAEAPTVRIGGPDCRQPVDISLMNISSMSFGSLSANAVQAMNKGAGL +GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNGDGTFSAEKFAAKAALPEVKGITI +KMSQGAKPGLGGMLPKEKITAEIAEAREIPMDQDCLSPASHSAFRTPREMVRFIGHLREL +SDGKPVGIKFCVGSRVDVLAMCKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT +EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ +KCHTNECPVGVATQDPRLMRALDVTDKSNRVFNYHRLTVREAVQIMASMGVTHPSQLNTR +MLRRRVDHLATRSYASIYHWLRTDELLNDPPAGWAMDWDEADGDHFGEHARVDYLTERDP +EWRSELLIPGRQEQGAPVQGSPASGAGSRVAVGDSRDTAPVTTSPLPRVSTLAEGETLYS +RSTRSHDPAREQAGVTQRVDTDGNDGLSPHAGEDPERQDGEEVTQRGTTGRVDAEPRGEG +RVG +>PROKKA_01592 +MNSKTLAAAAAALGVAGVAVRDLTQKQHALRHNFPVLARARWALETIGPELRQYIVAANN +EERPFSRDQRRWVYTSSKGKNNYYGFGTDNDVEHTSYAVVKHRTFSDVAPMSALALDPGK +ALPSAKVLGGPRGRRHAFRPNSVVNVSAMSFGSLSPQAITALNKGAALGGFMHNTGEGGL +SDHHRQGGDLMLQIGTGYFGCRDAHGNFDMEKLAAVVESAPVRALEIKLSQGAKPGLGGH +LPGAKVNAEIARIRGVEEGKDVASPSRHSEFSTVDEMLDFVERVAERTGLPVGIKSAVGD +LGFWHELADAMADGTRGVDFITIDGGEGGTGAAPLIFSDSVAFPFRVAFTEVYRIFAARG +LTDRVTWIGSGKLGLPDNALVAFALGVDMVNVAREAMLAIGCIQAQKCHLDTCPAGVATQ +NPWLAAGLDPQEKSQRLVGYVQTLRRDLIKVSEAAGVPHPALLSPDDVALVEQTRSQTPL +REIYGYERGWGVPGEEIRAEITRIMVDEDSSRADEDHLVQHEPLPQDDVDTTH +>PROKKA_01848 +MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV +LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG +YEFLLHSTAPVNPPEEPPTVRIGGPDCRRPVDISLMNISSMSFGSLSANAVIAMNKGAGL +GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKALLPEVKGITI +KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL +SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT +EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ +KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR +MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP +QWRSELLIPGRAAAGAPVQGSPISGTGSTLVDARQTESVPLTTSPMPRVSSLGEGESLSP +HGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTQRGTTGRVEGEHRGE +GRVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001561.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001561.fa new file mode 100644 index 0000000000000000000000000000000000000000..0f99cbc2c634e3b4c31a84c20bb39d146ed4884b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001561.fa @@ -0,0 +1,26 @@ +>PROKKA_01936 +MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE +DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR +VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA +EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEDGPAVASQA +>PROKKA_01632 +MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE +DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR +VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA +EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEAGPAVASPA +>PROKKA_00923 +MARTTRTSRGATPGSATRGHDDDGRAGLRLRALSVAYPDGATPVRGLDLELAPGEIVALV +GASGSGKSTVLRGIAGLEDVVGGVVEIDGEDVAAVPTHRRGVGMVFQDGQLFPHRSVARN +VAYGLEAAGWPRERRRARVAELLELVDLAELAERPVQSLSGGQAQRVALARSLAPRPRVL +LLDEPLSALDADLRARLAVQIREVLRAAGVTAVVVTHDLAEAAVMADRTVRLGAGGRLAG +PGEGEPDEGAGPGPEGDAR +>PROKKA_00857 +MPARMHHHDAAPALRLRGLAVAYPDGSVPVTRADLDLAPGEIVALLGPSGSGKSTVLRGI +AGLEDVPAGAVELAGRDVTAVPTHRRGVGMVFQDGQLFPHRTVARNVAYGVEAAGWDRSR +RDARVAELLELVDLAALADRPVQTLSGGQAQRVALARSLAPSPAVLLLDEPLSALDADLR +TRLAADIRTVLRAEGVSAVVVTHDAAEAAVMADRTVRMGADGVLHGAAADGARTAG +>PROKKA_01855 +MTPTTTGASLRLRDVAIRYPDGSTPVRGTDLDVAAGEIVALVGASGSGKSTILRGIAGLE +DVVAGTVELDGRDVAAVPTHRRGVGMVFQDGQLFPHRTVGRNVAYGLESAGWDRARRRAR +VAELLDLVGLTELTDRPVQRLSGGQAQRVALARSLAPAPRVLLLDEPLSALDADLRRRLA +EDIRAVLRAAGTTGVVVTHDLAEAAVMADRTVRLGAGGRIAAEEDGPAVASQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001564.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001564.fa new file mode 100644 index 0000000000000000000000000000000000000000..1a3f5fb8a54c94fa75660443a1f5dbd6b45b9c19 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001564.fa @@ -0,0 +1,15 @@ +>PROKKA_01941 +MATPHTPDPQDARRAREATDETSGAAFDGDTPPAEGAGVGPSNPGMDVEQTGERSAGKIV +LGLIIALVVIGVLLFILGRVAGLG +>PROKKA_01637 +MATPHTPDPQDARRAREATDETSGVAFDGDTPPAEGAGVGPHNPGMDVEQTGERSAGKIV +LGLIIALVVIGVLVFILGRVAGLG +>PROKKA_00918 +MAAPHTRRPHDSDPHDARRAADEHSGHTDRGGTPPAEGSGVGPTNPQMDVEQPGERSTGR +IVLFAIIALLVIGILLFVLGRVFDLFG +>PROKKA_00853 +MATPHHPDQPADAHRSDHLARATDENSGHAVAGDTPPAEGLGVGPTNPGMEADKSGEGGM +GRILLGLLIALVVIGVLLFVIGRISSIG +>PROKKA_01860 +MATPHTPDPQDARRAREATDETSGAAFDGDTPPAEGAGVGPSNPGMDVEQTGERSAGKIV +LGLIIALVVIGVLLFILGRVAGLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001565.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001565.fa new file mode 100644 index 0000000000000000000000000000000000000000..f922cf5982a9473c4658a69a2bbfa79887f0c104 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001565.fa @@ -0,0 +1,40 @@ +>PROKKA_01942 +MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVARQDIDSAEYDEVILGCIDQLG +PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAIMSGTADLVVAGGVQSMS +AIPLSLSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV +RSHERALAAQADSRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS +DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM +DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG +RYGLQTMCEGGGQANVTVIERL +>PROKKA_01638 +MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG +PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS +AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV +RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS +DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM +DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG +RYGLQTMCEGGGQANVTVIERL +>PROKKA_00914 +MPEAYIIDAVRTPVGRRGKGLAQVHPLDLAAAPLREIVGRQDIDSAEYDEVILGCIDQLG +PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS +AIPLSHSNRAAAEFGFADPFTGSESWAARYGNEEISQFRGAEMMARHWNLDRDVLEEFAV +RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS +DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM +DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG +RYGLQTMCEGGGQANVTVIERL +>PROKKA_00852 +MGEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPIRELVGRQDVDSAEYDEVILGCIDQLG +PQAMDVARSAWLAAGLSEDVPGSTIERQCGSGQQAIHYAAQAVMSGTADLVVAGGVQSMS +AIPLSRSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV +RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAASASQMS +DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAFALRRMGLGIDDM +DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG +RYGLQTMCEGGGQANVTVIERL +>PROKKA_01861 +MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG +PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS +AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV +RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS +DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM +DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG +RYGLQTMCEGGGQANVTVIERL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001566.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001566.fa new file mode 100644 index 0000000000000000000000000000000000000000..c429ac7fe3ce2d0abf6ea1ce5c28bb6462be3930 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001566.fa @@ -0,0 +1,50 @@ +>PROKKA_01943 +MPDQITHPTDAAAHPSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYTQLRDGAHRVA +RRLQDTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAE +LLVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLETARDETLDAAAPEAEVSA +TDLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSMIALDFTAEDRPLVAMPLYHSAAMHVF +LLPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRK +AQYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHV +EARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAG +YIQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVVGLPDERWIEAVTAVVVLKEG +AELTAETVRAHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR +>PROKKA_01639 +MPDQITHPTDAGHLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVAR +RLQDTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEL +LVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLETAQDETLDAAAPEAEVSAT +DLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVFL +LPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLHKA +QYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVE +ARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAGY +IQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEGA +ELTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR +>PROKKA_00913 +MTEQTSPAAPTADSPSPEDTIGRLFTRAAARHPETVALRFEDRDWTYAQLLDGVHRVARR +LLATGLPRGTRVAAYGANSDAYAVLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEVL +VADAGMLERVEQVRADGGGAGLRHVWTMLPAGHAEPSLLETARDEAADATAPDVPVTATD +LAQLLYTSGTTSTPKGAMMSHRALITEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVFLL +PYLSLGATVRLLATPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRKAQ +YGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVEA +RVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAGYI +QVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEGAE +LTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR +>PROKKA_00851 +MPDQITHPTDAAAHLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVA +RRLQGTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGTE +LLVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLETAQDEALDAAAPEAEVSA +TDLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVF +LLPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRK +AQYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHV +EARVMTADGVPAAPGMPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAG +YIQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEG +AELTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR +>PROKKA_01862 +MPDQITHPTDAGHLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVAR +RLQDTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEL +LVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLQTAQDETLDAAAPEAEVSAT +DLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVFL +LPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLHKA +QYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVE +ARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAGY +IQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEGA +ELTAETVRAHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001567.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001567.fa new file mode 100644 index 0000000000000000000000000000000000000000..55ecbb7b95b9fbf8f0e2067ff4e2f5b8ca8dd156 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001567.fa @@ -0,0 +1,40 @@ +>PROKKA_01944 +MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPFD +LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC +ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG +AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA +RLPDVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER +LAQMLDEVTAMQTRCVAVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL +LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA +>PROKKA_01640 +MTRRQKPTYDVVTPLDVDYLDAFGEATEEDRAHWDRARAYGREVLERIDGHWDRAEYPLD +LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC +ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG +AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA +RLPDVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER +LAQMLDEVTAMQTRCVAVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL +LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA +>PROKKA_00912 +MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPLD +LVARAGELDLLTDGLEVPGHPVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC +AGPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG +AAGGITIVWARDTGDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA +RLPNVATFKDAVRVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER +LAQMLDEVTAMQARCVAVARLQASGRLRDEQASLLKYACTRGARRVAQTARDMLGGNGIL +LEHRVIRHFADVEALHTYEGTESVQALILGRDLTGMSAFA +>PROKKA_00850 +MRRQKPTYDVVTPLDVDYLDAFGEATEEDRAHWDRARAYGREVLERIDGHWDRAEYPLDL +VARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHCA +SPEQQERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNGA +AGGITFVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDAR +LPGVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQERL +AQMLDEVTAMQTRCVVVARLQAAGRLRDEQASLLKYACTRGARRVAQIARDMLGGNGILL +EHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA +>PROKKA_01863 +MTRTQKPTYDVVTPLDVDYLDAFGEATDEDRAHWDRARAYGREVLERIDGHWDRAEYPLD +LVARAGELDLLTDGLEVPGHAVMSPLAAGLVAMEISRADGSMAAAAAVQGGLVLRALVHC +ASPEQKERYLEPVARGTLPGGFALTEPLHGSDSVSLETSARPDGAGGWVLNGAKKWIGNG +AAGGITIVWARDTEDGQVKGFVVEQSTPGYEAEVITGKGALRAIHQAEITLTDVRVGDDA +RLPGVATFKDAARVLVATRVNVGWSALGHATAMFEAALAYARQREQFGKPLGAHQMVQER +LAQMLDEVTAMQTRCVAVARLQAAGLLRDEQASLLKYACTRGARRVAQIARDMLGGNGIL +LEHRVMRHFADVEALHTYEGTESVQALILGRDLTGMSAFA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001576.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001576.fa new file mode 100644 index 0000000000000000000000000000000000000000..826c9510c77383ebfa3db476639e9efd05c48e09 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001576.fa @@ -0,0 +1,39 @@ +>PROKKA_01971 +MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAELLPADVPVIPLPSDL +VPGHEQPARSPLHWSPVGPEIRARFDALHAAAQRVGPDVCVVDVSVEAALFLRLAGWPVL +HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRT +TTTSTARAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA +EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF +VREIHRAAGVPWCAWEDPDADWAGAVRGALADPTAADRLAGLLLVAPDEYRRRWEAAIEG +ALG +>PROKKA_01665 +MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAELLPADVPVIPLPSDL +VPGHQQPARSPLHWSPVGTEIRARFDALHAAAQRVDPDVCVVDVSVEAALFLRLAGWPVL +HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRA +TTTSSAGAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA +EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF +VREIHRAAGVPWCAWEDPDADWAGAVRGALADPAAADRLAGLLLVAPGEYRRRWEAAIEG +ALG +>PROKKA_00888 +MSDGAAAVSRPGASARPSRRRRVLYYAHQHGSGHVRHAANLAATGAFDVTVVSAHPDAAR +MLLAGTPVLPLPSDVVPGHVQPERSPLHWTPVGPQIRDRFAALHDAARDVRPDVCVVDVS +VEAALFLRLAGWPVLHRRMHGERTDPAHALVYAEADGLFAHYAEELEDPAWREAHAGRTA +FLGVPDVTGRLGARATTTTATTTAAGGSAPRVAVIAGTGGGGVRAADLARAAAAVPEATW +EVYGPVAGADELQAPGGAAGSRSSDADATTGTAPTAGVALPANVTLHGWVEAPASRAAEA +DVVVVSAGHNAAVDAARSGRPVVLAPEPRPFDEQHVFAREARRAAGVPWCAWEDPDADWA +GAVRGALADPSAADRLAALLLVEPGEYRRRWEAAVEAALEATQG +>PROKKA_00829 +MSGRRLRVLHYAHQHGSGHVRHAATLIRADVADVTVATAHPDAARLLPTGTRIVPLPTDI +VPGHGQPEGSPLHHTPVGPAIQARFDALHDAARAVRPDVCVVDVSAEAALFLRLAGYPVV +HRRMHGDRTDPAHRLVYAEADALFAHYGEVLEDPAWQAEFGARTAHLGVPDADGRLGRTA +APARAGEAPRVVAVTGTGGGGVAARDIARAARSTPGARWHVIGPVRDAGGADLPENLELQ +GWVEDVPAALAAADVVVVSAGHNAAVDAAHSGRPVVLAPEERPFAEQRRFAEAVERAAGV +PWRAWEDPEADWAGAVARALGDPAAADRLAAALLRPPAEHAAGWGALLERAAASAQ +>PROKKA_01897 +MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAALLPADVPVIPLPSDL +VPGHQQPARSPLHWSPVGTEIRARFDALHAAAQRVDPDVCVADVSVEAALFLRLAGWPVL +HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRA +TTTSSAGAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA +EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF +VREIHRAAGVPWCAWEDPDADWAGAVRGALADPAAADRLAGLLLVAPDEYRRRWEAAIEG +ALG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001578.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001578.fa new file mode 100644 index 0000000000000000000000000000000000000000..49dad2f35db39ebd1f81e7ba75ea7ff61058839b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001578.fa @@ -0,0 +1,20 @@ +>PROKKA_01974 +MTVPPGSPAAPSAPASRRRRRALAAALAVAVVVQLVVLYLPGEQVPQAGFAAPGLDKAIH +VAVFALPAFLAVGRGRSAWWALPFAVHAPVSELVQHAWVPLRTGDPVDVVADLAGVVLGV +VAARSRRIGGSGASGV +>PROKKA_01668 +MTVPSGSPAAPSAPASPRRRRALAAALAVAVAVQLVVLYLPGEQVPEAGFTVPGLDKAIH +VAVFALPAFLAVGRGRSAWWALPFAVHAPVSELVQHAWVPLRTGDPVDVVADLAGVVLGV +VAARSRRIGGSGASGV +>PROKKA_00884 +MGDARPRVPVCPSSRRRRRALAALLAVVVVVHLVVLYLPGSDVPQTGFEVPGLDKTIHVL +AFAAPTWAAVRLGSSWWWALPFAVHAPVSEAVQHAWVPLRTGDAWDMVADLAGVVLGAAL +AWRAVRREVEAPGEVGEVGEAGRGDRIGGSGRPGV +>PROKKA_00826 +MPARSSAPAAPPPSAARRRTLALLLVIALAAHLVVLYLPGDDVPAVGFEVPGMDKAIHVA +TFGVPALLGVLLARRVWPAAVLAVHAPLSEVLQAVQGLGRTGDPADAVADLAGVALGLLA +ARAALRRGPTGRPIGAAPGRGV +>PROKKA_01900 +MTVPSGSPAAPSAPASRRRRRAVAAALVVAVVVQLVVLYLPGEQVPEAGFAVPGLDKAIH +VAVFALPAFLAVGRGRSAWWALPFAVHAPVSELVQHAWVPLRTGDPVDVVADLAGVVLGV +LAARSRRIGGSGASGV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001579.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001579.fa new file mode 100644 index 0000000000000000000000000000000000000000..1b9c206be48c84ca801e5ebcb472ccc528bed1b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001579.fa @@ -0,0 +1,25 @@ +>PROKKA_01978 +MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE +ETVAAAIAELLGPDARYVVPAGLEPDWLPTDSRGAGRERITEPAVGHTGERAAVRGAHDG +EREPLNVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV +ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR +>PROKKA_01672 +MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE +ETVAAAIAELLGPDARYVVPAGLEPDWLPADSRGAGRERITEPAVGHTGERAAVRGAHDG +EREPLSVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV +ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR +>PROKKA_00880 +MSEATPTTVPATPTPGPGGPGGEARAAILDRIRQALQDGPTPDPVERTYRRTSEAAPGDV +VEQLVDRLVDYKAGVHREDLTTVADRVADLLGEGARYVVPPGLDPAWLPGDGQGRVRVTE +PATADAGALGVRELDELDAVVTGSTVSCSETGTIFLTGRPEEGRRAISLVPDHHVCIVPL +DTVVELFPEALARVEPTAAITMISGPSATSDIELERVEGVHGPRRLDVILLDR +>PROKKA_00815 +MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE +ETVAAAIAELLGPDARYVVPAGLEPDWLPADSRGAGRERITEPAVGHTGERAAVRGAHDG +EREPLSVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV +ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR +>PROKKA_01904 +MSEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEVVEMLRDRLIDYRASVRDETE +ETVAAAIAELLGPDARYVVPAGLEPDWLPADSCGAGRERITEPAVGHTGERAAVRGAHDG +EREPLSVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGRRAITLVPDHHVCIVPLDSVV +ELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPRRLDVILLDRAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001582.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001582.fa new file mode 100644 index 0000000000000000000000000000000000000000..d30ef7ba7ed6c773e3f42e58f3678129cb2ebb90 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001582.fa @@ -0,0 +1,55 @@ +>PROKKA_01981 +MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM +PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV +LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT +AGTLTGIPATHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW +LASTHFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM +AVLPYIVVVAVFALAKLVPSITAALNSATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA +SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV +MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD +PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL +QSNVLAWMLPAAG +>PROKKA_01675 +MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM +PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV +LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT +AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW +LASTYFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM +AVLPYIVVVAVFALAKLVPSITAALNAATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA +SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV +MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD +PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL +QSNVLAWMLPAAG +>PROKKA_00877 +MDPLIQASAPVGTFTATTDAVAGSLGLSAALGTIPLLTFFVMLLLVKAKAWQAGLVSLTA +AVLVAILAFGMPADLTLLSASQGAVFGFFPIVWIVVMALWFYQVTVLSGRFEDMRAIFDT +VGGGDIRIQAVLIAFCFGGMLEALAGFGAPVAITATMLLALGLPPLKTAVVVLLANTAPV +AFGAVGIPITTAGQLTDIPAAEIGAIVGHQAPFVAVLVPFFLVWIIDGFRGIRETWPALL +TIGGTFALGIWWASTQFSYELTDVVASLLAMASAVVLLRFWRPKGAAEADARLGITPTRP +AGDLTPGRIWMAVLPYLLVITVFGIAKLWTLGFDLPGWLASTNVRIPWPGLDGRLVTAAG +EPITGTVYSFQWLSSPGTLLLITGLLVALIYSVFTGGGRFPLRFGDALAEIGRCFWKMRW +SGLTIVLVLSLAYVMNFSGQTLAMGTAVAGVGAAFAFLSPVLGWLGTAVTGSDTSANALF +ATLQQTAAEEAGLDPSLMVAANTSGGVVGKMISPQSLAIAATAVSMEGQESKILRTVLPW +SVALLLMVCTIVFLQSNVLSWMLP +>PROKKA_00812 +MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM +PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV +LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT +AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW +LASTHFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM +AVLPYIVVVAVFALAKLVPPITAALNSVTAKIPWPGLDGHLVNASGAPLASTVYKFEWLA +SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV +MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD +PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL +QSNVLAWLLPAAG +>PROKKA_01907 +MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM +PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV +LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT +AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW +LASTYFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM +AVLPYIVVVAVFALAKLVPSITAALNSATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA +SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV +MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD +PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL +QSNVLAWMLPAAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001584.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001584.fa new file mode 100644 index 0000000000000000000000000000000000000000..ec04b19e6792d943efe468c03ccccdeccd50e709 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001584.fa @@ -0,0 +1,40 @@ +>PROKKA_01984 +MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGAGSGASDQDYRDAGAELVDD +VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV +TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE +AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI +PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM +PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLPSVATAVAD +ELGLDPRKDVRVTSEVLAEA +>PROKKA_01678 +MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGVGSGASDQDYRDAGAELVDD +VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV +TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE +AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI +PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM +PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGALTLPSVATAVAD +ELGLDPQKDVRVTSEVLAEA +>PROKKA_00873 +MLIGVPTEVKNNEFRVALTQGGVLELVRRGHEVLVQAGAGVGSGISDQVYLDAGAQLVQD +PDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPECTRAILDSGTTAIAYETV +TRGRALPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE +AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIAETVADADLVVGSVLI +PGAAAPKLVTAEMVEQMRPGSVLVDIAIDQGGCFENSRPTTHQDPTYLVGDKIYYCVSNM +PGAVPQTSTAALTNATLPYIQRIADLGWREALAADEGFASGLNAHEGALTLPSVAEAMAG +PLGLDPRKDARTTADVLASA +>PROKKA_00809 +MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGVGSGASDQDYRDAGAELVDD +VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV +TRGRALPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE +AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRMRTLASSHLNIGETVADADLVIGSVLI +PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM +PGAVPQTSTAALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLSSVATAVAD +ELGLDPQKDVRVTSEVLAEA +>PROKKA_01910 +MLVAVPTEVKNNEFRVALTQGGVQELVRAGHQVLVQSGAGAGSGASDQDYRDAGAELVDD +VDELWERAELVLKVKEPQPEEYGRLRRGQVLFTYLHLAASPACTRAILDAGTTAIAYETV +TRGRSLPLLAPMSQVAGRLAPAAGAYHLLQPQGGSGVLMGGVPGTRRARVAVIGGGVAGE +AAAVIAAGMGADVTVLDISLERLAQLDAVHQGRIRTLASSHLNIGETVADADLVIGSVLI +PGAAAPKLVTAEMVESMRPGSVLVDIAIDQGGCFENSRATTHQDPTYLVGDKIYYCVSNM +PGAVPQTSTSALTNATLPYIKRIADLGWRAALAADEGFAGGLNAHDGVLTLPSVATAVAD +ELGLDPRKDVRVTSEVLAEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001585.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001585.fa new file mode 100644 index 0000000000000000000000000000000000000000..69dde4620064d109fd18513dc28c6d8a2a19134c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001585.fa @@ -0,0 +1,35 @@ +>PROKKA_01986 +MSDERARSFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV +AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF +IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA +VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVAETGALPVVMFTAGGVATPAD +AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV +GDLPAPHRLAERGW +>PROKKA_01680 +MSDERARNFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV +AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF +IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA +VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVAETGTLPVVMFTAGGVATPAD +AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV +GDLPAPHRLAERGW +>PROKKA_00871 +MSDERARSFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV +AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF +IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA +VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVAETGALPVVMFTAGGVATPAD +AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV +GDLPAPHRLAERGW +>PROKKA_00807 +MSDDRAQSFSASTGAAADDGARGTGTTRVKRGLADMLKGGVIMDVVTPEQARIAEDAGAV +AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF +IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA +VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVCEVAETGALPVVMFTAGGVATPAD +AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV +GDLPAPHRLAERGW +>PROKKA_01912 +MSDERARSFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV +AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF +IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA +VKHIRTIRKEIAQLQGLAQDELYVAAKELRAPYELVREVAETGTLPVVMFTAGGVATPAD +AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV +GDLPAPHRLAERGW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001586.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001586.fa new file mode 100644 index 0000000000000000000000000000000000000000..0209a547f35b03f87cea06d9065233eabd8678d6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001586.fa @@ -0,0 +1,30 @@ +>PROKKA_01988 +MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARRH +VVDALSGGMTAWVRISATSTDHWQRDLEALAGLDGVRGVVLAETKEPEQVTFTAMRLRAG +TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR +VGGLPGAIDGPPGNTDGEDAVIESSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW +ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA +>PROKKA_01682 +MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARQH +VVDALSGGMTAWVRISATSTDHWQRDLEALTGLDGVRGVVLAETEEPEQVTFTAMRLRAG +TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR +VGGLPGAIDGPPGNTDGEDAVIESSVVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW +ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA +>PROKKA_00869 +MPVRNRRAAALPAKLSRSWLLVNAARPEDFAPALASEADSVIFDLEAAVPEDKKDAARQH +VVDALSGGMTAWVRIAATSTDHWQRDLEALAGVDGVRGVVLAETEEPEQVTFTAMRLRAG +TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR +VGGLPGAIDGPPGNTDGEDAVVDSSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW +ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA +>PROKKA_00806 +MPVRNRRAAALPAKLSRSWLLVNAARPEDFAPGLASEADSVIFDLEAAVPEEHKDAARQN +VIEALSGGMTAWVRISATTSEHWARDLEALEGLSGVRGVVLAETEEPEQVTFTAMRLRAG +TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR +VGRLPGAVDGPPGAGDDEAAVAASSEVTHSMGMTGRLCLNRGQVEWVNRALSPSEDELTW +AHDLLDKHAAGAAVGDGSYLPRLRRAEKIADLADSYGLWNA +>PROKKA_01914 +MPVRNRRAAALPAKLSRSWLLVNAATPDAFAPALASEADSVIFDLEAAVPEEQKDAARQH +VVDALSGGMTAWVRISATSTDHWQRDLEALAGLDGVRGVVLAETEEPEQVTFTAMRLRAG +TPVIALLESALGIENATAVAKAPGTFRLAFGVNDFRKDVGVGEDPLAMAYARSRMVIASR +VGRLPGAIDGPPGNTDGEDAVIESSAVTASMGMTGRLVLNRDQVDWVNRAMSPSEDELAW +ARDLLEKHAQGAAVGDGSYLPRVLRAQKIADLADSYGLWNA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001587.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001587.fa new file mode 100644 index 0000000000000000000000000000000000000000..75dc48aa170e5ada5f632d7c281bc9f4db123c2b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001587.fa @@ -0,0 +1,32 @@ +>PROKKA_01989 +MRPPSPPRALRLMGAVAAACLLAGCAVDPGLAEDSASDDGVPLPATEGYQPLTVYLAVAE +TEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADAALDFLFADEQGWHGDPSLWNAVFDAR +ETLTPTGHRREGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL +DDVLGLEPLRLGESVDVPQGDPTPSGEPSDESGEQTWAPEGESPEDTWAPAEPSDETWAP +AEESSWGPAEPTQGTWSPGPEPSAP +>PROKKA_01683 +MRPTPPSRALRLTGAVAAACLLAGCAVAPDLAEDSASDDGVPLPATEGYQPLTVYLAVAE +PEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADAALDFLFADERGWHGDPSLWNAVFDAR +ETLTPTGHRRAGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL +DDVLGLEPLRLGESVDVPQGDPTPSGEPSDGSGEQTWAPEGESSEDTWAPAEPSTWAPTE +ESSWGPAEPTQGTWSPGQEPSAP +>PROKKA_00868 +MRQRPASRAVLLVGAAAAVGLLGGCAAEPGAPAADGSAQGDALPRPEVDGYAPLTVWLTV +PAAEAVPGSTGRAYGCDDLLVPVQTVPADAPDDADAALDFLFSDERGWHGDPSLWNAVFE +TRESLTPTGHRLEGDVDVFTFTGTVTAEGECEAERIRAQLQETAAAHTSAGQVRLEVDGR +PLDDVLGLAPLALGDEVDVPESGADPSESPTEPADEPWEEPAEDPWAEPTEDTWSEPTED +PWAESEESAEPSPTAWEEPAEETWEPQDETAPTEEDAPTEWDGTVDDGSASEDVPAEVEE +PPAQDEGADAADESAPAEDAGADGAGNLGIGDPDATEPSAP +>PROKKA_00805 +MRIRPTPRVRLAAVLATSAALTSGCGALTGQGLDEPKELTVHLTVPRADAASSFEGRPYG +CDDLLVPVTTAPSSGVDHGDAALDFLFSDLQGEHGDPALQNAVKATADTLHPTGHHRDGS +TEVFTFDGTVTAEDECAAQRIRAQLQETARAQSPVPDVRLEVGGRPLDEVLGLPALSLGD +PVKGGAASTPRATPTPESTPSPTATPTPTPTTVPGSSASPAPTSASPTATPAPSTSAAPS +TTGPSSASPTAETSSAAPASPDPASADPATAAPTSASATAGGASPSVEPTDGTSLRSPGA +GDATATTAPLDGLDGGAAGGTGTGGADATAPGGAPSAGAAAGAGAGSSATG +>PROKKA_01915 +MRPPSPSRALRITGAVAAACLLAGCAVDPGLAEDSASDDGVPLPATEGYQPLTVYLAVAE +AEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADTALDFLFADERGWHGDPSLWNAVFDAR +ETLTPTGHRRAGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL +DDVLGLEPLRLGEPVDVPRGVPAPSGEPSDGSGEQTWAPEGESSWGPAEPTQGTWSPAQE +PSTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001590.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001590.fa new file mode 100644 index 0000000000000000000000000000000000000000..ea092d97bcb6af18cd2241abd8882f8c2d9aac13 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001590.fa @@ -0,0 +1,25 @@ +>PROKKA_01992 +MRRTDIGTVGLAGAPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA +IRRLQSEKLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTGEDLAAARE +VNATMRAMTESETAWDPMAFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA +YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLEHSAEPSA +>PROKKA_01686 +MRRTDIGTVGLAGAPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA +IRRLQSEKLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLAAARE +VNATMRAMTESETAWDPVTFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA +YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLRAYLEHSAEPSA +>PROKKA_00865 +MSRTDIGTVGLAGTPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA +IRRLQSENLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLSAARE +VNATMRAMTASEKAWDPVAFTELNRRFHSILFEHHQNEHVHDLVHRGWTRLAALRSSTFA +YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLAHQGELS +>PROKKA_00803 +MRRTDIGTLGLAGTPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA +IRRLQSENLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLAAARD +VNAAMRAMTASEKAWDPVAFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA +YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLEHSAEPSA +>PROKKA_01918 +MRRTDIGTVGLAGAPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA +IRRLQSEKLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLAAARE +VNATMRAMTESERAWDPVAFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA +YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLEHGAEPSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001593.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001593.fa new file mode 100644 index 0000000000000000000000000000000000000000..96c93512a4274acbb4fb5b71f7050c4a1ad8910a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001593.fa @@ -0,0 +1,30 @@ +>PROKKA_01995 +MLDHETHVKIADELHRAGIDRVPVPRLTARYPQMEIEDSYAVQRIWAERQVEAGRRKVGH +KIGLTSKAMQDATGIDEPDYGVIFDDQVFESGHVYEWKKYTHPRIEMELAFVLKDELRGP +GLNLMDVLRATEYVVPALEVLDSRIEMAGRTITDTISDNAALGSLVIGGRPVGVDDVDLR +WVSGILSRNEEIIETGVAAGVLNHPANGVHWLANRIAGHGDALEAGEIVLAGSFTRPMWV +YEGDTVYADYGPLGTITCRFA +>PROKKA_01689 +MLDHETHVKIADELHRAGIDRVTVPRLTARYPEMQIEDSYAVQRIWAERQVEAGRRKVGH +KIGLTSKAMQDATGIDEPDYGVIFDDQVFESGHVYEWKKYTHPRIEMELAFVLRDELRGP +GLNLMDVLRATEYVVPALEVLDSRIEMAGRTITDTISDNAALGSLVIGGRPVGVHDVDLR +WVSGILSRNEEIIETGVAAGVLNHPANGVHWLANRIAGHGDALEAGEIVLAGSFTRPMWV +HEGDTVYADYGPLGTITCRFA +>PROKKA_00860 +MLDHETHVKIADELHEAGRTGTPVPLLTARYEGMEIEDSYAVQRIWAQRQVEAGRRVVGH +KIGLTSKAMQAATGITEPDYGVIFDDQVFESGHEYETARITNPRIEMELAFVLKDELRGP +HVNLFDVLRATEYVVPALEILDAHVELAGRTIVDTIADNAALGSMVLGGRPVAPDAVDLR +WVAGTLSRNQTIEETGVAAGVLNHPGNGVHWLANRLVDHGDALAAGEIVLAGSFTRPMHV +SAGDTVTADYGPLGTVTCHFA +>PROKKA_00798 +MLDHATHVKIADELFEAGRAGTPVPLLTARYADMEVEDSYAVQRIWAERRVEAGRRVVGH +KIGLTSKAMQAATGITEPDYGVIFDDQVFESGHVYETARITNPRIEMELAFVLKAELRGP +HVNLFDVLRATEYVVPALEILDAHIELAGRTIVDTIADNAALGSMVLGGRPVAPDAVDLR +WVAGTLSRNQTIEETGVAAGVLNHPGNGVHWLANRLGEHGDALAAGEIVLAGSFTRPMHV +SAGDTVTADYGPLGTVTCFFA +>PROKKA_01921 +MLDHETHVKIADELHRAGIDRVPVPRLTARYPEMEIEDSYAVQRIWAERQVEAGRRKVGH +KIGLTSKAMQDATGIDEPDYGVIFDDQVFESGHVYEWKKYTHPRIEMELAFVLKDELRGP +GLNLMDVLRATEYVVPALEVLDSRIEMAGRTITDTISDNAALGSLVIGGRPVGVHDVDLR +WVSGILSRNEEIIETGVAAGVLNHPANGVHWLANRIAGHGDALEAGEIVLAGSFTRPMWV +HEGDTVYADYGPLGTITCRFA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001594.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001594.fa new file mode 100644 index 0000000000000000000000000000000000000000..7cf52b4437ccafc90b63c8926a84e9bd9f62e983 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001594.fa @@ -0,0 +1,56 @@ +>PROKKA_01998 +MTTSAPTLSSHFADTFPELALPWQAQVTDGPQLVLLNAGLAAELGLDAEWLASDDGVRFL +TGEQPGPHARPVAQAYAGHQFGHYSPRLGDGRALLLGELTAPDGRLHDLHLKGSGRTPFA +RGNADGQAVLGPMLREYVVSEAMHALGVPTTRALAVVATGHPVRRETVLPGAVLARTAAS +HLRVGTAQYAAALPEQAHPTEVLRRIVDEAIARHHPHATDAEHPALALYEAVIAAQAELV +SRWMLVGFVHGVMNTDNMTLSGETIDYGPCAFIDAFDPAASFSSIDTQGRYAYGNQGPIA +AWNLARLGEALVPVLDDDPDRAVALAQEALGRFHGAHLAAWRGGLRDKLGLPASVAEDDV +AALTDRLFPWLAAARADWTSFWVRLAEHTAAPVDDDAARTEAARLVPGAPDPAGLAAWLA +DWRAMGPDPARMRAVNPVYIPRNHLLDEALTAAEGGDLAPVHRLLEAVTDPFTPRPGFER +YAEPGPADGAPFVTYCGT +>PROKKA_01692 +MTTSVPALSSHFADTFPELALPWQAQATDGPRLVLLNAGLAAELGLDAEWLASDDGVRFL +TGEQSGPDARPVAQAYAGHQFGHYSPRLGDGRALLLGELTAPDGRLHDLHLKGSGRTPFA +RGNADGQAVLGPMLREYVVSEAMHALGVPTTRALAVVATGHPVRRETVLPGAVLARTAAS +HLRVGTAQYAAALPEQAHPTEVLRRIVDESIARHHPHATDAEHPALALYEAVIAAQAELV +SRWMLVGFVHGVMNTDNMTLSGETIDYGPCAFIDAFDPAASFSSIDTQGRYAYGNQGPIA +AWNLARLGEALVPVLDDDPDRAVPLAQEALGRFHGAHLAAWRGGLRDKLGLPASVAEDDV +AALTDRLFPWLAAARADWTSFWVRLAEHTAAPVDDDAARTEAARLVPGAPDPAGLAAWLA +EWRAMGPDPARMRAVNPVYIPRNHLLDEALTAAEDGDLTAVHRLLEAVTDPFTPRPGFER +YAEPGPADGAPFVTYCGT +>PROKKA_00859 +MPVRHNTQPLVRDLFTTEAKAARGGRPAAGMFLSSGDCTAAEICAGAGLDYLLIDGEHAP +LSLENVQAQLRTIAGYGVPVMTRVPFLDWISIKQYLDLGAQTLLVPMIDTPEQAAEAVRA +LRYPPHGDRGVGSALARSGRWNRIEGYLQHDEEHVSLFVQIETVRGVENAAAIAAVPGVD +GVFVGPSDLSASMGLIGQQSHADVVAAVRRVIEACNAAGTTVGVNAFATDQAQAYADAGA +DFVNVGADVALMARGAEALADRWCPTPGTGADEGAGEGAGAGAGARANARPARRTDGGRP +TRPPAPHAWECGVMDDVAPAHPALAPQPGRPALRHRFADLFPELAVPWQAQETDGPELVL +LNTGLVTELGLDADWLASDDGVRLLTGEQLGPDARPVAQAYAGHQFGHYSPRLGDGRALL +LGELVPPRRTRDANDAPQALPTWRELHLKGSGRTPFARGDADGQAVLGPMLREYAVSEAM +HALGVPTTRALAVVATGRPVRRAGWQPGALLARTAASHLRVGSFQYAAALPERADPVAVL +RRLVDEAILRHHPHAAEAENPALALYEAVIAAQAELVARWMLVGFVHGVMNTDNMTLSGE +TIDYGPCAFLDAFDPAASFSSIDTQGRYAFGNQGPVAAWNLARLGEALVPVLDDDAGRAV +ELAQEALGGFQATHLAAWRGGLRAKLGLSEEVTDADVAALTDRLFPVLAAARTDWTGFWV +RLAEHVPGGRGRGRAGRGRRRTECPAECRSGRADGRRAGGGADAGPGRGRPGCRGRVAAR +LAGAGPRRGPDAGGEPRLHPAEPPARRGPHRRRGRGPGAGAPPAGGRHRPVHPAPGPRAV +RRAGPVGRGPVRDVLRDVRRGRRGLPYSRSPLPAPRPNSHRPTAFVWESGNLPPLSCGET +GVPVSHTKGDEGRTLLLTRGCGGARPLTPGRATSAARSGRRGPAGPPRSRGR +>PROKKA_00795 +MPVPALQHRFADRLPELAVPWQARPAPAPTLAALNAPLAAELGLDPAWLATDAGLAFLTG +TEPGPGARPVAQAYAGHQFGSYSPLLGDGRALLLGELTAPDGTLHDVHLKGSGLTPFSRE +GSDGLAALGPMLRELVVSEALHALGIPTTRALAVVATGGPVRRQRVLPGAVLVRVADSHL +RVGTFQHAAALVHAGRAPEDLLTRLVAESLERHHPGHADDAAPALALLRAVVAAQAELVA +RWMLMGFVHGVMNTDNMTVSGQSIDFGPCAFLDGFDPDAVFSSIDRGGRYAYGAQPRIAL +WNLNRFAETLLPLLAPDPEAAVAAAEEALGGFAPAFDAAWQGGLAAKLGLARSADSDALA +AELLRLLAQDRADWTASWANLSDLPLPADWLARWRALDPDPELARAANPLRVPRNRPLQA +ALDAAEDGDLADVERILAAVREPFTPRADASDLDVPPAPGAGGEAPFVTFCGT +>PROKKA_01924 +MTTSVPALSSHFADTFPELALPWQAQATDGPQLVLLNAGLAAELGLDAEWLATDDGVRFL +TGEQPGPGARPVAQAYAGHQFGHYSPRLGDGRALLLGELTAPDGRLHDLHLKGSGRTPFA +RGNADGQAVLGPMLREYVVSEAMHALGVPTTRALAVVGTGHPVRRETVLPGAVLARTAAS +HLRVGTAQYAAALPEQAHPTEVLRRIVDEAIARHHPHATDAEHPALALYEAVIAAQAELI +SRWMLVGFVHGVMNTDNMTLSGETIDYGPCAFIDAFDPAASFSSIDTQGRYACGNQGPIA +AWNLARLGEALVPVLDDDPDRAVALAQEALGRFHGAHLAAWRGGLRDKLGLPASVAEDDV +AALTDRLFPWLAAARADWTLFWVRLAEHTAAPVDDDAARTEAARLVPGAPDPAGLAAWLA +DWRAMGPDPARMRAVNPVYIPRNHLLDEALTAAEDGDLTAVHRLLEAVTDPFTPRPGFER +YAEPWPEDGAPFVTYCGT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001596.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001596.fa new file mode 100644 index 0000000000000000000000000000000000000000..3b1cd9f3b9a55101b64e52ef12580d0190b55598 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001596.fa @@ -0,0 +1,15 @@ +>PROKKA_02000 +MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW +LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA +>PROKKA_01694 +MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW +LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA +>PROKKA_00857 +MAEPIHIGAAADIPEGEAVVVPAATAGTSDDVAVFHAEDGAFYAIDDTCTHEDASLAEGW +LEGTQVECPLHSAQFCLKSGEALCLPATRPVGTHPVQERDGQLYLTPGA +>PROKKA_00793 +MSREINVGPASAVPEGESLLVPNDTTGTKDHIGVFHAEDGAFYAIDNTCTHQDYALSEGF +VEDCRVECPLHGASFDLRTGEALSLPATKPVGTHRVEERDGDLWLTVEDGE +>PROKKA_01926 +MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW +LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001597.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001597.fa new file mode 100644 index 0000000000000000000000000000000000000000..4bb2e0c42b9268c8dbd1d2b0f56df1f891c5b5d9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001597.fa @@ -0,0 +1,40 @@ +>PROKKA_02003 +MGRITASAARITLVAMTDDAQQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE +NPYAPVSGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL +GALAQVITAFAGHGEAGEGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML +EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL +EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL +EHLDEVLERVQIVVDERERVAAALAEAGWDLPASQANFVWLPLGERTQAFAEAAQARALS +VRAFAGEGVRVSIGEKEANDRFLEVARDFLA +>PROKKA_01713 +MVPLTASAARITLVAMTDDAQQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE +NPYAPVPGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL +GALAQVITAFAGHGEAGEGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML +EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL +EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL +EHLDEVLERVQVVVDERERVAAALAEAGWDLPSSQANFVWLPLGERTQAFAEAAQARALS +VRAFADEGVRVSIGEKEANDRFLEVARDFLT +>PROKKA_00839 +MTDDAQLTPAAVAPHKKVGMLPPYAAGKPPVAVPGLRPYKLSSNENPHAPVAGVIERVRG +VVTGPEGAPSTLCRYPDTLSTGLREALAAHLDVPADDVVTGAGSLGALSQVITAFAGHGE +AGRGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAMLAAITDRTRVILLCTP +NNPTGPVLTTAEVEGFLAEVPEHVLVVIDEAYVEFVRDEDAVRGLDMYRKHANVVVLRTF +SKAHGLANLRVGYSVSRPEITKALRTVATPFAVSTVAEEAAIASLEHLDEVLEGVQLVVD +ERERVAAALAEAGWDVPASQANFVWLPLGERTADFAAAAQAKALSVRAFAGEGVRVSIGE +QEANDRFLEVARDFLK +>PROKKA_00776 +MTDVTSGSSGVAAHRKVSLLPPYAAGKPPVAVPGLRPYKLSSNENPFAPVPAVVERIHEV +VAGAEGEPSPVCRYPDPLSTALRERLAAHLDVPADDIVTGGGSLGALTQVITAFAGDGGE +DGAPDEVVFAWRSFEAYPIVVRTAGAKDVQVPLTADGRHDLPAMLAAITERTKVMLLCTP +NNPTGPVLTTAEVEDFLAQVPPHVLVVIDEAYVEFVRHPDAVDGPAMYRRHPNVVVLRTF +SKAHGLANLRVGYSVSRPEVTASLRTVAVPFAVSTVAEQAAIASLDHLDEVLERVQTVVD +ERERVVAALAEAGWDVPETHANFVWLPLGERGADFAAAAGERALSVRAFPEGVRVSISER +EANDRFLEVARAFQR +>PROKKA_01941 +MGRITASAARITLVAMTDDAPQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE +NPYAPVSGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL +GALAQVITAFAGHGEAGEGDEVIFAWHSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML +EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL +EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL +EHLDEVLERVQVVVDERERVAAALAGAGWDLPSSQANFVWLPLGERTQAFAEAAQAQALS +VRAFAGEGVRVSIGEQEANDRFLEVARDFLT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001598.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001598.fa new file mode 100644 index 0000000000000000000000000000000000000000..463b348015c909fa13f38427a7309408f5e65521 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001598.fa @@ -0,0 +1,30 @@ +>PROKKA_02004 +MAEHDGGPVREGAPSQTLSRALTLLEAVVEAPEPPTIADLADGLGVHRSVAYRMLRTFET +HGLLRRDGLGRVHAAPGLAVLARRVEQDLRAAAMPHLTAVSTDLGMTAFLVVWDGAHCLT +LATAEPPSGNLVTQRPGTRHPLGVGAPGMAIAVALTGQEWARLPGEAAPERPELDDVRER +GWAVSSDEVITGVSSVAVPLRVPGQLPAALAVVYATRPEDPARLGDRLGEAARAVAVAFG +AA +>PROKKA_01714 +MAEHDGGPVREGAPSQTLSRALTLLETVVEAPEPPTIADLADGLGVHRSVAYRMLRTFEA +HGLLRRDGLGRVHAAPGLAVLARRVEQDLRAAAMPHLTAVSTDLGMTAFLVVWDGAHCLT +LATAEPPSGNLVTQRPGTRHPLGVGAPGMAIAVALTGQEWARLPGEAPPERPELDDVRER +GWAVSSDEVITGVSSVAVPLRVPGQLPAALAVVYATRPEDPARLGDRLGEAARAVAVAFG +AA +>PROKKA_00838 +MAEDDGGPAPAREGAPSQTLSRALALLEAVVEAAEPPTIAELADGLGVHRSVAYRVLRTF +EAHGLLRRDPLGRVHSAPGLAVLARRVEQDLRTAAMPHLSAVSADLGMTAFLVVGDGSTC +LTLATVEPPRGNLVTQRPGTRHPLGIGAPGMAVALALPEQEWEQRRGDAAPERPELGEAR +ERGWAVSRDEVITGVSSVAVPLSVPGQLPAALAVVYATRPEDPERLGGRLKEAAQAVAAS +LGAA +>PROKKA_00775 +MDPHDDSVPAVSAPPPSAPGVRPGAPSQTLSRALTMLELVADRPTPPSIAELADDLGVHR +SVAYRMLRTFEVHGLLRRDAAGLVHGAPGLVTLAGGVEQDLRAAAVTELSRVSDALAMTA +FLVVWDGRDCLTLATVEPPRGNLVTQRPGTRHPLGVGAPGIAIASVLPAEGQDRPAVREA +RARGWAASRDEVITGVGSVAAPVPAAAGMPAALAVVFTSPAVDEEAVGAELAAAARRLGA +VLGEG +>PROKKA_01942 +MAEHDGGPVREGAPSQTLSRALTLLETVVEAPEPPTIADLADGLGVHRSVAYRVLRTFET +HGLLRRDGLGRVHAAPGLAVLARRVEQDLRAAAMPHLTAVSTDLGMTAFLVVWDGAHCLT +LATAEPPSGNLVTQRPGTRHPLGIGAPGMAIAVALTGQEWARLPGEAPPERPELDDVRER +GWAVSSDEVITGVSSVAVPLRVPGQLPAALAVVYATRPEDPARLGDRLGEAARAVAVAFG +AA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001599.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001599.fa new file mode 100644 index 0000000000000000000000000000000000000000..1762a19b1b4e39964d07b0708751a39278cd6c02 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001599.fa @@ -0,0 +1,51 @@ +>PROKKA_02006 +MTGGRGAGPGAVAFSTHGGPGSIYAEAEEMRVVAGRHEHAAEEAAGASWQVDAAAFGLGR +SATWLASAALLQDRLAEAVGRVRSLSEQCAELHRDLLSAAARYEEAERAAAGIMAAEDAS +LEELPGLLWRDGHDGLTTREAERLVRDLVQAVPEAIVSAALAATGFPLLAALARIDVKML +TRAQKRVLKRPVSTAAKKGTDAASDLTEALRVSPDEAWTVAADALALAGAAPRGAVTPHG +APQDRPAAPARLDGSAAGLASLIPRGEGDGDLTVTEVVQENGSRAWVVGLPGTRGGLIPD +PESTDPWDAGGLLDALGSESEITAPAVRAALEAAGVPHGVPLVLAGYSQGGVHAVNLAGR +EDFTSVYPVAGVMTIAAPSGNAVETGRTAVLEFSADGDLAVAADGAPTPVSARRAEVVFH +PAGHGWDAPGGGFRTGSPLAVKADLDAAHDFEGQVDLIRQFEAAEPAARAEVAGLSAALA +GLTAGTVASSRAVRLRRTPPEGGHRPPGSR +>PROKKA_01716 +MTGGRGASPGAVAFSTHGGPGSIYAEAEEMRVVAGRHEHAAEEAAGASWQVDAAAFGLGR +SAAWLASAALLQDRLAEAVGRVRSLSEQCAELHRDLLSAAARYEEAERAAAGIMAAEDAS +LEELPALLWRDGHDGLTTREAERLVQDVVQAVPEAIVAAMLAAAGFPLLAALARIDVKML +TRAQKRVLKRPVSSAAKKGTDAASDLTEALRVSPDEAWTVAADALTLAGAAPRGAVTPHG +APQDRPTAPALLDGSATGLASLIPREEGDGDLTVTEVVRENGSRAWVVGLPGTRGGLIPD +PESTDPWDAGGLLDALGSESEVTAPAVRAALEAAGVPHGAPLVLAGYSQGGVHAVNLAGR +EDFTSVYPVAGVMTVAAPSGNAVETGRTEVLEFSSDGDLAVAADGAPAPVSARRAEVVFH +PAGHGWDAPGGGFRPTSPLAAEDDLGAAHAFDAQVDLIRQFETAEPASRAEVAGLSAALA +GLTAGTVASSRAVRLRRTPPERDHLPPGSR +>PROKKA_00836 +MTGGRGAGPDGVAFSTHGGPGSLYAETEQMRAVAAGHDRAAGEALRVAGTAESAGAGLVR +APRVSPTAAVLQARLWEGLERVRALSDRCARMDRDLRAAAVRYEEAERAAAGIVAAEDVG +LGALPLEAWRRGRDGLTTREAERLGEAAVQAVPEAVASAVLTAAGFPALAALARIDLKKL +SWWQRKALKRPVSRGASRLVEEASEGTDLLRVSPDEAWTAVGAVARALSIAADREVAVAG +PPEDRPDAPARLDGSASDLLGLIPRGGVEGELTVTRVERERGGPAWVVGLPGTQGGFAPD +HASRNPWDASGLADALTADSAATAPAVRAALEAAGVPHGAPLVLAGYSQGGVHAVNLAGD +AGFTAAYPVAGVVTVAAPSGNAARTGGAAVLEFSSDADLATAVDGAPVPASRHRAEVVFH +PGGQGWGPPPAPGEEPGAAPAGGFRTAGPDAVGEDLAATHDFDGHLAMVRQFEAADPAAR +AEVAGLSATLAGLSAGAVASSRSVRLRRAPAPREAAGSTSPVAPGGPGRR +>PROKKA_00773 +MSAPAFRVTGGPGSVYADLGSLEAVAQRQRDNGDLARRAGQWCTVLGLDLVSPARTAPSA +EVLRARLEDGRAGLERLAERLEDMRRSLEHTAQAYRQVESGNAAMIGLIDPALAGVPEVT +PESLRDGATASETAGVISEELRAAQEKAYVDAAQRLLLALVGGVPGIPESLAALDFQAKQ +LPWWHPAKHAWNKGKGEAVDRVTGALPAIVEEGVDSGVLPTATAQDASRELARALVSAGA +LPRGEGEVRVEPGARDRPAPPLLDGRASTLLSLVPEQDGADGAGAVTVTRVDRPDGPGGT +ASTWIVGLPGTTTRGGAGDNPFDTLGIVESLADEPGVTRAVQEALEREGVPHGSTVVLAG +YSQGGMRALDLAADEQFASAYRVEGVLTAGAPANDAAAPAEAAVLQFASEADLIWGLGGG +HDRPAASRATVMFDAPAQVPLPQPGEVRPFDGLDEFDGALAGHARSEYARLIEGFERAPA +QDRAEVADLQARLALLTGGAVVSSRVLTLRRTSTEPAVDQRAREVREAAEAAGQRPGPRF +GPRLP +>PROKKA_01944 +MTGGRGAGPGAVAFSTHGGPGSIYAEAEEMRVVAGRHEHAADEAAGASWQVDAAAFGLGR +SAAWLASAALLQDRLAEAVGRVRSLSEQCAELHRDLLSAAARYEEAERAAAGITAAEDAS +LEELPALLWRDGHDGLTTREAERLVQDLVQAVPEAIVAALLTAAGFPLLAALARIDVKML +TRAQKRVLKRPVSSAAKKGADAASDLTEALRVSPDEAWTVAADALTLAGAAPQGAVTLHG +APQDRPTAPALLDGSATGLASLIPRAEGDGDLTVTEVVRGNGSRAWVVGLPGTRGGLIPD +PESTDPWDAGGLLDALGSGSEVTAPAVRAALEAAGVPHGAPLVLAGYSQGGVHAVNLAGR +EDFTSVYPVAGVMTIGAPSGNAVETGRTAVLEFSSDGDLAVAADGAPTPVSSRRAEVVFH +PAGHGWDAPGGGFRTASPLAVEDDLGAAHDFDAQVDLIRQFEAAEPASRAEVAGLSAALA +GLTAGTVASSRAVRLRRTPPERDHLPPGSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001601.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001601.fa new file mode 100644 index 0000000000000000000000000000000000000000..94be86bcba4dfab637c3c47df4311400d519e8c9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001601.fa @@ -0,0 +1,35 @@ +>PROKKA_02008 +MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE +IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA +KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG +WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPTDEDSPNSRQSMAWKVKRFSNDDLR +QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR +IQAHEDGAWVREAAAAYARRQAEQNAPAETHLIGA +>PROKKA_01718 +MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE +IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA +KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG +WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPPDEDSPNSRQSMAWKVKRFSNDDLR +QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR +IQAHEDGAWVREAAAAYARRQAEQNAPAETHLIGA +>PROKKA_00834 +MTQTSSTTRLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE +IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDVLNDQLLEGKA +KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRSSYGPYGRAMVRICKEESFHQRQG +WEILYELSHGTPEQKQMAQDAVDRFYGPALQMFGPPDEDSPNSKQSMAWKVKRFSNDELR +QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDELMSVIKGNGPMNTQRLARR +IQAHEDGAWVRDAAAAYARRQAEQHAPAETHLIGA +>PROKKA_00771 +MTQTSSSPHLASVPSPDDAAGQENFDRLIQEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE +IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA +KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG +WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPPDEDSPNSQQSMAWKVKRFSNDELR +QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGNGPMNTQRLARR +VQAHEDGAWVREAAAAYARRQAEQHVPADTQLIGA +>PROKKA_01946 +MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE +IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNAQLLSGRA +KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG +WEILYELSHGTPEQKQMAQDAVDRFYGPALQMFGPPDEDSPNSRQSMAWKVKRFSNDDLR +QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR +IQAHEEGAWVREAAAAYARRQAEQNAPAETHLIGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001602.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001602.fa new file mode 100644 index 0000000000000000000000000000000000000000..c43979d4431890501355e89c993d0fc05d4c1c58 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001602.fa @@ -0,0 +1,15 @@ +>PROKKA_02009 +MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV +PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL +>PROKKA_01719 +MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV +PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL +>PROKKA_00833 +MGENTAASNAWPLWEVFVRANRGLSHVHAGSLHAPDASLALRNARDLYTRRNEGTSVWVV +PAEAIAASDPDSKGGFFESPQGKSYRHATYYQQSEGVPHL +>PROKKA_00770 +MTENTAPSNEWPLWEVFVRANRGLSHVHAGSLHAPDATMALRNARDLYTRRNEGTSVWVV +PADAVAASDPDSKGGFFESPQGKSYRHATYYQKSEGVPHL +>PROKKA_01947 +MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV +PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001603.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001603.fa new file mode 100644 index 0000000000000000000000000000000000000000..46c84507a29f3291187fb82b84d92041d97d4c3f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001603.fa @@ -0,0 +1,30 @@ +>PROKKA_02010 +MSFATNDSATRHSAGVAITAEEIAAGEQKANDDVARYALALGDDALMLGQRLSWWISRAP +EIEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA +KTIARQLYYSFYSYELYTRLRESTDPTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES +KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEACLTVP +TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW +>PROKKA_01720 +MSFATNDSATRHSAGVAITAEEIAAGEQKASDDVARYALALGDDALMLGQRLSWWISRAP +ELEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA +KTIARQLYYSFYSYELYTRLRESTDSTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES +KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEAGLTVP +TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW +>PROKKA_00832 +MSFATNDSATKHSAGVAITAEEIASGEQKASEETARYALYLGDDALMLGQRLSWWISRTP +ELEEDIALGNIALDLVGHARFLLSYAGTAWGQSEDELAYFRDEEEFRSVRLVEAENGDFA +KTIARQLYYSFYAFELYTRLKESTDATLAAIADKALKEVLYHQDHAALWLNRLGLGTDES +KFRMQRGLDELWPYLPELFHDDETTRPLAEQGIAVLPSSLEEPTMTRIREAIEAAGLEVP +TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGASW +>PROKKA_00769 +MSFATNDSATRHSAGVANTAEEIASGGQKASDEVARYAVYLGDDALMLGQRLSWWISRAP +ELEEDIALGNIALDLVGHARFLLSYAGTAWDKSEDDLAYFRDEEEFRSTRLVEAENGDFG +KTIARQLYYSVYAHGLYTRLKDSKDATLAAIADKALKEVEYHLDHAEQWVNRLGLGTEES +NARLQRGLDELWPYLPELFHDDELTRSLAEQGIAVLPSSLEESTMARIRAAIEGADLKVP +ETGAARGGDRSGQMSEYRGYILAEMQSLARRHPGASW +>PROKKA_01948 +MSFATNDSATRHSAGVAITAEEIAAGEQKASDDVARYALALGDDALMLGQRLSWWISRAP +ELEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA +KTIARQLYYSFYSYELYTRLRESADPTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES +KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEAGLTVP +TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001604.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001604.fa new file mode 100644 index 0000000000000000000000000000000000000000..a14d8f437780ba95dd3e957d622fc1340d1eb119 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001604.fa @@ -0,0 +1,20 @@ +>PROKKA_02011 +MTTASELRPADPAGARVWDAASTVHDPEIPVLSIADLGILREARVEGERAVVVITPTYSG +CPAMDTITTDVARALGRAGFPDAEVRLVLQPAWTTDWMTDEGKAKLNEYGIAPPVARTTD +GPVRIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH +>PROKKA_01721 +MTTASELRPADPADARVWDAASTVHDPEIPVLSIADLGILREARAEGERAVVVITPTYSG +CPAMDTITTDVTRALERAGFPDAEVRLALQPAWTTDWMTDEGKAKLNEYGIAPPVARTTD +GPVMIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH +>PROKKA_00831 +MTTASELRPADPADARVWDAASTVHDPEIPVLSIADLGILREARAEGEKAVVVITPTYSG +CPAMDTITTDVSRALERSGFEESEVRLVLQPAWTTDWMTDEGKAKLAEYGIAPPSARTTD +GPVMIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH +>PROKKA_00768 +MTTAAELRPSDPAAAQVWDAAATVHDPEIPVLSIADLGILRDVQVEDGRAVVVITPTYSG +CPAMGTITADVTTALGRAGYPDAEVRTVLQPAWTTDWMTDEGKAKLAEYGIAPPSARTDE +GPVRVGLAVKCPRCHSLNTREITRFGSTSCKALYTCQECLEPFDYFKVH +>PROKKA_01949 +MTTASELRPADPADARVWDAASTVHDPEIPVLSIADLGILREARVEGERAVVVITPTYSG +CPAMDTITTDVTRALERAGFPDAEVRLVLQPAWTTDWMTDEGKAKLNEYGIAPPVARATD +GPIRIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001606.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001606.fa new file mode 100644 index 0000000000000000000000000000000000000000..803b3e2e2b93471938ca0b2465ffcf235967bf26 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001606.fa @@ -0,0 +1,30 @@ +>PROKKA_02013 +MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF +CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV +YVAKDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA +LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDRRVGLWESLDAENIAQGELCGTA +DYAEGFQAFQEKRKPEFTGRG +>PROKKA_01723 +MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF +CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV +YVAEDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA +LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDHRVGLWESLDAENIAQGELCGTA +DYAEGFQAFQEKRKPEFTGRG +>PROKKA_00829 +MTVADGVAEVRLNAPKKMNSLDEAALADLHEAYRRAAAGVESGEVRAVLLHGEGRGFCAG +RDISAVDPAEDDATAYLRDKVTPVLRAMSEIGVPTFAAVQGACLGVGLGLAIATDVVYVA +EDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELISGEEAVRAGLFSRSVPA +DELLEFTRAKAAKAAQGATLAFRASKELVRQIRDERVGLWESLDAENIAQGDLCNTADYA +EGFKAFQEKRRPEFTGRG +>PROKKA_00766 +MIELAIADRVAVITLNAPQKMNSLDEQALADLADAYAQASAGAESGEVRAILLRGEGRGF +CAGRDISNVVPADDDATAYLRDKVTPVLKAISEAPVPTFAAVQGACLGVGLGLAIASDVV +YVAENAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELISGAEAVQAGLFSRA +VPAEELDGFTREKVAKVADGATLAFRASKELVRQIRDRRVGLWESLDAENVAQGELCDTA +DYAEGFTAFQEKRKPEFTGRP +>PROKKA_01951 +MIEITVENGVAEIVLDAPQRMNALDEAALAELQAAYERAAAGVESGEVRAVLLRGEGRGF +CAGRDISAVVPAEDDATAYLRDRVTPVLRAMSEIPVPTFAAVQGACLGVGLGLAIATDVV +YVAEDAKIGSPFANLGATLDSGGHWLFTERLGAHRTLDLIYTAELLSGAEAVQAGLFSRA +LPADELLEFTRAKVAQVASGATLAFRASKELVAQVRDHRVGLWESLDAENIAQGELCGTA +DYAEGFQAFQEKRKPEFTGRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001609.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001609.fa new file mode 100644 index 0000000000000000000000000000000000000000..19d6fe7e29c3636748c2fae2ce6837b2505fdc24 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001609.fa @@ -0,0 +1,16 @@ +>PROKKA_02019 +MDEPTLLRVALPVANTPGHHLDQRLWLSRAARPVDPETFGRA +>PROKKA_01728 +MDEPTLLRVALPVANTPGHHLDQRLWLSRAARPVDPETFGRA +>PROKKA_02537 +MDALDLPALAGARALELPGSELTHPFGPEADVYKVRGRVFMLVLEARGAMLVNLKAVPED +GAALREAYPAQVTPGYHMSKRHWISLGPPPADPHDDDAPARLDAALVRDLVTESYLLVLE +RSVPRRDWPVDPATFGRG +>PROKKA_00761 +MDEPTLLRIARDRALELPGSAASHPFGPDTEVVKVQGKLFVVFIDHDGRRLVNVKARPED +GAQLRAALPAAITPGYHMDKRHWLSLAAHPDLDEQLVRDLVTESYLLVVAKLPRTRRPVD +PDTFGRA +>PROKKA_01956 +MDEPTLLRIARDRALELPGSAASHPFGPDTEVMKVQGKLFAVFIDHDGRRLVNVKARPED +GAQLRAALPAAITPGYHMDKRHWLSLAAHPDLDEQLVRDLVTESYLLIVAKLPRTRRPVD +PETFGRV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001610.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001610.fa new file mode 100644 index 0000000000000000000000000000000000000000..52bb128bb37e7ddfa40f15adf5e951db98305e05 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001610.fa @@ -0,0 +1,20 @@ +>PROKKA_02020 +MSVDRPFRFTHRWAVPADARSVLALLADPAGYPRWWPAVPRVRRLGPDRAAVRLRGFVPV +RLTMERLIDDRARGLLVARLSGGLTGTVRATVHDDGAPAGHAPRCIVVWEQEVVLTSPWM +RAVARVPGARTAMGLSHAAAMRSARRALGAKAVPTADPA +>PROKKA_01729 +MSADRPFRFTHRWAVPADARSVLALLADPAGYPRWWPAVPRVRRLGPDRAAVRLRGFVPV +RLTMERLIDDRARGLLVARLSGGLTGTVRVTVHDDGAPAGHAPRCIVAWEQEVVLTSPWM +RAVAHVPGARTAMGLSHAAAMRSARRALGAKAVPTADPARTSRP +>PROKKA_00802 +MPASARRPFRFTHRWAVPRPAAEVAALLADPLGYPTWWPSVPRARRIDGAGHDGDPRVAV +LLRGLVPVRLVMARELDDRERGRLVARLDGDLRGTVRVTVHDDDGPAGGTGGCTVAWEQE +VVLGAGRLRAAARLPGARAAMRLSHAWAMRSARRALGARALPAGR +>PROKKA_00760 +MSVDRPFRFTHRWSVPADARSVLALLADPAGYPRWWPAVPRVRHLGPDRAAVRLRGFVPV +RLTMERLIDDRARGLLVAHLSGDLTGTVRVTVHDDGAPAGHAPRCIVVWEQEVVLTAPWM +RAVDRVPGARTAMGLSHAAAMRSARRALGAKAMPTADPAPTTRP +>PROKKA_01957 +MSVDRPFRFTHRWAVPADARSVLALLADPAGYPRWWPAVPRAHRLGPDRAAVRLRGLVPV +RLTMERLIDDRARGLLVAHLSGDLTGTVRVTVHDDGAPAGHAPHCVVTWEQEVVLTSPWM +RAVARVPGARTAMGLSHAAAMRSARRALGAKAVPTADPARTTRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001611.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001611.fa new file mode 100644 index 0000000000000000000000000000000000000000..7f4d2fb56a7689ed1256791daaff9112dab21b69 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001611.fa @@ -0,0 +1,20 @@ +>PROKKA_02021 +MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI +AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARHFQPKVVHVDADNRIVELGVD +PADGLLDGLSRPPLSREWNEAQAEL +>PROKKA_01730 +MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI +AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARNFQPKVVHVDADNRIVELGID +PADGLLDGLSRPPLSREWNEAQAEL +>PROKKA_00798 +MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAAQILPGELVSIVDVTNGARLETYTI +AGERGSGVIGINGAAAHLVHPGDIVILIAYAQMDEEEARHIQPRVVHVDGENKIVELGAD +PADGLLDGVSRPPLSREWNEAQAEL +>PROKKA_00759 +MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI +AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDAEARHFQPKVVHVDADNRIVELGVD +PADGLLDGLSRPPLSREWNEAQAEL +>PROKKA_01958 +MLRTMFHAKIHRATVTQADLHYVGSVTVDQDLLDAADILPGELVSIVDVTNGARLETYTI +AGERGSGVLGINGAAAHLVHPGDIVILIAYGQMDDDEARNFQPKVVHVDADNRIVELGVD +PADGLLDGLSRPPLSREWDEAQAEV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001612.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001612.fa new file mode 100644 index 0000000000000000000000000000000000000000..ce5a40836221aaa0bcad6b71efa998685fec0917 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001612.fa @@ -0,0 +1,35 @@ +>PROKKA_02022 +MRCGLDGLLRDPTVFSTPAAREAGVSAARLRRGDVVSLGWGLWGRRGIEPDPMDHVRALQ +DLHPEGVFSHVTAARVLGLWLTGPLAADRSVHVATPRGHGTASSRAGVRSHRLRADAPVR +IVDGVRVTAPGWIFVDLAAQAGPLEHLVALGDSMVRTAPTEARRRRLPPGVTDVAELRAA +VEERGRVRGIRAAREALELVRPGADSPQESRLRVRLVLDGVPEPAVNPCIRLATGQRLRV +DLVWADAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVFRPGHWELFVR +QLRGLVAARTPPGRVPPSWI +>PROKKA_01731 +MRCGLDGLLRAPTVFSTPAARETGVSAARLRRGDVVSLGWGLWGLRGVEPDPMDHLRALQ +DLHPEGVFSHVTAARVLGLWLTGPLAADRSVHVATPRGHGTASSRAGVRSHRLRADAPVR +IVDGVRVTAPGWIFVDLAAQAGPLDHLVALGDSMVRTAPTEARRRRLPPGVTDVAELRAA +VEERGRVRGIRAAREALELVRPGADSPQESRLRARLVLDGVPEPAVNPCIRLATGQRLRV +DLVWAEAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVFRPGHWELFVR +QLRGLVAARTPPGRVPPSWI +>PROKKA_00797 +MRCGLDETEREPTVFSTNAAQEAGVPPGRLRRSDLEPWGRGLWRVRDAVPDVMDHLRALQ +DLHPEGVFTHVTAARVLGLWLTGPLARDPAIHLGAPRHHGTGSRREGVRSHRLYGDVPVR +IVDGVRVTATGWTFVDLAAAAATVETLVALGDSAVRSAPTERRRRDLPPGVTSLEELRGA +VAERPRVKGIRLARDAVDLVRPGADSPQESRLRVGLVLDGVPEPQVNPRIVLSTGQWLRV +DLAWPAARLVVEYDGDQHRTEQRQWREDRSRDAGLRADGWEVLRVTADVFRPAEWELFVR +RVRARLGRDAAGRAAAG +>PROKKA_00758 +MPRSPAPLPPMRCGLDGLLRAPTVFSTPAAREAGVSAARLRRGDVVSLGWGLWGRRGVEP +DPLDHVRALQDLHPEGVFNHVTAARVLGLWLTGPLAADRSVHIATPRGHGTASSRAGIRS +HRLRADAPVRIVDGVRVTAPGWTFVDLAAQAGPLEHLVALGDSMVRTAPTEARRRRLPPG +VTDVAELRAAVEERGRVRGIRAAREALELVRPGVDSPPESRLRVRLVLDGVPEPAVNPCI +RLATGQRLRVDLVWAEAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVF +RPGHWELFVRQLRGLVAARTKPGRVPPSWI +>PROKKA_01959 +MRCGLDGLLRAPTVFSTPAAREAGVSAARLRRGDVVSLGWGLWGRRGVEPDPMDHVRALQ +DLHPEGVFSHVTAARVLGLWLTGPLAADRSVHIATPRGHGTASSRAGIRSHRLRADAPVR +IVDGVRVTAPGWTFVDLAAHAGPLEHLVALGDSMVRTAPTEARRRRLPPGVTDMAELRAA +VEERGRVRGIRAAREALELVRPGADSPQESRLRVRLVLDGVPEPAVNPCIRLATGQRLRV +DLVWADAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVFRPGHWELFVR +QLRGLVAARTPPGRVPPSWI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001614.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001614.fa new file mode 100644 index 0000000000000000000000000000000000000000..90c04a6dd7c527a32c50c8e3c52646f500f313e0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001614.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001616.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001616.fa new file mode 100644 index 0000000000000000000000000000000000000000..9c2fa2214b0ff0046bff81f04fde2bf1c6866e28 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001616.fa @@ -0,0 +1,25 @@ +>PROKKA_02026 +MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLATHLGISKSAIYHHVESKE +AILDHAVTEALDALEACLDDVVASGVDAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS +AVEVAAVERRREITRRFGDLLEAAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDRGV +PGQEGPGQMIDAVTGVVLGGLRG +>PROKKA_01735 +MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLAAHLGISKSAIYHHVESKE +AILDHAVTEALDALEACLDDVVASGADAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS +AVEVAAVERRREITRRFGDLLEAAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDRGV +PGQQGPDQMIDAVTGVVLGGLRG +>PROKKA_00793 +MPHSSTAPRRGRPGYDRQTLLTVCVDVFNRHGYEATSMGMLAQHLGISKSAIYHHVESKE +AILEQALDDALDALEASLDGVMADFAGPGEQVEAAVRGTLRVLVEKMPEVTLLLRLRGNS +AVELAAMERRRAITRRLGEMIAAAQEAGAVRGDITPRNLARLALGMINSIVDWYRPESDS +PGHKSVTEMVDAVTRVVLGGLRG +>PROKKA_00754 +MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLATHLGISKSAIYHHVESKE +AILDHAVTEALDALEACLDDVVASGADAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS +AVEVAAVERRREITRRLGDLLESAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDGAD +PGHKSVEEMVAAVTGVVMGGLRG +>PROKKA_01963 +MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLAAHLGISKSAIYHHVESKE +AILDHAVTEALDALEACLDDVVASGADAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS +AVEVAAVERRREITRRFGDLLEAAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDRGV +PGQQGPDQMIDAVTGVVLGGLRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001617.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001617.fa new file mode 100644 index 0000000000000000000000000000000000000000..1a36f191526a655613f993617f9aa670b8b971a6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001617.fa @@ -0,0 +1,45 @@ +>PROKKA_02027 +MLEASIPNPYTPAPLPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYREH +FDAHGVHPSDFTELGDLAKFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV +GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG +GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTEEMRR +EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRH +GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ +IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHATLEEAQACAAHLRMEIKTKIGS +SCVINVVEPETLARSSGKLKRIYDLRDQA +>PROKKA_01736 +MLEASIPNPYTPAPLPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYREH +FDAHGVHPSDFTELGDLAKFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV +GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG +GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTEEMRR +EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRH +GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ +IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHASLEEAQACAAHLRMEIKTKIGS +SCVINVVEPESLARSSGKLKRIYDLRDQA +>PROKKA_00792 +MLEASIPNPYTPAPLPAPADRGAQDPEETMSRDQIEALQFERLRWSLHHAYENVPAYTEH +FDAHGVHPSDFKALEDLAKFPYTDKEFLRKNYPFGAFAAQGPELRRIHASSGTTGQPTVV +GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG +GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTDEMRR +EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRH +GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ +IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHATLEEAQACAAHLRMEIKTKIGS +SCVINVVEPETLARSSGKLKRIYDLRDKG +>PROKKA_00753 +MLEASIPNPYSPAPVPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYKEH +FDNHGVHPSDFTALEDLELFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV +GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG +GQTEKQVQLITDFQPRAILSTPTYLLTIADGFRKLGLDPRESSLEVAILGAEPWTEAMRR +EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRP +GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ +IEELALKEPALSPHFTLEITRPDRMDQMAVNIERREHATLEEAQACAAHLRMEIKTKIGS +SCVINVVEPETLARSSGKLKRIYDLRDQA +>PROKKA_01964 +MLEASIPNPYTPAPLPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYREH +FDAHGVHPSDFTELGDLAKFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV +GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG +GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTEEMRR +EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRP +GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ +IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHATLEEAQACAAHLRMEIKTKIGS +SCVINVVEPESLARSSGKLKRIYDLRDQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001619.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001619.fa new file mode 100644 index 0000000000000000000000000000000000000000..5ad9859ef26acdaa659f1ee05e46b86ca7705851 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001619.fa @@ -0,0 +1,27 @@ +>PROKKA_02033 +MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA +DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP +TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW +EGRRWDSVQLAVLRRDWWPASTDG +>PROKKA_01740 +MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA +DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP +TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW +EGRRWDSVQLAVLRRDWWPASTDG +>PROKKA_00787 +MTELDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKWWDAPYFHAA +DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGSGWWELGILLFDP +TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW +EGRRWDSVRLALLRRDWDSARASV +>PROKKA_01226 +MDTHRSTPVVALRPVEAGDEEFLWTWIHGTPDAEWKRWDAPYFHAAEQAAPMGRAAFARS +FAPWPDDADRRIITADGAAIGLVTRHEEAPAGGGWWELGILLFDPSRWGGGIGTRALAAW +TEATLTETDAHVLTLTTWSGNARMAGAAERAGFRMCARVPESRAWDGRRWDSLRFALLRG +DHEGEQASAPEPPARRPELADLTVVTGRIPDAAALRALYDAVGWTAYTRNPDALAAGVAG +SACVATAWAGQELVGLARVVSDGHTIAYLQDVLVHPERRRQGVAGKLLDAVFAPFAHVRQ +QVLITDEEPGQRAFYEACGFRQFGGGGPVPGRTFVRFAG +>PROKKA_01968 +MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA +DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP +TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW +EGRRWDSVQLAVLRRDWWPASTDG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001620.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001620.fa new file mode 100644 index 0000000000000000000000000000000000000000..e3ec5f9306f08fcd77648d226ae8cb13cac7f9f4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001620.fa @@ -0,0 +1,49 @@ +>PROKKA_02034 +MGAMTSQPAPASTAHRRPLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEW +FIHLAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVAELAATEKVTVHDVKAVEYFIADR +LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET +PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDA +DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF +AQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR +NIGVALGHSVLALTNVTKGMGQLQVADPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGM +DNPYERLKELTRGHRVDGARMREFVQGLGLSEGAQARLLELTPAGYTGVASELAKEFGPA +QD +>PROKKA_01741 +MTSQPAPASTAHRRPLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEWFIH +LAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVAELAATEKVTVHDVKAVEYFIADRLEG +LGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAETPML +SRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDADWP +ALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYFAQI +PVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQRNIG +VALGHSVLALTNVTKGMGQLQVADPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGMDNP +YERLKELTRGHRVDGARMREFVQGLGLSEGAQARLLELTPAGYTGVASELAKEFGPAQD +>PROKKA_00783 +MTTQPAGPSPASTDHRRSLADSGAALGPLDGRYRAAVAPLVEHLSEAALNRNRIHVEVEW +FIHLAEHAVLPGLTPLTDEQKAGLRAIVTDFDADSVAELAATEKVTVHDVKAVEYFIADR +LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET +PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAAQEYLGKINGATGTYAAHLAAAPDA +DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF +TQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR +NIGVALGHSVLALTNVTKGMGQLQVAEPVLAEDLDTNWEVLGEAIQTVMRAEAIAGVPGM +DNPYERLKELTRGHRVDGERMREFVRGLGLSDGAQARLLELTPAGYTGVAADLAREFGPA +QG +>PROKKA_00749 +MGAMTSQPAPASTAHRRSLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEW +FIHLAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVSELAATEKVTVHDVKAVEYFIADR +LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET +PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDA +DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF +AQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR +NIGVALGHSVLALTNVTKGMGQLQVAEPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGM +DNPYERLKELTRGHRVDGARMREFVQGLGLSEGAQARLLELTPAGYTGVASELAKEFGPA +SAQG +>PROKKA_01969 +MGAMTSQPAPASTAHRRSLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEW +FIHLAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVAELAATEKVTVHDVKAVEYFIADR +LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET +PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDA +DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF +AQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR +NIGVALGHSVLALTNVTKGMGQLQVAAPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGM +DNPYERLKELTRGHRVDGARMREFVQGLGLSEAAQARLLELTPAGYTGVAAELAKEFGPA +QG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001621.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001621.fa new file mode 100644 index 0000000000000000000000000000000000000000..347fdf157b0c63140cca9deac49e263ea80782de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001621.fa @@ -0,0 +1,30 @@ +>PROKKA_02035 +MLLPLLPVWLLSAAPKDPAELERDVPEPIDAHGELADAVTAAITAVDLVGVFFFAISGAV +LAVRKGYDIVGSLLLALMVGTGGGVVRDLVVGRDVPAAFDNPWYLILPAVASLAVFLRIF +DGERGHHAVMAFDAIGLAVYCVVGTRIALLAGLSPVAAAVLGLVTAVGGGILRDVVAGEP +PAVFGGRGWYALPAILGAGTTAALGQAEVLNPLTSAAVMVLVLVLRVVSLRREWLAPGAE +ISGETQRQRMDPHDEPPVPDIRDRKGRDGPPAAPGEDGPPANEETPGADEDVTPRGTPG +>PROKKA_01742 +MLLPLLPVWLLSAAPKDPAELERDVPEPIDAHGELADAVTAAITAVDLVGVFFFAISGAV +LAVRKGYDIVGSLLLALMVGTGGGVVRDLVVGRDVPAAFDNPWYLILPAVASLAVFLRIF +DGERGHHAVMAFDAIGLAVYCVVGTRIALLAGLSPVAAAVLGLVTAVGGGILRDVVAGEP +PAVFGGRGWYALPAILGAGTTAALGQAEVLNPLTSAAVMVLVLVLRVVSLRREWLAPGAE +ISGETQRQRMDPHDEPPVPDIRDRKGRDGPPAAPGEDGPPANEETPGADEDVTPRGTPG +>PROKKA_00781 +MLLPSLPVWLLSATPKDPAELERDVPEPIDAHGELADAITAAITAVDLVGVFFFAISGAV +LAVRKGYDIVGSLLLALMVGTGGGVVRDLVVGRDVPAAFDNPWYLILPAVASLAVFLRIF +DGERGHHAVMAFDAIGLAVYCVVGTRIALLAGLSPVAAAVLGLVTAVGGGILRDVVAGEP +PAVFGGRGWYALPAILGAGTTAALGQAELLGPLTSAAVMVLVLVLRVVSMRREWLAPGAE +ISGETQRQRMDPHDEPPVPDIRDRKGRDGPPADPGEDGPPANEETPGAGEGVPPGTPG +>PROKKA_00748 +MLLPLLPVWLLSAAPKDPAELERDVPEPIDAHGELADAITAAITAVDLVGVFFFAISGAV +LAVRKGYDIVGSLLLALMVGTGGGVVRDLVVGRDVPAAFDNPWYLILPAVASLAVFLRIF +DGERGHHAVMAFDAVGLAVYCVVGTRIALLAGLSPVAAAVLGLVTAVGGGILRDVVAGEP +PAVFGGRGWYALPAILGAGTTAALGQAELLGPLTSAAVMVLVLVLRVVSLRREWLAPGAE +ISGETQRQRLDPHDEPPVPDIRDRKGKDGPPADPGEDGPPATEETPGADEGVPPGTPG +>PROKKA_01970 +MLLPSLTVWLLSATPKDPAELERDVPEPIDAHGELAEAITAAITAVDLVGVFFFAISGAV +LAVRKGYDIVGSLLLALMVGTGGGVVRDLVVGRDVPAAFDNPWYLILPAVASLAVFLRIF +DGERGHHAVMAFDAVGLAVYCVVGTRIALLAGLSPVAAAVLGLVTAVGGGILRDVVAGEP +PAVFGGRGWYALPAILGAGTTAALGQAEVLNPLTSAAVMVLVLVLRVVSLRREWLAPGAE +ISGETQRQRMDPHDEPPVPDIRDRKGRDGPPAAPGEDGPPANEETPGADEDVTPRGTPG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001623.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001623.fa new file mode 100644 index 0000000000000000000000000000000000000000..39af5ef694f1344e94dfd7ac207d1095719c1c33 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001623.fa @@ -0,0 +1,50 @@ +>PROKKA_02040 +MTGTHETARPASTTTEAAASGPLHRVGFDRAKYIELQSQHIQERRRQIGGKLYLEMGGKL +FDDLHASRVLPGFTPDNKIAMLDRIKDETEILVCFNAKDLERNKVRADLGITYEDDVLRL +VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHAMSTIVSEQ +GFGANEWSETTRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLE +HPVNAAYEAATVDLDDINLIDPFHLAEYGERVTSYNRDVEVFPLLSALLEKVTGTTPYKS +PTDMGVNMAGAAIVDDEVCQEAAKQEIIRRYYKAQVNEALEGADDTESERVALVMSKLGL +SSEDRPVVGAAQLVAERTGEPGAAVQLADGTLVTGKTSELLGCSAAVLLNALKVLAGIED +DVHLLSPASIEPIQTLKTVHLGSKNPRLHTDEVLIALSVSAATDANARAAVEQLASLEGC +DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR +>PROKKA_01744 +MTGTHETARPASTTTEAAASGPLHRVGFDRAKYIELQSQHIQERRRQIGGKLYLEMGGKL +FDDLHASRVLPGFTPDNKIAMLDRIKDETEILVCFNAKDLGRNKVRADLGITYEDDVLRL +VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHAMSTIVSEQ +GFGANEWSETTRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLE +HPVNAAYEAATVDLDDINLIDPFHLAEYGERVTSYNRDVEVFPLLSALLEKVTGTTPYKS +PTDMGVNMAGAAIVDDEVCQEAAKQEIIRRYYKAQVNEALEGADDTESERVALVMSKLGL +SSEDRPVVGAAQLVAERTGEPGAAVQLADGTLVTGKTSELLGCSAAVLLNALKVLAGIED +DVHLLSPASIEPIQTLKTVHLGSKNPRLHTDEVLIALSVSAATDENAKAAVEQLASLEGC +DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR +>PROKKA_00778 +MTGTHETALPASTTDGRAASAPLRRIGFDRAKYIDLQSQHIQERRREIGGKLYLEMGGKL +FDDLHASRVLPGFTPDNKIAMLERIKDETEILVCFNAKDLERNKVRADLGITYEDDVLRL +VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHATARIVSEE +GFGRNEWSQTTRDLVVVTAPGPGSGKLATCLSQVYHDHQRDIPSSYAKFETFPIWDLPLE +HPVNVAYEAATADLDDINLIDPFHLAAHGEQVTSYNRDVEVFPLLAALLEKLTGTSPYRS +PTEMGVNMAGAAIVDDEACREAARQEIIRRWYKAAVEEAANGESDEVSERIALIMSRLGL +TSEDRPVVGASLLVAERTGEPGAAVQLADGTLVTGKTSALLGCSAAMLLNALKVLAGLSD +EVHLLTPESIEPIQTLKTVHLGSTNPRLHTDEVLIALSVSAATDPNAKAAVEQLASLAGC +DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR +>PROKKA_00746 +MTGTADMAPQKISRPLGFDREQYIALQSQHIQERRRQLGGKLYLEMGGKLFDDLHASRVL +PGFTPDNKIAMLDRIKDETEILVCFNAKDLERNKVRADLGITYEEDVLRLVDVFRERGFL +VEHVVVTQLEDSNHLALAFIEKLGRLGLKVARHRVIPGYPHAMATIVSEQGFGANEWSET +TRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLEHPVNAAYEAA +TVDLDDINLIDPFHLAEYGEKVTSYNRDVEVFPLLSALLEKVTGTTPYKSPTDMGVNMAG +AAIVDDAVCRAAAEQEIIRRYYKAQVNEALEGADDTESERAALVMSKLGLSSEDRPVVGA +AQLVAERTGEPGAALELADGTIVTGKTSELLGCSAAMVLNALKVLAGIDDDAHLLSPASI +EPIQTLKTQHLGSKNPRLHTDEVLIALSVSAATDENAKAAVEQLASLEGCDVHTTTILGS +VDEGIFRSLGMLVTSEPVFQKKGLYRKR +>PROKKA_01972 +MTGTHETARPASTTTEAAASGPLHRVGFDRAKYIELQSQHIQERRRQIGGKLYLEMGGKL +FDDLHASRVLPGFTPDNKIAMLDRIKDETEILVCFNAKDLGRNKVRADLGITYEDDVLRL +VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHAMSTIVSEQ +GFGANEWSETTRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLE +HPVNAAYEAATVDLDDINLIDPFHLAEYGERVTSYNRDVEVFPLLSALLEKVTGTTPYKS +PTDMGVNMAGAAIVDDEVCQEAAKQEIIRRYYKAQVNEALEGADDTESERVALVMSKLGL +SSEDRPVVGAAQLVAERTGEPGAAVQLADGTLVTGKTSELLGCSAAVLLNALKVLAGIED +DVHLLSPASIEPIQTLKTVHLGSKNPRLHTDEVLIALSVSAATDENAKAAVEQLASLEGC +DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001625.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001625.fa new file mode 100644 index 0000000000000000000000000000000000000000..ab71ca7ca94cd7327bfae20bfae63b5e15dddea8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001625.fa @@ -0,0 +1,25 @@ +>PROKKA_02052 +MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALHRRLPGHPSAMTL +GGLLKHLAFVEFWWFEAVALGEPTSAPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV +ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE +GIDGQTGE +>PROKKA_01758 +MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALHRRLPGHPSAMTL +GGLLKHLAFVEFWWFEAVALGEPTSTPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV +ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE +GIDGQAGE +>PROKKA_00770 +MTTVFYDDQGRPEPPETAGEAETLLGFLEFLRATFAWRTGGLDEAALRRRLDGHPSEMTL +GGMLKHLAFVEFWWFEAVALGAPTSEPWVSVDWAADEDWDWHSAAEDSAADLRALWEGQV +ERSRQAVQELLAADGDPLGRVLESYDGRRRVTLRWILTHMIEEYARHNGHADLLREQIDG +QTGE +>PROKKA_00740 +MTTVFYDEQGRPEPPHAADEAATLLAFLDFQRATFAWRTSGLDDAALRRRLDGHPSEMTL +GGMLKHLAFVEFFWFEVTAHGKPTSEPWVSVDWDADADWDWHSAAEDAAEELRDLWRESV +ERSRAVVVRLLADGPAALDTTHPAWGGRADVSLRWILTHMIEEYARHNGHADLLREQIDG +QTGE +>PROKKA_01986 +MTTVFYDDQGRPEPPFAAGEAATLLGFLDFLRATIEWKTADLDTAALRRRLPGHPSAMTL +GGLLKHLAFVEFWWFEAVALGEPTSAPWVGADFDADPDWDWHSAAQDSAADLRALWQGQV +ERSRQIVVDLLAADGDDGAAALARAHRIREGRDPVSLRWILTHMIEEYGRHAGHADLLRE +GIDGQTGE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001626.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001626.fa new file mode 100644 index 0000000000000000000000000000000000000000..7bdcbdb79755e0ef53dca334da7aca5ab9a3ca4c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001626.fa @@ -0,0 +1,79 @@ +>PROKKA_02053 +MASPSPASAHPSAPESGTGLGFTGVEGITGLTASEVAEREAAGLVNVQSRDTSRSLGQIL +RVHVFTLFNLAIALCAVVVILMGRWLDLLFSLAAVANVVIGVVQEYSAKRKLDRIALLHQ +DDVLVIRDGARVPLPMAQIVRDDVVVLRRGDQVPVDGEVLVSDGLDMDEALLTGENDPVP +KTPGDAVLSGSAVVAGAGLVRATAVGSASHAARLSAEARRYSAIHSELRGALEKVARWLT +IALVPIIAVIVHGQMTAVGGWSLALSQPREAALEPALIASVAAVTSMIPQGLALMTTIAF +AVSALKLAQQEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFDRLAAPASADASPDAH +DDGAPAEVGDGARAVLAWFGADPDVNPTAAALREPFTAVPAVDPAAQVAFSSARRWSAVA +FGPEAGAAAGTWLLGAPEALVDERLLGPDAAEAVRAQVHADADAGRRVLLLARTDEPLIG +DALPAGGVPVAVVTFRENVRPDAAETLGYFHAQGVRAVVISGDSPRTVAAVAREVGLEVA +GQAYDGRTLPDDPDALADVMEEHSVFGRVSPDQKKAMVQALQSRGHVVAMTGDGVNDALA +LKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPRVLGEGRQVIANMERLAHIYLTKTTY +ALLFGVVFSLFAWQFPLLPRQASTVDFIMIGAPTFFLALLPNPRRYVPGFLGRALRFAIP +SGAVILLSMVALQTYVRLTAGDVDLARQQAAFMITLTLVGLWVLSVMSRPLSARVVVLIL +AMYAVLAAVVLVPVSRWYHQMEVPPTDVLVAALVIAAVGCGLIELIHQVHRRHVARMLAA +AGA +>PROKKA_01759 +MASPSPASAHPSAPESGTGLGFTGAAGITGLTAAEVAEREAAGLVNVQSRDTSRSLGQIL +RVHVFTLFNLAIALCAVVVILMGRWLDLLFSLAAVANVVIGVVQEYSAKRKLDRIALLHQ +DDVVVIRDGARVPLPMARIVRDDVVVLRRGDQVPVDGEVLVSDGLDMDEALLTGENDPVP +KTPGDAVLSGSAVVAGAGLVRATAVGSASHAARLSAEARRYSAIHSELRGALEKVARWLT +IALVPIIAVIVHGQMTAVGGWSLALSQPREAALEPALIASVAAVTSMIPQGLALMTTIAF +AVSALKLAQQEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFDRLTAPASADASPDAH +DDGAPAEVGDGARAVLAWFGADPDVNPTAAALREPFTAVPAVDPAAQVAFSSARRWSAVA +FGPEAGAAAGTWLLGAPEALVDERLLGPDAAEAVRAQVHADADAGRRVLLLARTDAPLIG +DALPAGGVPVAVVTFRENVRPDAAETLDYFHAQGVRTVVISGDSPRTVAAVAREVGLEVA +GQAYDGRTLPDEPGELAAVMAEHDVFGRVSPDQKKAMVQALQSRGHVVAMTGDGVNDALA +LKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPRVLGEGRQVIANMERLAHIYLTKTTY +ALLFGVVFSLFAWQFPLLPRQASTVDFIMIGAPTFFLALLPNPRRYVPGFLGRALRFAIP +SGAVILLSMVALHAYVRLTAGDVDLARQQAAFMITLTLLGLWVLSVMSRPLSARVVVLIL +AMYAVLAAVVLVPASRWYHRMEVPPTDVLVAALVVAALGCGLIEVIHQVHRRHVARVLAA +AGA +>PROKKA_00769 +MTPPAPAPPPAAAPGALSGVSGLTSAEVAEREAAGLTNRQSKDTSRSLAEILRVHVLTLF +NLAIALCAVVVISLGRWLDLLFSLAAIANVVIGVVQEYSAKRKLDRIALLHQDDAVVVRD +GARVSLPMARIVRDDVVVLRRGDQVPVDGEVLASDGLDLDEALLTGENDPVPKAPGDAVL +SGSSVVAGTGLMRATAVGPASHAARLSAEARRFSAIRSELRGALEKVARWLTIGLVPIIA +VIVHGQMTAVGGWAHALAQPREAALEPALIASVAAVTSMIPQGLALMTTIAFAVSALKLA +QHEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFHELLAPASASPSTSTSTDDDGAPA +DVDAAARAVLAWFGADPDANPTAAALHEPFADAPPHEPADHVAFSSARRWSAVAFGPEVG +AATGTWLLGAPEALLGDADARPGEAGTGRDDVAAVRAQADALSDEGLRVLLLARTDAPLA +GNALPAGRVPAAVVTFRENVRPDAAETLGYFHAQGVRTVVISGDSPRTVAAVAREVGMDV +PGHARDGRTLPEDPEALADVMAEHDVFGRVSPDQKKAMVAALQSRGHVVAMTGDGVNDAL +ALKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPAVLGEGRQVIANMERLAHIYLTKTT +YALLFGVVFSLLAWQFPLLPRQASTVDFIMIGLPTFFLALLPNPRRYVPGFLGRALRFAI +PSGVVILLSMVALQVYVRLAADHVDLAQQQTAFMITLTLVGLWVLSVMSRPLTRRVVLLV +LAMYAVLAAVVLVPASRWYHQMEVPPADVLVAALVIAAVGCALIELIHQVHRRHVARVLA +AAGA +>PROKKA_00126 +MTHTPPSPAPAADAGPAALAGLTSAQVAERVAAGRVNVQPKDTSRSFGTILRSHVLTLFN +LVIALCATVIVVLGRWFDLLFSLAAVANVVIGVVQENSARRALDRIALLHQDGVLVVRDG +ARREVRIEEVVLDDVVVLRRGDQVPVDGAVLTSEGLDVDESLLTGESDPVPKAPGDAVLS +GSAVVAGTALVRATAVGADSHAAKLAVQARRFTRAHSELRAALEKVARWLTIALVPIVAV +ILHGQVTAAGGWSRVLGSEDQPALEAALVATVAAVTAMIPQGLALMTTISFALAALKLAR +RAVLIQEQPAVEILARVDTVCLDKTGTLTEGGIVFHGAHAPVGAPALPHDDDAAVALDPG +ARAVLAWFGADPDANPTAAALREPFPAAPASSPTGVVPFSSVRRWSAVTFGPDADAAHPG +MAGTWLLGAPEALADAAHLGPERTAALTEACTAPADRGLRTVLLCRASDAPAGETLPAGR +EPVAVLTFAEDVRPDAAQTLGYFREQGVAVKVISGDSPRTVAAVARAVGMEVPGDAVDGR +TLPADPAELADVLESHEVFGRVAPEQKQAMVAALQSRGHVVAMTGDGVNDALALKTADLG +IAMGNAAPATKAVSRMVLLDGRFDRLPDVLREGRQVIANMERLAHIYLTKTSYALLFGLV +FSLLAWPFPLLPRQASTADFLMIGAPTFFLALLPNPRRYVPGFLRRALLFAVPAGVTIVA +AMLAVSWYARHLSSKPVDTAQLQTASLITLTLLGLWVLTCISRPLRPLMCGVVAGMYALL +AAAVLVPASRWYHQMELPAPDLLAASLAIALGGCVVVEAVHRIHHARVTVPGRRAAEG +>PROKKA_01987 +MASPSPASAHPSAPESGTGLGFTGVAGITGLTAAEVAEREAAGLVNVQSRDTSRSLGQIL +RVHVFTLFNLAIALCAVVVILMGRWLDLLFSLAAVANVVIGVVQEYSAKRKLDRIALLHQ +DDVVVIRDGARVPLPMAQIVRDDVVVLRRGDQVPVDGEVLVSDGLDMDEALLTGENDPVP +KTPGDAVLSGSAVVAGAGLVRATAVGSASHAARLSAEARRYSAIHSELRGALEKVARWLT +IALVPIIAVIVHGQMTAVGGWSLALSQPREAALEPALIASVAAVTSMIPQGLALMTTIAF +AVAALKLAQQEVLIQEQPAVEVLARVDTVCLDKTGTLTEGGVRFDRLTAPASADASPDAH +DDGAPAEVGDGPRAVLAWFGADPDVNPTAAALREPFTAVPAVDPVAQVAFSSARRWSAVA +FGPEAGAAAGTWLLGAPEALVDEWHLGPDAAEAVRAQVHADADAGRRVLLLARTDEPLIG +EALPAGGVPVAVVTFRENVRPDAAETLDYFHAQGVRTVVISGDSPRTVAAVAREVGLEVA +GQAYDGRTLPEDPGALADVMAEHDVFGRVSPDQKKAMVQALQSRGHVVAMTGDGVNDALA +LKTADLGIAMGNAAPATKAVSRMVLLDGRFDRLPRVLGEGRQVIANMERLAHIYLTKTTY +ALLFGVVFSLFAWQFPLLPRQASTVDFIMIGAPTFFLALLPNPRRYVPGFLGRALRFAIP +SGAVILLSMVTLQTYVRLTAGDVDLPRQQAAFMITLTLLGLWVLSVMSRPLSARVVVLIL +AMYAVLAAVVLVPASRWYHQMEVPPTDVLVAALVIAALGCGLIEIIHQVHRRHVARVLAA +AGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001627.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001627.fa new file mode 100644 index 0000000000000000000000000000000000000000..1ac3a756fef17ca48b37b207cdef3290d18f9784 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001627.fa @@ -0,0 +1,21 @@ +>PROKKA_02055 +MDSTLFTRSADRAAHNDVNFRTRKWVKPEDLNANNTLFGGSLLRWVDEEAAIYATLQLGN +PRCVTKLISEINFLASAKQGDMIEMGLRATEFGRTSLTMRAKVRNIVTGEMILTIDKIVF +VSLGEDGKPVPHGFTEITYDRDRLPLDNPL +>PROKKA_01761 +MDSTLFTRSADRAAHDDVNFRTRKWVKPEDLNANNTLFGGSLLRWVDEEAAIYATLQLGN +PRCVTKLISEINFLASAKQGDMIEMGLRATEFGRTSLTMRAKVRNIVTGEMILTIDKIVF +VSLGEDGKPVPHGFTEITYDRDRLPLDNPL +>PROKKA_00711 +MDTSTAPGADHGRAADDISYRTRKWVKPEDLNANGTLFGGSLLRWIDEEAAIYAIIQLGN +PRSVTKLISEINFRSSARQGDMIEMGLRAVEFGRTSLTMRAKVRNIISGEVILTIEKIVF +VSLDEDGNPVPHGYTDITFDRDRLPQDTAR +>PROKKA_00726 +MATHHAPNLTAHEDDDVSYRTRKWVKPEDLNANGTLFGGSLLRWIDEEAAIYSIIQLGNP +RSVTKLISEIEFSASARQGDMIEMGLRAVKFGRTSLTMRAKVRNIVTGEVILTIDKIVFV +SLDEEGRPQPHGYTDITYDRDRLPLDTSR +>PROKKA_01989 +MPAATVKPSTGTSRQVASGVAGSGWGRMVIGRVPPVWSVADPSGDPTARSSTSPHRAPSL +VPASASLYRGAMDSTLFTRSADRAAHDDVNFRTRKWVKPEDLNANNTLFGGSLLRWVDEE +AAIYATLQLGNPRCVTKLISEINFLASAKQGDMIEMGLRATEFGRTSLTMRAKVRNIVTG +EMILTIDKIVFVSLGEDGKPVPHGFTEITYDRDRLPLDNPL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001635.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001635.fa new file mode 100644 index 0000000000000000000000000000000000000000..b5597ca2560e323f2243aa87ec7c311e7eb91940 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001635.fa @@ -0,0 +1,20 @@ +>PROKKA_02083 +MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS +TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG +WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG +>PROKKA_01788 +MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS +TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG +WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG +>PROKKA_00700 +MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQQSSPELWGRLIAAVFALDGVEEGHS +TVSPATSRAVHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG +WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG +>PROKKA_00610 +MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS +TVSPATSRAVHLTGRPKERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLPPERGVRLAELG +WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG +>PROKKA_02022 +MDPDASPRVRLTADDPRPGSRPVTSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS +TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG +WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001636.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001636.fa new file mode 100644 index 0000000000000000000000000000000000000000..86998b768f7668b44e54bd82d89b6ce0985803cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001636.fa @@ -0,0 +1,35 @@ +>PROKKA_02084 +MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGKLDALALAVADQERAGIDIVC +DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR +ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP +AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP +LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF +VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE +>PROKKA_01789 +MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGKLDALALAVADQERAGIDIVC +DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR +ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP +AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP +LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF +VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE +>PROKKA_00699 +MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGEQLREGQLDALALAVADQERAGIDIVC +DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPASVFVDDAKALR +ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP +AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGQEWRQYETSFP +LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDVVETPEEVAATLRETLEF +VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE +>PROKKA_00609 +MTTLIPTTLVGSLPKPGWLAEEETLWSPWKLEGERLREGKLDALALAVADQERAGIDIVC +DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR +ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAVGVDVVQFDEP +AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGVKANNDWKATLGEEWRQYETSFP +LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF +VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE +>PROKKA_02023 +MTTLIPTALVGSLPKPGWLAEEETLWSPWKLEGERLHEGKLDALALAVADQERAGIDIVC +DGEQTRQHFVTTFIEHLGGVDFDRRETVRIRDRYDASVPTVVGEVGRPAPVFVDDAKALR +ARTDRPIKWTLPGPMTMIDTLADRHYGSREKLAWEFARILNEEARELAAAGVDVVQFDEP +AFNVFFDDVRDWGVATLERAAEGLTCETAVHICYGYGIKANNDWKATLGEEWRQYETSFP +LLRESTIDTIALERHHSRVPAELIGLLRGKKVMVGAIDVASDEIETPEEVAATLRETLEF +VDADKLIASTNCGMAPLARSVARDKTAALVAGARILREELGGE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001637.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001637.fa new file mode 100644 index 0000000000000000000000000000000000000000..be71b76834baef02041ac061428b07e3d2dad5e0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001637.fa @@ -0,0 +1,35 @@ +>PROKKA_02085 +MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGTDRRENLRAAL +AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG +AVLGRSVGNNFSSYVRDHDFSVVLPAHAVTSPGTEEPDGFGDLHGRLFRHLLDSQAYRER +FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA +PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT +RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDNEETR +>PROKKA_01790 +MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGTDRRENLRAAL +AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG +AVLGRSVGNNFSSYVRDHDFSVVLPAHAVTSPGTEEPDGFGDLHGRLFRHLLDSQAYRER +FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA +PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT +RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDNEETR +>PROKKA_00698 +MSHATLAPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL +AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG +AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDKHGRLFRHLLDSQAYRER +FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEASRTDRYFGRMGLGIRCFLPRGAVA +PLAFYSRGDLLNDHANLSLAGLVATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT +RIAYDREERARLGREQGEYTQAHFVGPHRDLLERWAAAHAARDTEETR +>PROKKA_00608 +MSHATLVPSTVPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL +AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERETG +AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDLHGRLFRHLLDSQAYRER +FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA +PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT +RIAYDREERARLGREQGEYTQEHFVGPHRDLLERWAAAHAARDTEETR +>PROKKA_02024 +MSHATLVPSTAPTRVDDLTFSIHTTPFDEDYTPAASTRATTNFANLARGADRRENLRAAL +AMIDGRLNDLAPWDNPERDRYTARIEIVSIDVHFTADDGADVDFPLMEMLDVRVVERATG +AVLGRSVGNNFSSYVRDHDFSVVLPAHAATSPGTEEPDGFGDLHGRLFRHLLDSQAYRER +FPQPPVICISVSTSRTYRRLTNEHPVLGVEYRQDEPSRTDRYFGRMGLGIRCFLPRGAVA +PLAFYSRGDLLNDHANLSLAGLIATMETFQRIYRPEIYNANAGAGEVYRPRLDHGDFSQT +RIAYDREERARLGREQGEYTQAHFVGPHRDLLERWAAAHAARDTEETR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001639.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001639.fa new file mode 100644 index 0000000000000000000000000000000000000000..1f3a063b72d10db531593c8dbc018d5176c1d64e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001639.fa @@ -0,0 +1,45 @@ +>PROKKA_02087 +MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT +VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA +DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD +STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK +ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAAASAAQFIQGLETLDLRVARHTATAL +AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE +LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLIADLDRA +LAVVTAAGPAVPATTPAVPETAAVTQEVR +>PROKKA_01792 +MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT +VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA +DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD +STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK +ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAAASAAQFIQGLETLDLRVARHTATAL +AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE +LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLIADLDRA +LAVVTAAGPAVPATTPAVPETAAVTQEVR +>PROKKA_00696 +MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT +VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA +DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD +STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK +ARYGGQTLVERHGRGAYLTLTRSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL +AVAEHLAGHPAVARVHHPGVAGHPSARLAARDFPDGVGSVFSFDLACGPEAVAPFLDALE +LFQLVVNVGDARSLVSHPATMTHCRLTRQQREDAGIAETTVRLSIGLECPDDLITDLDRA +LAVVSAAGPAVLATTPAVPETTAVTQEVR +>PROKKA_00606 +MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT +VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA +DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALAGLAHAAGVPVVVD +STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK +ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL +AVAEHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPETVAPFLDALE +LFQLVVNVGDARSLVSHPATMTHCRLTRQQREAAGIAETTVRLSIGLECPDDLIADLDRA +LAVVSAAGPAVPAATPAVPETAAVTQEVR +>PROKKA_02026 +MPRHATQQVHAGYEPAAPHRPVVPPIHQTTAFRFPDHATAASMFRLETPGFTYSRTGNPT +VAVFENRLAALEGGIGAIATATGQAAVALSLLALLQGGKHLVASSQLYGGTVDLLTDTFA +DFGIEVTFADPADPPAWAAAVRPDTRAFFLEAITNPLATLPDLPALADLAHAAGVPVVVD +STLATPALYRPLEHGADVVVHSATKFLGGHGAVLGGAIVDGGTFDYGAAPDRWPQLARPK +ARYGGQTLVERHGRGAYLTLARSKFLHDLGPTLAPASAAQFIQGLETLDLRVARHTATAL +AVAQHLAGHPAVARVHHPGVAGHPSAALAARDFPDGVGSVFSFDLACGPEAVAPFLDALE +LFQLVVNVGDARSLVSHPATMTHCRLTREQREAAGIAETTVRLSIGLECPDDLIADLDRA +LAVVTAAGPAVPAATPAVPETAAVTQEVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001644.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001644.fa new file mode 100644 index 0000000000000000000000000000000000000000..a6c23962f6ccc3fed67b8dc96a59acd21044af88 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001644.fa @@ -0,0 +1,16 @@ +>PROKKA_02102 +MTFLDLVLVFVGFALAVLVGAALVGRVRGEHLRAVAATLVALWALTAVFDNVMIAAGLFD +YGHELLVGAYVGQAPVEDFAYPLGSALLLPALWLLLTSRGRAGRRGRRPGRRPHPGDR +>PROKKA_01809 +MTFLDLVLVFVGFALAVLVGAALVGRVRGEHLRAVAATLVALWALTAVFDNVMIAAGLFD +YGHELLVGAYVGQAPVEDFAYPLGSALLLPALWLLLTSRGRAGRRGRRPGRRPHPGDR +>PROKKA_00677 +MTFLDLILVFVGLAAAVLAAVALTGRVRARHAAAIAVAIAALAVLTAVFDNVMIAAGLFD +YGHDLLSGIYVGLAPIEDFAYPVGSALLLPAVWLLMTGRRRRGGERSPDGGAEPTGDGSS +TADAGR +>PROKKA_00592 +MTYLTISLPFLAVAAAVLLASALTGRLDRRRRLGLVLAVALLVVLTAVFDSVIIGLGIVD +YTQANINGARIGLAPVEDFLYPLAGVALLGGLWTLVRGGTR +>PROKKA_02042 +MTFLDLVLVFVGFALAVLVGAALVGRVRGEHLRAVTATLVALWALTAVFDNVMIAAGLFD +YGHELLVGAYVGQAPVEDFAYPLGSALLLPALWLLLTSRGRAGRRGRRPGRRPHPGDR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001645.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001645.fa new file mode 100644 index 0000000000000000000000000000000000000000..413a0610d5b7120b23f02ba7398f869defb11ca6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001645.fa @@ -0,0 +1,15 @@ +>PROKKA_02103 +MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ +SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRRGDARAATPADPTDGGSR +>PROKKA_01810 +MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ +SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRRGDARAATPADPTDGGSR +>PROKKA_00676 +MVYLLTLLAVIGCMALLDWRHRLFLWARPGAATAVLAVGMAYFLAWDVWGIAEGVFLHRD +SPYMTGIMLAPQLPLEEGFFLLFLSQITMVLFTGAVRILEHRAGGTTAAGGTR +>PROKKA_00591 +MYLAALLLLCGCYLAIDARWRLALFSATPGRALAVLAAGLAFFLAWDLTGIAADVFWHGA +DDVSVGLFLAPELPVEELVFLWFLCHQTLVYVEGLPRLTAWARARRAGRGEGATAS +>PROKKA_02043 +MIYLLALLGVIGCMLLVDRRFELFLWHRPLPALLVLAAGVAYFFAWDLWGIAEGVFLHRQ +SPYMTGVMLAPQLPLEEGFFLLFLSQITMVLFTGALRLLRGRGRDARAATPADPTDGGSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001646.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001646.fa new file mode 100644 index 0000000000000000000000000000000000000000..d18a84a127930a9ff076cbeafe5cf35890a089ea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001646.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001647.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001647.fa new file mode 100644 index 0000000000000000000000000000000000000000..3c1b489bfdfc4745aac9846ffb316f963d899369 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001647.fa @@ -0,0 +1,55 @@ +>PROKKA_02105 +MSARDTALGPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDT +GPSWYLMPEVIDRWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHEPPVDVRTGHAETLFE +SLEPGAGRRLRAYLDSASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLR +SHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHLMSHLDLADGVQYPLGGFAALVDAM +AEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPGRVTG +VAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVR +GSLPQLAHHTLLFTADWEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILV +PAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVADRALDQLARWAGIPDLAERIVVRRT +YGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVPMCLI +SAEVVRDELRHDARRVRPAGPGGSGT +>PROKKA_01812 +MSARDTALGPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDT +GPSWYLMPEVIDRWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHEPPVDVRTGHAETLFE +SLEPGAGRRLRAYLDSASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLR +SHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHLMSHLDLADGVQYPLGGFAALVDAM +AEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPGRVTG +VAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVR +GSLPQLAHHTLLFTADWEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILV +PAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVADRALDQLARWAGIPDLAERIVVRRT +YGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVPMCLI +SAEVVRDELRHDARRVRPAGPGGSGT +>PROKKA_00674 +MSAAPNVASGAAAHDDGPRAVVIGGGFAGLATAGLLARDGHRVTLLERNDGLGGRSGRWS +AEGFAFDTGPSWYLMPEVIDRWFRLMGASAAERLDLRRLDPGYRVYFEDHLDAPPVDVRT +GHAEELVESLEPGAGERLRAYLDSAGRVYELAKEHFLYTDFRRPADLARPAVLRALPSLG +PQLLGGLRAHVAARFRDPRIRQILGYPAVFLGTSPDRAPAMYHLMSHLDLRDGVQYPIGG +FAALVDAMADLVREAGVEVVTGAEATRIEVEDAERRRRRRGRVTGVVVRQDGTERRLSAD +VVVAAADLHHVQTALLPPAQRVAESAWDRRDPGPSGVLVCVGVRGALPQLAHHTLLFTAD +WEDNFGRIERGEDLAADTSLYVSRTSATDPGVAPDGDESLFVLVPAPAEPGWGRGGIRVR +EGDGWRVEREGDAQVEAVADRALDQLARWAGIEDLHERIVVRRTIGPGDFAADVHAWRGS +MLGPGHTLAQSAMFRPSVRDADVAGLLYAGSSVRPGIGVPMCLISAEVVREELRHAARRD +ALRAQRRGRSQDDDDGARRGRVAAS +>PROKKA_00590 +MTPTTPAARPAAAPSGSRRVVVIGGGFAGLATAGLLAQDGHRVTLLEKNPVLGGRSGRWS +AEGFTFDTGPSWYLMPEVIDRWFRLMGTSADEALDLRALSPAYRVYFQEHAADDAAAPGD +GSTPGARAPLDVVSGREESLALAEELEPGAGGRLAAYLDSAERIYALAKRRFLYTDFQDL +TELLRPDVLRALPALAPQLLGDLRGFVARRFEDGRLRRVLGYPAVFLGTSPGKAPAMYHL +MSHLDLADGVQYPIGGFAALVDAMAELVRAAGVEIVTAAEVTAVDVVSDPRPRGRLPRLL +DGAPRPWEPRTPAGGRRRSGHVRGVSWRDAEGGSHRLDADAVVAAADLHHVQTALLPGDQ +RVAERTWDRRDPGPSAVLVCVGVRGRLPELLHHTLLFTEDWDENFRRIDEGEDLQEETSL +YVSMTSATDPGVAPEGDESLFLLVPAPAVPEWGRGGVRTPEEDRAGDAQVETVADRALAQ +LARWAGVPDLGERIVVRRTWGPADFTADVHAWRGSLLGPGHVLRQSALFRPPVRDPRVAG +LVYAGSSVRPGIGVPMCLISAELARDAVSGVRPGGAAPGAPAMAGR +>PROKKA_02045 +MSARDTALGPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDT +GPSWYLMPEVIDRWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHEPPVDVRTGHAETLFE +SLEPGAGRRLRAYLDSASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLR +SHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHLMSHLDLADGVQYPLGGFAALVDAM +AEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPGRVTG +VAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVR +GSLPQLAHHTLLFTADWEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILV +PAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVADRALDQLARWAGIPDLAERIVVRRT +YGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVPMCLI +SAEVVRDELRHDARRARPAGPGGSGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001648.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001648.fa new file mode 100644 index 0000000000000000000000000000000000000000..c7b463f67170dfef0ae720dd4b82504f65b6b4fa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001648.fa @@ -0,0 +1,32 @@ +>PROKKA_02106 +MAAPTPSPAALYTRTAHTAAAQVIRRYSTSFSWACRTLPRQARQDVATIYAMVRVADEVV +DGVAVAAGLDEAGVRAALDDYERACEAAMASGFATDPVLHAFADVARRHGITPELTRPFF +ASMRADLGIREHGAESLDAYIHGSAEVVGLMCLQVFLSLPGTRARTPGQRQELRAQASRL +GAAFQKVNFLRDLAADHHELGRTYLPGAAPGVLTEARKAELVAEVRADLDAALPGIRVLD +PGAGRAVALAHGLFAALVDRIEATPAAELAHRRVRVPDHQKARIAARVLARGRRGGRR +>PROKKA_01813 +MAAPTPSPAALYTRTAHAAAAQVIRRYSTSFSWACRTLPRQARQDVATIYAMVRVADEVV +DGVAVAAGLDEAGVRAALDDYERACEAAMASGFATDPVLHAFADVARRHGITPELTRPFF +ASMRADLGIREHGAESLDAYIHGSAEVVGLMCLQVFLSLPGTRARTPGQRQELRAQASRL +GAAFQKVNFLRDLAADHHELGRTYLPGAAPGVLTEARKAELVAEVRADLDAALPGIRVLD +PGAGRAVALAHGLFAALVDRIEATPAAELAHRRVRVPDHQKARIAARVLARGRRGGRR +>PROKKA_00673 +MPADAPLYTRTARAAAGRVIRRYSTSFSWACRTLPREARRDVEAIYAMVRVADEAVDGVA +QAAGLDSQRVRAALDDYERACEAAMASGFSTDLVLHAFGDVARRHGITPELTRPFFASMR +ADLGVSEHGAESLAAYIHGSAEVVGLMCLQVFLSLPGTRARTPAEREAIRAQAARLGAAF +QKVNFLRDLAADHDGLGRTYLTGAAPDELTEARKAELVAEVRADLAAALPGIRALDPRAG +RAVALAHGLFAALADRIETTPAAELARRRVRVPDAQKARIAARVLAEQAGLAVARRRRGG +RR +>PROKKA_00589 +MTGTTTPPAPAGPECGTVRARTGETDLELYTATALRVAGEVIGRYSTSFSWACRVLPPDA +RRDIAAIYAMVRVADEVVDGAAEEAGLPVARVAAGLDAYERACEDAMDTGFSTDLVLHAF +ADVSRRHGITAELTRPFFVSMRADLTVAEHGEDSLAAYIHGSAEVVGLMCLQVFLSMDGT +RADGPADRAALRAAASRLGAAFQKVNFLRDLAADHDALGRTYFSGAAPEALTEERKAELL +ADLDADLDASLPGILALDPRAARAVLLAHGLFAELSRRLAATPAAELARRRVRVPDPVKA +RIAVRVLAASPVGIGRRGRPLPAGCAEDLAAHQDGDRRP +>PROKKA_02046 +MAAPAPIPAALYTRTAHAAAAQVIRRYSTSFSWACRTLPRQARQDVATIYAMVRVADEVV +DGVAVAAGLDEAGVRAALDDYERACEAAMASGFATDPVLHAFADVARRHGITPELTRPFF +ASMRADLGIREHGAESLDAYIHGSAEVVGLMCLQVFLSLPGTRARTPGQRQELRAQASRL +GAAFQKVNFLRDLAADHHELGRTYLPGAAPGVLTEARKAELVAEVRADLDAALPGIRVLD +PGAGRAVALAHGLFAALVDRIEATPAAELAHRRVRVPDHQKARIAARVLARGRRGGRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001650.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001650.fa new file mode 100644 index 0000000000000000000000000000000000000000..82c81143e12e5ef8ab32ec8b5a385d57b4b7528f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001650.fa @@ -0,0 +1,25 @@ +>PROKKA_02109 +MQTPATPSPHDRPSPVARPWMAASDVPVAGPDDVERVVLLSPAGEAVGTEAKATVHRRTE +DGGTPLHLAFSCHVYDEAGRFLLTRRALGKAAFPGVWTNGFCGHPGPGEPPAEAVLRRAP +QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA +DLAAALAAVPRAFSPWLVEQWQQGAFDPR +>PROKKA_01816 +MQTPATPSPPDRPSPVARPWLAASDVPVAGPDDVERVVLLSPEGEAVGTEAKATVHRRTE +DGGTPLHLAFSCHVYDEADRFLLTRRALGKAAFPGVWTNGFCGHPGPGESPAEAVLRRAP +QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA +DLAAALAAVPRAFSPWLVEQWQQGAFDPR +>PROKKA_00669 +MQTPATPSPHDRPSPVVRPWMAAPDLPIAGPDGVERVVLLSPAGEAVGTEAKAAVHRRTE +DGGTPLHLAFSCHVYDDAGRFLLTRRALGKKAFPGVWTNGFCGHPGPGESPAQAVLRRAP +QELGAEVSDVVEVLPDFRYRAADASGMEEHEICPVFQARMHGDPAPERDEVAEWCWVEPA +DLAAALAAVPRAFSPWLVEQWQQGAFEAR +>PROKKA_00586 +MQQGPSDPRTVEEVEERVVLLGADGAPIGTEAKASVHRNAADGGTPLHLAFSCHVYGPDG +RFLLTRRALGKKAFGGVWTNGFCGHPAPGEAPAEAVLRRAPQELGVGVREVTPLLPGFRY +RAADAGGVEEHEVCPVFRAECDGDPVPERDEVAEWCWVEVADLTAALASVPRVFSPWLVM +QWEQGAFGPR +>PROKKA_02049 +MQTPATPSPHDRPSPVVRPWMAASDVPVTGPDDVEHVVLLSPAGEAVGTEAKATVHRRTE +DGGTPLHLAFSCHVYDEADRFLLTRRALGKAAFPGVWTNGFCGHPSPGESPAEAVLRRAP +QELGVEVSDVVEVLPDFRYRAADASGMEEHEICPVFRARMHGDPAPERDEVAEWCWVEPA +DLAAALAAVPRAFSPWLVEQWQQGAFDAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001651.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001651.fa new file mode 100644 index 0000000000000000000000000000000000000000..016059e3ce13a851fc66c8e0faf3875eca2091e0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001651.fa @@ -0,0 +1,20 @@ +>PROKKA_02110 +MATKDLTLEEFGSTVAENDTVLVDFWAGWCGPCRQFAPVFEAASEKHEDVVFAKVDTEDQ +QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGTALEQLLDQVKGLDIAEVRRLAEEQQG +QQGDAEPGQDEAVQSTAAHLDDVNGR +>PROKKA_01817 +MATKDLTLEEFGSTVAENDTVLVDFWAGWCGPCRQFAPVFEAASEKHEDVVFAKVDTEDQ +QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGAALEQLLDQVKGLDIAEVRRLAEEQQG +QQGDAEPGQDDAVQSTAAHLDDVNGR +>PROKKA_00668 +MATKDLTLEEFGTTVSENDTVLVDFWADWCGPCKQFAPVFDAASEKHEDIVFAKVDTEDQ +QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPAPALDQLLEQVKGLDIAEVRAMAEQQAG +EAEAEPSQDEAVQSTASHLDEVNGR +>PROKKA_00585 +MATTDLTLEAFGTTVSENDTVLVDFWAEWCGPCKMFGPVFETASEKHQNVVFAKVDTEDQ +QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGQALDQLIDQVTALDIAEVRAMAEQQGA +QDAEPSEEEAVQSAAAQLDDVNGR +>PROKKA_02050 +MATKDLTLEEFGSTVAENDTVLVDFWAGWCGPCRQFAPVFEAASEKHDDVVFAKVDTEDQ +QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGTALEQLLDQVKGLDVAEVRRLAEEQQG +QQDDAEPGQDDAEPGQDEALQSTAAHLDDVNGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001652.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001652.fa new file mode 100644 index 0000000000000000000000000000000000000000..f3edfa1ba841224fd52a5e243e11cbd20e7c56a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001652.fa @@ -0,0 +1,20 @@ +>PROKKA_02113 +MTGAPILPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG +ELIDWIQEARTSHAGVLINPAAYSHTSIAIRDALAAVDRPIAEVHISNIHRREAFRHHSH +VSAVADVVIAGAGVQGYTLAVDWLAAAVRR +>PROKKA_01820 +MTGAPILPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG +ELVDWIQEARTSHGGVLINPAAYSHTSVAIRDALAAVDRPIAEVHISNVHRREAFRHHSH +VSAVADVVIAGAGVQGYALAVDWLAAAVRR +>PROKKA_00667 +MRETGASPRTFVRETGASVVVRSYTGPMTTAPSALPLLVLNGPNLNLLGTREPEIYGSDT +LDDVRSRTEARAAGHGLAVDFRQSNHEGELVDWIQEARTSHAGILINPAAYSHTSVAIRD +ALSAVGRPIVEVHISNIHRREPFRHHSHVSAVADAVIAGAGVLGYELGIDWLAAAVRR +>PROKKA_00583 +MTDSMPAATAARLPLLVLNGPNLNMLGTREPEKYGFETLEDVRALTAARAAEHGLEVDFR +QSNHEGELVDWIQEARTGFSGILINPAAYSHTSVAIRDALAAVPVPIVEVHITNIHAREE +FRHHSVVSAVATTVIAGAGTQGYALGVEVLAARLAR +>PROKKA_02051 +MTATPALPLLVLNGPNLNLLGTREPEVYGTATLDDVRALTEARAAEHGLTVDFRQSNHEG +ELIDWIQEARTSHAGVLINPAAYSHTSIAIRDALAAVDRPIAEVHISNVHRREAFRHHSH +VSAVADVVIAGAGVQGYALAVDWLATTVRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001657.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001657.fa new file mode 100644 index 0000000000000000000000000000000000000000..30fc514e2598b01579b72c5f320967b56488d483 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001657.fa @@ -0,0 +1,30 @@ +>PROKKA_02119 +MAPIPPDPHADHAPAVDDMPLDTTAAPDIPAAVDPVPHGMAAHVLEREVGPLRARFPGVA +DEATVRQLLFDSYAELAETSRHPEMLPTISVQHAASRLRARAINQGSIESRHPRVLFVCH +GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD +VLRAAEIVVLFDGADPFEIPEGAQVQKWSVPSIRGMSLEQVRGVRDALDLEVRGLIADLG +EAATPLPEEGTRVGRPLDLYPPGV +>PROKKA_01827 +MTPIPPDPHADHAPAVDDMPLDTTAAPDIPAAVDPVPHGMAAHVLEREVGPLMARFPGVA +DEATVRQLLFDSYAELAETSRHPEMLPTISVQHAASRLRARAINQGSIESRHPRVLFVCH +GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD +VLRAAEIVVLFDGADPFEIPEGAQVQKWSVPSIRGMSLEQVRGVRDALDLEVRGLIADLG +EAATPLPEEGTRVGRPLDPYPPGV +>PROKKA_00661 +MAAIPPDPHADRTPAVDDLPLDAASPDGRAAAPVGLEPEGMAANVLEREIEHLMERFPCV +GDEETVRAVVMDSYAQLAATSRHPDMLPNTTVQHASARLRAMAINQGSIESRHPRVLFVC +HGNAGRSQMAAALLENRTGGAVKSRSAGTSPAGEVISTAFDAMSEIGIPLHHSYTKGVDE +DVLKAAEVVVLFDGAEPLDIPEGTEVQEWSVPSIRGMSLEQVRGVRDALDLQVRGLIADL +GEEGSDAPPPGEGAPVA +>PROKKA_00578 +MAPHPSDPAADLPAADVPLDPTGALPVVAPAPEGMASHVLDREAEHLHARYPEVGDVAMA +RALLEDSYARLARTTRHPEMLPVTAANYAAARLRARAIAQGSVESRHPRVLFVCHGNAGR +SQMAAALLENRSGGTVASRSAGTSPAGSVLPMALDVMNEIGLPLHHAFPKGVDRDILQAA +QLVVLFDGAEEDLLDVPAGVEVQHWSVPSIRGLALEQVRGVRDALDLQVRGLIAELTALE +GEEQGGAADPAA +>PROKKA_02057 +MTPIPPDPHADHAPAVDDMPLDTTAAPDTPAAVDPVPHGMAAHVLEREVGPLMARFPGVA +DEATVRQLLFDSYAELAATSRHPEMLPTTAVQHAASRLRARAINQGSIESRHPRVLFVCH +GNAGRSQMAAALLENRTHGEVRARSAGTEPAGEVISTAFEAMNEIGIPLHHTYTKGLDPD +VLRAAEIVVLFDGADPFEIPEGAQVQNWSVPSIRGMSLEQVRGVRDALDLQVRGLIADLG +EAAADAPLPDADTRAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001659.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001659.fa new file mode 100644 index 0000000000000000000000000000000000000000..6ff5ad53a8a31ac18d4d7e685bc00b58e0d3bada --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001659.fa @@ -0,0 +1,15 @@ +>PROKKA_02121 +MTTTDLKITGMTCGHCVASVQEELGEIAGVSAVDVDLNSGGVSTATVTSEAPLDPAAARA +AVEEAGYTLVEA +>PROKKA_01829 +MTTTDLKITGMTCGHCAASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLDPAAARA +AVEEAGYTLVEA +>PROKKA_00659 +MTTTDLKITGMTCGHCVASVQEELGEIAGVTAVDVDLTAGGVSTATVTSESPLDPAAARA +AVEEAGYRLVEG +>PROKKA_00576 +MTTTDLKITGMTCGHCVASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLGPAAARA +AVEEAGYTLVEG +>PROKKA_02059 +MTTTDLKITGMTCGHCAASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLDPAAARA +AVEEAGYTLVEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001660.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001660.fa new file mode 100644 index 0000000000000000000000000000000000000000..5153ffc66313589f7feb43a8207348b3a92d5007 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001660.fa @@ -0,0 +1,20 @@ +>PROKKA_02123 +MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRRNFRRDEDEGYLTASQGAALLTLGALVR +IARNEDHADLEALLEHAEADEVDLTAFIGQFSDEDIETLRELIGVVIREPSCSELYQLWE +ESGELEQWLEYSRECLP +>PROKKA_01831 +MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRKNFRRDEDEGHLTASQGAALLTLGALVR +IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDVETLRELIGVVIREPSCSELYQLWE +ESGELEQWLEYSRECLP +>PROKKA_00656 +MGAWGRNVFQNDTALDLVDEVLDGSFDLDEFRKDFRREEDEGYLDASQGAALLALGALVR +IARNEDHADLDVLLEHAEAEEVDLTDFIDQFSDEDIQTLRELIGVVIREPSCSELYELWE +ESGELEQWLEYSRQCLP +>PROKKA_00574 +MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRRNFRRDEDEGYLTASQGAALLALGALVR +IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDIETLRELIGVVIREPSCSELYQLWE +ESGELEQWLEYSRECLP +>PROKKA_02061 +MGAWGRNVFQNDTALDIVDEVLDGTFDLDEFRKNFRRDEDEGHLTASQGAALLTLGALVR +IARNEDHADLEALLEHAETDEVDLTAFIDQFSDEDVETLRELIGVVIREPSCSELYQLWE +ESGELEQWLEYSRECLP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001663.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001663.fa new file mode 100644 index 0000000000000000000000000000000000000000..68409c4c9c54258e0bb4fcd00a44ab90c13fdf8e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001663.fa @@ -0,0 +1,32 @@ +>PROKKA_02127 +MTQTTSTPARLRARDGFVLAARHFAPTTAPQARPAGAVVIAPATGVKATYYRRYAEFLAG +HGFHAVTFDYRGVGESREPFAVARQARWADWGALDADAVLGWARTHLPGPLLTVGHSYGG +FGIGLADEARHVARHVAVGGQHAHWRDYRARPGRARMWARWHAAMPVVTLARGHLPGRRL +GWLEDLPRGVALDWARSRRDFTASARTAAGRDELRRRLAAFTADALIVAPVDDDFGTEAA +LDRADAYSPGRRTVRWRVRPEELGVAEIGHFGLFHARFAPTFWPATLEWLRDGVAPDAAR +>PROKKA_01835 +MTQTTSTPVRLRARDGFVLAARHFAPTTTTPPARPAGAVVIASATGVKATYYRRYAEFLA +GHGFHAVTFDYRGVGESREPFAVARRARWADWGALDADAVLGWARTRLPGPLLTVGHSYG +GFGIGLADEARHVARHVAVGGQHAHWRDYRARPGRARMWARWHAAMPAITLARGHFPGRR +LGWLEDLPRGVALDWARSRRDFTASARTTAGRDELRRRLAAFTADALIVAPVDDDFGTDA +ALDRADAYSPGRRTVRWRVRPEELGVAEIGHFGLFHARFAPAFWPATLEWLRDGVAPAAA +R +>PROKKA_00653 +MTQTTSTPVRLRAPDGFVLAARHFTPTTTTPPASPAGTVVIASATGVKATYYRRYAEFLA +GHGFHAVTFDYRGVGESREPFAVARRARWADWGVLDADAVLGWARTHLPGPLLTVGHSYG +GFGIGLADEARHVARHVAVGGQHAHWRDYRARPGRVRMWARWHAAMPAITLARGHFPGRR +LGWLEDLPRGVALDWARSRRDFTASARTAAGRDELRRRLAAFTADALIVAPVDDDFGTDA +ALDRADSYSPGRRTVRWRVRPEELGVAEIGHFGLFHARFAPTFWPATLEWLRDGVVPAAA +R +>PROKKA_00569 +MTQTTSTLVRLRARDGFVLAARHFAPTTTPPARPAGAVVIAPATGVKATYYRRYAEFLAG +HGFHAVTFDYRGVGESRAPFAVARRARWADWGALDADAVLGWARTHLPGPLLTVGHSYGG +FGIGLADEARHVARHVAVGGQHAHWRDYRARPGRARMWARWHALMPMVTLARGHFPGRRL +GWLEDLPRGVALDWARSRRDFTASARTVAGRDELRRRLAAFTADALIVAPVDDDFGTDAA +LDRADSYSPGRRTVRWRVRPEELGVGEIGHFGLFHARFASTFWPATLEWLRDGVAPAGAR +>PROKKA_02065 +MTQTTSTPARLRARDGFVLAARHFAPTTAPQARPAGAVVIAPATGVKATYYRRYAEFLAG +HGFHAVTFDYRGVGESREPFAVARQARWADWGALDADAVLGWARTHLPGPLLTVGHSYGG +FGIGLADEARHVARHVAVGGQHAHWRDYRARPGRVRMWARWHAAMPAITLARGHFPGRRL +GWLEDLPRGVALDWARSRRDFTASARTAAGRDELRRRLAAFTADALIVAPVDDDFGTDAA +LDRADAYSPGRRTVRWRVRPEELGVTEIGHFGLLHARFAPTFWPATLEWLRDGVAPDAAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001664.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001664.fa new file mode 100644 index 0000000000000000000000000000000000000000..9859adb293bc368f06c7a4b70470d6d5c424ddbc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001664.fa @@ -0,0 +1,35 @@ +>PROKKA_02128 +MTTMKAAVVTQFGTEADVTEVERPTPGQHEALVKLISSGVCHTDLHAMEGDWPVKPTPPF +IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD +GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG +HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT +AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE +FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD +>PROKKA_01836 +MTTMKAAVVTQFGTEADVTEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF +IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD +GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG +HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT +AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE +FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD +>PROKKA_00652 +MTTMKAAVVTQFGKEADVQEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF +IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSAD +GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG +HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT +AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE +FYAAGKIHPTFHTRPLTEINDVFEEMRHGKIEGRVVIDYAMQD +>PROKKA_00568 +MTTMKAAVVSQFGKEADVKEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF +IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWGACGHCQYCRTGWETLCEEQINGGYSMN +GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG +HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT +AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE +FYAAGKIHPTFHTRPLTEINDVFEEMRHGKIEGRVVIDYAMQD +>PROKKA_02066 +MTTMKAAVVTQFGTEADVTEVERPTPGQHQALVKLISSGVCHTDLHAMEGDWPVKPTPPF +IPGHEGVGIVEEVGPDVENLKVGDMVGNAWLWRACGHCQYCRTGWETLCEEQVNGGYSVD +GSFGEYMLVDARYAPVIPEGADPMEVGPILCAGVTVYKGLKQTEVRPGQWVVISGIGGLG +HIAVQYAVAMGMRVVAVDVADDKLALASRHGAELTVNANVADPSVEIQEKIGGAHGVLVT +AVHPQAFGQAIAMTRRGGTIVFNGLPPGDFPAPIFDIVLKGLTIRGSIVGTRQDMVEALE +FYAAGKIHPTFHTRPLTEINDVFDEMRHGKIEGRVVIDYAMQD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001667.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001667.fa new file mode 100644 index 0000000000000000000000000000000000000000..ee50410465063cd7005987e4af6438c3fb9e4def --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001667.fa @@ -0,0 +1,20 @@ +>PROKKA_02131 +MTVPSSSAEHAPALEARPEMPGETVSRVAMTPAALELIRRLLPIHGPLMFHQSGGCCDGS +APMCYPAGDFTTGAADVLLGTFALPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR +GSGFSVEAPEGKRFLIRSRLMAGSG +>PROKKA_01839 +MTVPSSSAEHAPALEARPEMPGETLSRVAMTSAALELIRRLLPIHGPLMFHQSGGCCDGS +APMCYPAGDFTTGAADVLLGTFALPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR +GSGFSVEAPEGKRFLIRSRLMAGSG +>PROKKA_00649 +MTVPSSSAEHAPALEARPELPGETVSRVAMTPAALELIRRLLPIHGPLMFHQSGGCCDGS +APMCYPAGDFTTGAADVLLGTFALPAEGDQDAVEIPFWMSAAQFEYWKHTHLTLDVVDGR +GSGFSVEAPEGKRFLIRSRLMAGSG +>PROKKA_00565 +MTVSSSSAEHAPALEARPELPGETVSRVAMTPAALALIRRLLPIHGPLMFHQSGGCCDGS +APMCYPAGDFTTGAADVRLGTFVVPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR +GSGFSVEAPEGKRFLIRSRLMAGSG +>PROKKA_02069 +MTVPSSSAEHALDARPELPGETVSRVAMTPAALELIRRLLPIHGPLMFHQSGGCCDGSAP +MCYPAGDFTTGAADVLLGTFALPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGRGS +GFSVEAPEGKRFLIRSRLMAGSG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001668.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001668.fa new file mode 100644 index 0000000000000000000000000000000000000000..aaacdcd50ddadcb5cd15c68b9dc27d1f3ae435c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001668.fa @@ -0,0 +1,25 @@ +>PROKKA_02132 +MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAVRRAFAAEA +RGDVEPGRAPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR +LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD +VPTTAA +>PROKKA_01840 +MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAAEA +RGDVEPGRVPASFYVGVDEAGHLVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR +LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD +VPTTAA +>PROKKA_00648 +MLPDPSPTVTVDGLLLRPLRTADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAADA +RGDVEPGRVPASFYVGVDEAGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAVR +LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVETGLDGAPFPEPKLRFD +VPTTAA +>PROKKA_00564 +MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAIRRAFAAEA +RGDVEPGRVPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAVR +LLRGALTLLAAHGVSTALLTCDETNTASVATIRACGGVLRDRVEAGLDGAPFPVPKLRFD +VPTTAA +>PROKKA_02070 +MLPDPSPTVTVDGLLLRPLRAADEIAAREADAELHREGFDFLMAGTRSFPAVRRAFAAEA +RGDVEPGRAPASFYVGVDENGELVGRVSVRWELNEALRHVNGHVGYAVRPAFRRRGHAAR +LLRGALTLLAARGVPAALLTCDETNTASVATIRACGGVLRDRVEADLDGAPFPVPQLRFD +VPTTAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001669.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001669.fa new file mode 100644 index 0000000000000000000000000000000000000000..6ca69ef8adf3d8bbe94cfeb8176bfcdde2661ba2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001669.fa @@ -0,0 +1,55 @@ +>PROKKA_02133 +MSQTSQATGRLSAGHVIVKTLESHGVKRVYSVPGESYLDVLDGLHDSGIENVVCRHEGGA +TYMAEADGKMNVVPGVAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHRDREAFQ +EFDPHAWFGTGAKRVMVLDHPERASEIVAEAMFAASSGRPGPVVVGLPEDVIREEIDAHL +HPQIPVASGGMTVGDWKSLHAALKESRKPLFITGGNDWTDEGAQTLTTWLEEHKIPAAAE +WRTEGTVPFSSPSYVGPIGYGRPKPTYDMLEETDLIVFVGTVPGDVVTNGFTIRQNWDKK +NFLVTIDPSLRGRSGPVSHQIVAKPDGFIRDLVRMELEVKPEWEEWTSRMRGEQEKFAAL +PPAEPSEGQAKMATLMANLVPKLPKDSMISLGAGEHTNWAHRYFPTEGYRSMISARNGSM +GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIRT +HQERQYPGRVSGTQLKNPDFAAMAQAFGGFGVRVERDADVPAAVDAALKAVQEEGRFALI +HLIVEQRVKAY +>PROKKA_01841 +MSQTSQATGRLSAGHVIVKTLESHGVKRVYSVPGESYLDVLDGLYDSGIENVVCRHEGGA +TYMAEADGKMNVVPGVAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHRDREAFQ +EFDPHAWFGTGAKRVMVLDHPERASEIVAEAMFAASSGRPGPVVVGLPEDVIRQEIDAHL +HPQIPVAPGGMTVEDWKSLHAALKESRKPLFITGGNDWTDEGAQTLTTWLEEHKIPAAAE +WRTEGTVPFSSPSYVGPIGYGRPKPTYDMLEETDLIVFVGTVPGDVVTNGFTIRQNWDKK +NFLVTIDPSLRGRSGPVSHQIVAKPDVFIRDLVRMELEVKPEWEEWTSRMRGEQEKFAAL +PPAEPSEGQAKMATLMANLVPKLPKDSMISLGAGEHTNWAHRYFPTEGYRAMISARNGSM +GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGAKPLVIVMDNQEYGTIRT +HQEREYPERVSGTQLKNPDFAAMAQAFGGFGVRVERDADVPAAVDAALKAVQEEGRFALI +HLIVEQRVKAY +>PROKKA_00647 +MSQTTEAGGRLSAGHVIVKTLESHGVRRIYSVPGESYLDVLDGLHDSQIENVVCRHEGGA +TYMAEADGKMNEVPGIAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHREKEAFQ +EFDPHAWFGTGAKRVMVLDHADRASEIVAEAMFAATSGRPGPVVVGLPEDVIREQIDATL +HPVIPVATGGMTVEDWKSLHSALKESKKPLFITGGNDWTDEGAQQLTQWLEGHKIPAAAE +WRTEGTVPFSSPSYVGPIGYGRPKPTYDLLEETDLIVFIGTVPGDVVTNGFKIRQNWDKK +NFLVTIDPSLRGRSGPVSHQIVAKPDVFVRDLVRMDLDVKPEWEEWTSRMRGEQETFAAL +PPAEPSEGQAKMATLMANLMPKLPKDSMISLGAGEHTNWAHRYFPTEGYRAMISARNGSM +GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIRT +HQEREYPERVSGTQLKNPDFAGMAEAFGGLGIRVEKDADVPAAVDAALKAVQEEGRFALI +HLIVEQRVKAY +>PROKKA_00563 +MSQNSEAPGRLSAGHLIVKTLESHGVRRVYSVPGESYLDVLDGLHDSAQIENVVCRHEGG +ATYMAEADGKMNEVPGIAMVTRGPGAANAHVGLHTAWQDSTAMVLFVGLIPFEHRDREAF +QEFDPHAWFDSGAKRVMVLDHPERASEIVAEAMFAAASGRPGPVVVGLPEDIIRVEVDAH +LHPQIPVAPGGMTVEDWKSLHAALKESQKPLFITGGNDWTDAGAEALTSWLEDHKIPAAA +EWRCEGTVPFSSPSYVGPIGYGRPDFTQHLLEETDLIVFVGTVPGDVVTDGFTIRQNWDK +KNFLVTIDPSLRGRSGPVSHQIVAKPDVFVRDLVRMDLAVKPEWEAWTSRLRGQQEEFAA +LPAAEPGDGQAKMATLMATLMPKLPKDSMISLGAGEHTNWAHRYFPTEGYRAMISARNGS +MGYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIR +THQEREYPERVSGTQLKNPDFAAMAEAFGGFGVRVEQDADVPAAVDAALKAVQEEGRFAL +IHLIVEQRVKAY +>PROKKA_02071 +MSQTSQATGRLSAGHVIVKTLESHGVKRVYSVPGESYLDVLDGLHDSGIENVVCRHEGGA +TYMAEADGKMNVVPGVAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHRDREAFQ +EFDPHAWFGTGAKRVMVLDHPERASEIVAEAMFAASSGRPGPVVVGLPEDVIREEIDAHL +HPQIPVAPGGMTVEDWKSLHAALKESRKPLFITGGNDWTDEGAQTLTTWLEEHKIPAAAE +WRTEGTVPFSSPSYVGPIGYGRPKPTYDMLEETDLIVFVGTVPGDAVTNGFTIRQNWDKK +NFLVTIDPSLRGRSGPVSHQIVAKPDGFIRDLVRMELEVKPEWEEWTSRMRGEQEKFAAL +PPAEPSEGQAKMATLMANLVPKLPKDSMISLGAGEHTNWAHRYFPTEGYRSMISARNGSM +GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIRT +HQERQYPGRVSGTQLKNPDFAAMAQAFGGFGVRVERDADVPAAVDAALKAVQEEGRFALI +HLIVEQRVKAY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001671.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001671.fa new file mode 100644 index 0000000000000000000000000000000000000000..d1e9b49f4e5803e7b6272a85b946f3fe9f68e084 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001671.fa @@ -0,0 +1,20 @@ +>PROKKA_02136 +MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRID +IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAARER +REQGGTGGDAPRA +>PROKKA_01844 +MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRVD +IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAAAER +REQGGTGGDAPRA +>PROKKA_00636 +MSAPSPRPSADRAGTGRPARGGLRTTVKGPLVFSAVLGVIGGVIAGITASGGTQNPLRID +IALIAFGVFFMTSLVVVAMLQLAARENPDHLSAGSGINRSSEETFQKAAAERRAQVARER +REQDGTGGDAPRA +>PROKKA_00560 +MSAQSPRPSDDRTRPGAGRPARGGLRTTVKGPLVFSAVLGLVGGVVAALTASGGTANPLR +IDIGLIAFGVFFMTSLVVVAMLQLASRENPDHLSRGSGVNRSSEETFQRRAAERRAKAAA +ERRAAQGDAGR +>PROKKA_02074 +MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRVD +IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAAAER +REQGGTGGDAPRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001672.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001672.fa new file mode 100644 index 0000000000000000000000000000000000000000..c3e9500243a1702a79a199727fdcc870537ca2ef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001672.fa @@ -0,0 +1,25 @@ +>PROKKA_02137 +MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWEYLR +RDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARHRRE +FIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFHHEV +RRDRGTARGL +>PROKKA_01845 +MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWEYLR +RDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARHRRE +FIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFHHEV +RRDRGTARGL +>PROKKA_00635 +MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAAPGLTWMKVSLALYLAFSGSAMWEYLR +REPVPVAMRSPLSMAAAASMLGVIVLLFLGTPAGVGLAAAAALVLGGAAELVAWARHRRE +FIPARDQLWTGLVGLLSGLGVAFGALQGFGPHALLGIAGGGAIIIGVLLLVSGLGFHHEV +RRDRGTAKGL +>PROKKA_00559 +MTSPQTPLEISSEVFKPVLIRAGVALIFGLTTVFVQNPGLTWMKVAFALYLVFSGSALWE +YLRRDPVPVGMRSPLSLAAAAWMLGTVVLVIMGSPAAVGIVVGLALLAGGAAELTAWARF +RREFIPARDQLWTGLVGALSGLGVLVGAVQGFGPHALLGIAGGGAIIVGVLMLISGLGFH +HEVRRDRGTAKGL +>PROKKA_02075 +MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWEYLR +RDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARHRRE +FIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFHHEV +RRDRGTARGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001679.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001679.fa new file mode 100644 index 0000000000000000000000000000000000000000..57fdcb321e41a5c89078c86eb6befd683867cd97 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001679.fa @@ -0,0 +1,35 @@ +>PROKKA_02145 +MTRPLRWATLAGVLLIVAVLAFWAGRATLTPPAQAEQRPSEDALVTVAEQELGRVITLGV +SVTREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVITVQGELPQWRALGEGATG +SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAADTVELGQLVVLESLPAA +LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAIIPAGTAVTVPHGEHEWEAV +AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL +RTQPDGAARVTVVRDGVQEERTVIVRGSADGLAVVDGVDAGETVRVLNGAP +>PROKKA_01852 +MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV +SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG +DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP +LSVDAKTTAVGTTLAGGENVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV +AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL +RTQPDGAATVTVVRDGAAEDRAVTVLGSADGLAVVDGVDAGEQVRVLNGTR +>PROKKA_00627 +MSKVTRWAALVLTLVLVAALAFWAGRATLTPPAQADQRPSEDAVVTVAEQELGRVITLGV +SVAREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVIAVQGELPQWRALDEGATG +SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAAGTVELGQLVVLESLPAA +LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWEAV +AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL +RTQPGGAVVVTVVQDGVEEERTVTVRGSADGLAVVDGVDAGETVRVLNGAP +>PROKKA_00551 +MTRPARWAALVLAVVLVAALAFWAGRVTLTPPAQAEQRPSEDAVVTVAEQELGRVITLGV +SVTREQAPAAVNALSGVVTRAGQSGEVAAGDVLYAVAQKPVIAVQGELPQWRALGEGATG +SDVTAFQRMLTATGTKVKATGTWDEATATAWNAWLTTRGYPAADTVELGQLVVLESLPTA +LSVDAKATAVGGTLAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWKAV +AGESISDEQGLIRITLTAPDGGVVCGEDCDTLPADPTTSLLSQVSVVPPVSGPVVPVSAL +RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR +>PROKKA_02082 +MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV +SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG +DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP +LSVDAKTTAVGTTLAGGEKVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV +AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL +RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001682.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001682.fa new file mode 100644 index 0000000000000000000000000000000000000000..48e906bf7769f379e3c0588cd1b8f76393aad334 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001682.fa @@ -0,0 +1,55 @@ +>PROKKA_02148 +MLWTLLRRHGRRYRGDVAAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTARIWDIGLV +MLGVALVQVVAAIAAVWFGAKASMGVGRDLRRAVYTRVDAFSAEELGRFGAATLITRGTN +DVNQVQMLTLMALNFMVAVPIMAVGGIVMAIREDPGLSWLVWVSVPVLLVIVAWIVARLM +PLFQQMQDNIDDVNGVLREQIQGIRVVRAFVRERHETRRFTDANAALTETSVRIGRLFVL +LGPVITMILHLATAAVLWFGGQRVDAGLVQVGALTAFMQYLLQILMAVMMGTFMMMMLPR +AVISARRIGEVLDTVPTLGEPVRPVTPERRDGAVELRHVTFQYPGAEAPVLDDVSFAVAP +GTTTAIIGSTGSGKSTLISLLPRLYDATSGEVLVDGVPVTDLARAELTEAVALVPQKPYL +FSGTVRENMQFGAPDASDERIWAALETAQAADFVRARTTGKGEAAASGLDSRLSQGGTDV +SGGQRQRLSIARALVAEPRILVFDDSFSALDVTTDARLRAALDRAAAGVTRIVVAQRVAT +ITDADQIIVLDEGRVVGRGTHAELLADNQTYREIVDSQLTAEDVA +>PROKKA_01856 +MLWTLLRRHGRRYRGAVAAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTARIWDIGLV +MLGVALVQVVAAIAAVWFGAKASMGVGRDLRRAVYTRVDAFSAEELGRFGAATLITRGTN +DVNQVQMLTLMALNFMVAVPIMAVGGIIMAIREDPGLSWLVWVSVPVLLVIVAWIVARLM +PLFQRMQDNIDDVNGVMREQIQGIRVVRAFVRERHETRRFTDANAALTETSVRIGRLFVL +LGPVITMILHLATAAVLWFGGERVDAGLVQVGALTAFMQYLLQILMAVMMGTFMMMMLPR +AVISARRIGEVLDTVPTLAEPVRPVTPARRDGAVELRHVTFQYPGAEAPVLDDVSFAVAP +GTTTAIIGSTGSGKSTLISLLPRLYDATSGEVLVDGVPVTDLARAELTEAVALVPQKPYL +FSGTVRENMQFGAPDASDERIWAALETAQAADFVRARTTGKAETAASGLDSRLSQGGTDV +SGGQRQRLSIARALVAEPRILVFDDSFSALDVTTDARLRAALDRAAAGVTRIVVAQRVAT +ITDADQIIVLDEGRVVGRGTHAELLADNQTYREIVDSQLTAEDVA +>PROKKA_00621 +MLWTLLRRPRRPDLGAVTAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTDRIWDLGLV +MLGVALVQVVAAIVAVWFGAKVAMGIGRDLRRAVYTRVDGFSAEELGRFGAPTLITRGTN +DVNQVQMVTLMGLNFMVAVPIMAIGGIIMAVREDPGLSWLVWVSVPVLLVIVAWIVAKLM +PLFQRMQDDIDRVNGVMREQVMGIRVVRAFVREPHESARFSGANAALTRTSVLIGRLFVL +LGPVITMILHLATAAVLWFGGHRVADGLVEVGALTAFMQYLLQILMAVMMGTFMMMMLPR +AVVSAGRIGEVLDTVPTLAEPVNPVTPADPRGAVELRDVTFAYPGAEAPVLDGVSFTVAP +GSTTAIIGATGSGKSTLVNLIPRLYDATSGQVLIDGVPVTELARAELTRAVALVPQKPYL +FSGTVAENMRFGAPEATEEEIWAALETAQAAGFVRERTTGEGETAAGGLDSRLSQGGTDV +SGGQRQRLSIARALVARPRILLFDDSFSALDVATDARLRGALDATAAGTTRIVVAQRVAT +ITEADQIIVLDEGRVVGRGTHAELLAGNETYKAIVDSQVREEELA +>PROKKA_00546 +MLWTLLRRHLNPYAGAVTAVIVLQLVSTLAMLYLPSLNARIIDEGVARGDTARIWDLGLV +MLGVAAVQVVAAISAVWFGAKASMGVGRDLRRAVYTRVDGFSAEELGRFGAATLITRGTN +DVNQVQMLTLMALNFMVAVPIMAVGGIVMAVREDAGLSWLVWVSVPLLLVIVGFIVSRLM +PLFQRMQDDIDAVNGVMREQVMGIRVVRAFVRQDHEAARFTDANQALTDTSVRIGRLFVL +LGPVITMVLHLATAAVLWFGGHRVDQGLVQIGSLTAFMQYLLQILMAVMMGTFMMMMLPR +AVISARRIGEVLDTAPTLGEPVHPVTPERREGRVELRDVTFAYPGAEAPVLDGVSFTAEP +GTTTAIIGATGSGKSTLVNLIPRLYDATSGQVLVDGVPVTDLARAELTDAVAIVPQKPYL +FSGTVRDNMRFGAPEATDEQIWAALETAQAADFVRERTTGEGETAASGLDSSLSQGGTDV +SGGQRQRLSIARALVADPRILLFDDSFSALDVTTDATLRAALDASAAQTTRVVVAQRVAT +ITDADQIVVLEAGRVVGRGTHAELLAGNETYRQIVDSQVREEELA +>PROKKA_02086 +MLWTLLRRHGRRYRGAVAAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTARIWDIGLV +MLGVALVQVVAAIAAVWFGAKASMGVGRDLRRAVYTRVDAFSAEELGRFGAATLITRGTN +DVNQVQMLTLMALNFMVAVPIMAVGGIIMAIREDPGLSWLVWVSVPVLLVIVAWIVAGLM +PLFQRMQDNIDDVNGVMREQIQGIRVVRAFVRERHEARRFTDANAALTETSVRIGRLFVL +LGPVITMILHLATAAVLWFGGQRVDAGLVQVGALTAFMQYLLQILMAVMMGTFMMMMLPR +AVISARRIGEVLDTVPTLGEPARPVSPARRDGAVELRHVTFQYPGAEAPVLDDVSFAVAP +GTTTAIIGSTGSGKSTLISLLPRLYDATSGEVLVDGVPVTDLARAELTEAVALVPQKPYL +FSGTVRENMQFGAPDASDERIWAALETAQAADFVRARTTGKGEAAASGLDSRLSQGGTDV +SGGQRQRLSIARALVAEPRVLVFDDSFSALDVTTDARLRAALDRAAAGVTRIVVAQRVAT +ITDADQIIVLDEGRVVGRGTHAELLADNQTYREIVDSQLTAEDVA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001687.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001687.fa new file mode 100644 index 0000000000000000000000000000000000000000..88f5f0f1626b4560f595db697499ee4461abd626 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001687.fa @@ -0,0 +1,100 @@ +>PROKKA_02154 +MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALP +ANAAVVAADPDVLRPFDAAADYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPEL +TVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGVPVALVTSSKNSRAVLTAGGV +LDFFPVIVDGNTAVERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFG +LVIGVDREPELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDHFDPASEGTR +EVLSTLANGYWGTRGAVPGTRISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWT +PLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTFEDEQGRRTTVHTRQFTSLANR +HLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLLE +TATNQSGIHVAVATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKVAA +VATSHDHASASVWESAVKDAQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHHRRS +TAAETGGEYAPPVVAAGHSAPVGSAVPMGKDGASLRQQLALNLHTFHVLQTAYGRRRDLD +ASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAAGWA +GAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFI +SDYGAEMLVEISRFFMSMTLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL +TSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEEVSTRLTVPFFEEGEEAGILAQF +EGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSSEELDR +ILRRMGYELPQEAFERMVTYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDL +SDTQGGTTKEGIHLGLMAGTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQ +PVVIHMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGEKLTVPLD +>PROKKA_01867 +MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALP +ANAAVVAADPDVLRPFDAAADYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPEL +TVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGVPVALVTSSKNSRAVLTAGGV +LDFFPVIVDGNTAVERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAASDGRFG +LVIGVDREPELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDRFDPASEGTR +EVLCTLANGYWGTRGAVPGTHISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWT +PLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTFEDEQGRRTTVHTRQFTSLANR +HLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLLE +TATNQSGIHVAVATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKIAA +VATSHDHANASVWESAVKDVQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHQRRS +TAAEAGGEYAPPVVDAGHSAPVGSAVPMGKDGASLRQQLALNLHTFHVLQTAYGRRRDLD +ASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAEGWA +GAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFI +SDYGAEMLVEISRFFMSMTLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL +TSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEEVSTRLTVPFFEEGEEAGILAQF +EGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSAEELDR +ILRRMGYELPEEAFERMVTYYEARSTHGSTLSRLVHAWVSARTDPDRSWDLFTEALESDL +SDTQGGTTKEGIHLGLMAGTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQ +PVVIQMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGEKLTVPLG +>PROKKA_00609 +MDGVVTDTAGVHAQAWKELFDEALPAVGALPANAAAVAADPEALRPFDAAADYLHHVDGR +PREDGVRTFFHSRGLRVPEADSPEAATTPQLTVLALAERKQGYFEQVLARDGVRVFPEAQ +DLLEKLRAKGVPVALVTSSKNSRAVLGAGGVLDFFPVIVDGHTAIERGLPGKPDPAMFWE +AARELGVDVADAMVLEDAVSGVKAAADGRFGLVIGVDREPDLGKGRLKGAGAHLVVQDYG +TLCLEQRTTTPFDPAWVLRWDEFDPASEGTREVLCTLANGYWGTRGAVPGTRISDVHYPG +TYMAGVFNRLTSMVQGRAVDTEHMVNIQDWTPLVVTPRGGRPLLPGEETLVDFSQEMDLR +RGVLSRTMAFEDEQGRRTSLHTRQFTSLANRHLAAIELTVVAENWTGELTVRSTIEGRVA +NLNVSDDRTLANQHLEPSQAREIDGETVLLETTTSQSRIDIAVATRTRQMAPVGHHEPIR +RPVDGSDLRVGQDIRLHVEEGVPLVIEKIAAVATSHDHAQASVWESAVKDVQRANNFRNL +LTLHEQRWGTNWDRFSVRIDIAEPYRHQRRSAAAAEGAEYAPPVVDAGRSASVGSAVPMG +KDGASLRQQLALNLHTFHVLQTAYGRRRDLDASVGARGLHGEGYRGHIFWDEIYVYPMLT +LRRPEITRGILMYRYRRLNEARANAQAEGWAGAMYPWQSGADGSEETPTELWNPRSRMWM +PDNSHNQRHVSLDIAYSVLRYIEITKDTSFISDYGAEMLVEVSRFFMSMALHNADTDRYE +IHGVMGPDEFHDGYPETPGSGLRNNAYTNVLTSWVLSETARLVRWLDTLDDGLPEIMEIT +EEEIERWEDVSARLTVPFFEDGEEAGILAQFEGYQDLKEFDWEAYRAKYGNIGRMDLILQ +AEGDATNRYKLSKQADTLMLGYLFSAEELDGILRRMGYELPQEAFERMVTYYEARSTHGS +TLSRLVHAWVAARTDPDRSWDLFTEALESDLSDTQGGTTREGIHLGLMAGTVDTVIRCYA +GLETREDVVRVDPRMPSQLPGASFTIRFRQQPVQIHMRRSEVTVRAGSGMWHDVPMIIAG +QEHTLSPGAEITVPLG +>PROKKA_00533 +MTQTLTPVDQQDRNARRHRLRRYRAVIFDMDGVITDTAGVHAAAWKELFDQALPAVGALD +ANRAAVAADPGVLRPFDPEADYLHHVDGRPREDGVRAFFASRGLTVPEVDDADAPVDLTV +LALAERKQGFFEKVLERDGVRVFPEATDLLEKLRDKGVPVALVTSSKNSRAVLTAGGVLD +YFPVIVDGHTAIERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFGLV +IGVDREHGEGGKPRLKDAGAHIVVKDYGTLRLADRTTAPFDAAWVLRWDHFDPATEGTRE +VLCTLANGYWGTRGSIPGTRISDVHYPGTYLAGVFNRLTSMVQGRQVETEHMVNMQDWTP +LQVIPAGGRPLIPGEETLLDYHQEMDLRRGVLSRSMRFEDAQGRITTLHTRQFQSLADRH +LGAIELTVEAENWSGDLVVRTLVDGRVANLNVSDDRTLANQHLEPVAAREVDGETLLLET +VTSQSRVHVAVAARTRQMAPKGHHQPIRRPVEGSDLMVGQDIHLHVEQDVPLVLEKVAAV +ANTHDHALASVDASAIKKVQRAQNFRNLLTLHEQRWGMNWDRFSVRIDLAEEHRNQRRST +AVLAEGEEFEAPVFEAGRSASVGSAATMGKDGASLRQQLALNLHTYHVLQTAFGKRRDLD +ASVGARGLHGEGYRGHIFWDEIFVYPMLTLRRPEITRGILMYRYRRLNEARANAQAEGWA +GAMYPWQSGSDGREETPAELWNPRSHMWMPDNSHNQRHVSLDIAYSVLRYIEITKDASFI +SDYAAEMLVEISRFFTSMTLHNAETGRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL +TSWVLSETARLLRWLDTLDDGLPEVMEVTEEEIARWEEIAAKLTVPFFTEGPEAGILAQF +EGYQDLLEFDWEGYRAKYGNIGRMDLILQSEGDATNRYKLSKQADTLMLPYLFSGAELEQ +ILGRMGYELHQEALERTVEYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDL +SDTQGGTTREGIHLGLMAGTVDTVIRCYSGLETRDDVVRLDPRLPRQLPGARFTIRYHQQ +PVVIHMTQRDVTVTAGEGMWHEVPMVIAGREHTLEPGGEVTVALG +>PROKKA_02097 +MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALP +ANAAVVAADPDVLRPFDAAADYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPEL +TVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGVPVALVTSSKNSRAVLTAGGV +LDFFPVIVDGNTALERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFG +LVIGVDREPELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDRFDPASEGTR +EVLCTLANGYWGTRGAVPGTHISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWT +PLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTFEDEQGRRTTVHTRQFTSLANR +HLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLLE +TATNQSGIHVAMATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKIAA +VATSHDHANASVWESAVKDVQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHQRRS +TAAEAGGEYAPPVVDAGHSAPVGSAVPMGKDGASLRQQLALNLHTFHVLQTAYGRRRDLD +ASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAAGWA +GAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFI +SDYGAEMLVEISRFFMSMTLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL +TSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEEVSTRLTVPFFEEGEEAGILAQF +EGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSAEELDR +ILRRMGYELPQEAFERMVTYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDL +SDTQGGTTKEGIHLGLMAGTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQ +PVVIHMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGDKLTVPLD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001693.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001693.fa new file mode 100644 index 0000000000000000000000000000000000000000..92b052749866f745dc7b844d8d1317d7e6ed20fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001693.fa @@ -0,0 +1,80 @@ +>PROKKA_02164 +MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL +PGGSEDVSDLAGTGAEPGPLARLDGVEEAYALRMAWATARAADAEFGTTVMPLPRDPALA +GLTVTAGTLPAADDARGVTLDAQTADRHGVAVGDVVTLAGESGPAPATTPLDAVVTGLTQ +PSPDPMLSGQAQVWASSAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA +GVDVDVATPDEAVRSAVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD +LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG +LHPAGLAVSVAVGVAVTVLAALAPAVAATRVAPLEALRPKDEVTAGSRGGRVRAAIGLVL +AVGGTALMLGGVSVREPVSAIGGGALCFVGVLLLARLFVPAAVRGAAVLARPAGVPGHLA +GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD +PARAAEAVAATEDVQAVALATPVGTTENGSPVLATPAADLRAVVARLPEGVTGLGDPGTA +LVPDWVEADPVRAEVAGAAQTFAPVRAGSLSSGVYVAAEPLREAGWDGAADAAVPGQLLV +ALDPGVPVDRLQGLSEDVTRAAGDGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI +ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGAIAIEAVLIAAVAAVLGCALGVCYG +WAGAQLVLADLSATAGAGTAVRPVVPWLELGLVVAVAALAGLAASLLPARRAARLSPVAG +LAAV +>PROKKA_01878 +MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL +PGGSEDVSDLAGTSAEPGPLARLDGVEEAYALRMAWAAARAADAEFGAAVMPLPRDPALA +GLTVTAGALPAADDARGVTLDAQTADRHGVAVGDVVALASESGPDSTTTPVDAVVTGLTQ +PSPDPMLSGQAQVWASPAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA +GVDVDVAAPDEAVRSVVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD +LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG +LHPAGLAVSVAVGVAVTVVAALAPAVAATRVAPLKALRPRDEVTAASRGGRVRTAIGLAL +AVGGTALMLGGVSVREPVSAIGGGALSFVGVLLLARLFVPAAVRGAAVLARPAGVPGRLA +GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD +PARAAEAVAATADVQAVALATSVGATEDGSPVLATPAADLRAVVARLPEGVTGLGDPGTA +LVPDWVDTDQVRGQVAGAERTFVPVRAGSLSSGVYVAAEPLREAGWDGAAGAAVPGQLLV +ALDPGVPVDRLQGLSEDVTRAAGTGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI +ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGTIAIEAVLIAAVAAVLGCALGVFYG +WAGAQLVLADLSATAGAGTAVRPAVPWLELVLVVAVAALAGLAASLLPARRAARLSPVAG +LAAV +>PROKKA_00593 +MWTVALSQLRAQPRRYVSLVLAILIGTMFLAASFLVSASAQATLRTTLGNTYSAADLVVL +PEPSDHADEDPTAAFPGLAGTPAEPGALGRVDGVEEAYATQFTWAGGSAGGTEFTATLLP +VPGDVSLLPVTLTEGAFPAADDARGVTLDTGTAERTGVAVGDEIALTGAPGAGGETATVV +GLTTRSPDPTLSSGAQIWAAAPVIAAVNPPQDGEAGGSGAYSPHVLLRLTDGADRDAVAD +AAAAVLAQEGVAASVTTPDEAVRDTLAEAGGGTDVFGWVLGGFAALALLVTALVIGNTFQ +VLVAQRTRDLALQRTLGSTAGQVRGSVLTEAVVVGLVGSVLGVALAVVGLLAGVAFVRSA +FDLPTLTFGMDPAGLAITVVVGVLVTLVAALSPAVAATRVSPLQALRPREEVTVASRVGV +VRTVVGAVLAVGGTALMLWGAFRPEPLTAVGGGALSFIGVLLLATLFVPAAVRGAAVLAR +PAGVPGRLAGLNATRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDL +VLSLPADGDAARAAEAVAARDDVAAVALALPVGATENGSPVLATPGADLRKVVAELPDGE +DGLGDPGTAFVPGWVDEDTVTATVAGTEQTFSAVRAGDLSSGVYVEADSLRAAGWDGSPL +ATDGVEVPGQLLVALAGDVPVDRLQALSEDITAAAGEGASIIDGGAPTRAVYAQVIDVML +WIVVGLLAVSVLIALIGVANTLSLSVIERTRENALLRALGLPRGGLRGMIAIESVLIAAV +AALLGCVLGVFYGWAGSQLILGELVETVGRGGTVLPTIPWLELALVVGVAAVAGLAASLL +PARRAARLSPVAGLATV +>PROKKA_00516 +MWTVALSQLRARRRRYASVVLAVLIGTMFLAASFLVASTAQATLRTTLGSVYAGADLVIQ +PEDDPETSADASGPPPGQRLAALAGTPETPGALARLDDVAEAWAPTPGFAEAAAPGGGTP +RPAAVIPAPAHPDLLGVRAVAGALPDPADARGVAVDEETARALGVGVGDELPLTGEPTRA +PVRATVTGLTSVSPDPMLSSQAQVWASRPVAQDLAPDGQVPYTTAVLLRLAPGADREAVA +EAAARALHDDGVPAAVQTPDQAVRDQLASLSGGTDLLGWVLGGFALLALVVTALVIANTF +QVPVAQRTRELALLRAVGAEARQVRGAVLLEAVATGLTGAVAGVVLAVGLTAAVVAVARG +ALGADALTLGVDWLPLAGAVALGTAVAAVAALGPARAATRVAPVQALRPVDEAPVRSRVG +LVRAGLGLLLAVGGAALMWWGAWGSAFAAALGGGVLSFLGVLLLARLFVPGAVRAAAVLA +RPAGVPGRLAGLNAVRHRRRTAATASALLIGTTLVALVLTGGRTAQIRLDALLDEEYPVD +LVVSVPAGGDLAAATRALGAVDGVGSVAAASPVGATVNGSPAYAVEADALRSVVAALPDG +QDRALGDGASVLVPAWAGATTEVVVDGRVSGLASVRGSGLTTGVFLTPETAEWVRRHGVA +ADAGTASDAAGPAAEDQAVAGLVLVAAADDVSVNRLQEMSAALTAAAGAGASIVDGGAAE +RAVYAQIIDALLWIVVGLLAVSVLIALIGVANTLSLSVIERTRENALLRALGLTRGGLRG +MIAVEAVLVAGVAAVLGCGLGVLYGWAGSQLVLGQLVAQLGEDRALVWPEVPWAELALVV +AVAAVAGLLASLAPAGRAARLSPVEGLATV +>PROKKA_02109 +MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL +PGGSEDVSDLAGTSAEPGPLARLDGVEEAYALRMAWAAARAADAEFGAAVMPLPRDPALA +GLTVTAGALPAADDARGVTLDAQTADRHGVAVGDVVALASESGPDSTTTPVDAVVTGLTQ +PSPDPMLSGQAQVWASPAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA +GVDVDVAAPDEAVRSVVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD +LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG +LHPAGLAVSVAVGVAVTVVAALAPAVAATRVAPLKALRPRDEVTAASRGGRVRTAIGLAL +AVGGTALMLGGVSVREPVSAIGGGALSFVGVLLLARLFVPAAVRGAAVLARPAGVPGRLA +GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD +PARAAEAVAATADVQAVALATSVGATEDGSPVLATPAADLRAVVARLPEGVTGLGDPGTA +LVPDWVDTDQVRGQVAGAERTFVPVRAGSLSSGVYVAAEPLREAGWDGAAGAAVPGQLLV +ALDPGVPVDRLQGLSEDVTRAAGTGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI +ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGTIAIEAVLIAAVAAVLGCALGVFYG +WAGAQLVLADLSATAGAGTAVRPAVPWLELVLVVAVAALAGLAASLLPARRAARLSPVAG +LAAV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001697.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001697.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a87133c352778785b093cc8c2f7766b226537b8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001697.fa @@ -0,0 +1,30 @@ +>PROKKA_02173 +MAELKKVLPELSHPDGAPVRVLVVDDEPMIADLLSMGFTLCGWEVIVAHDGATAAELGTA +GRPDLAILDVMLPDMDGLDVLDRLRAHWSEMPAMFLTAKDATEDRVAGLAAGSDDYVTKP +FSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGDEIELTATQYNLLKF +LMANVRTVLSKERILQDVWGYDFGGRANIVELYISYLRKKIDADRDPMIHTIRGAGYVIR +PA +>PROKKA_01887 +MAELKKVLPELSHPDGAPVRVLVVDDEPMIADLLSMGFTLCGWEVIVAHDGATAAELGTA +GRPDLAILDVMLPDMDGLDVLDRLRAHWSEMPAMFLTAKDATEDRVAGLAAGSDDYVTKP +FSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGDEIELTATQYNLLKF +LMANVRTVLSKERILQDVWGYDFGGRANIVELYISYLRKKIDADRDPMIHTIRGAGYVIR +PA +>PROKKA_00579 +MSRIQSTTSPSSMAELKKVLPELSHPDGSPVRVLVVDDEPMIADLLSMGLSLCGWDVVVA +HDGASAVEQGTARRPDLAILDVMLPDMDGLEVLERLRAHWPEVPAMFLTAKDATEDRVAG +LASGGDDYVTKPFSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGQVI +DLTATQYNLLKFLMANVRTVLSKERILQEVWGYDFGGRANIVELYISYLRKKIDADRDPM +IHTIRGAGYVIRPA +>PROKKA_00506 +MTSAEHTVSPASMAELRESLPDLTHQDGSPVRVLVADAEGLEADLLSMGYSLLGWETVVA +KDTAAAVQEGTARRPDLALLDAGLPDGGGLEVLARLRAHWAEMPAIVLASPAEAEDRIAA +LLAGADDVVAKPFAVEEILLRSHHLVRRAGLNASTGEELVVGDLVMNTRTHEVTRGGDLI +ELTATQFNLLKFLMANVRTVLSKDRILQDVWGYDFGGRANIVELYISYLRKRIDAGREPM +IHTVRGAGYVIRPAEG +>PROKKA_02118 +MAELKKVLPELSHPDGAPVRVLVVDDEPMIADLLSMGFTLCGWEVIVAHDGATAAELGTA +GRPDLAILDVMLPDMDGLDVLERLRAHWSEMPAMFLTAKDATEDRVAGLAAGGDDYVTKP +FSMEEVLIRAHRLVQRSGVVSGGSEVLVVGDLVMNTRTHEVTRGGDEIELTATQYNLLKF +LMANVRTVLSKERILQDVWGYDFGGRANIVELYISYLRKKIDADRDPMIHTIRGAGYVIR +PA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001698.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001698.fa new file mode 100644 index 0000000000000000000000000000000000000000..6a4aa1aebd0b62864876874d397c0067c4c85795 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001698.fa @@ -0,0 +1,35 @@ +>PROKKA_02175 +MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH +VYGTTEIPQRPTRVATVSWVNQDVTLALGVVPVGMAAVEFGGNAEKSTDWFDAKLAETEG +AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS +WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHADLQGASFVYGTIDPAAADQISIY +TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA +IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG +>PROKKA_01889 +MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH +VYGTTEIPQRPARVATVSWVNQDVALALGVVPVGVAAVEFGGNAEKSTDWFDAKLAETEG +AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS +WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHAGLQGASFVYGTIDPAAADQISIY +TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA +IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG +>PROKKA_00577 +MATVSWVNQDVALALGVVPVGMAAVEFGGNAEKSTDWFDAALEKVEGAERPVTWSEAAGI +DAEAVASVRPDVILAAYSGLTREDYDRLSKIAPVVAYPKDVPAFGTPWQQSTRMIGQALG +KDAEAEALVEDVEGRIAAAAQKHPDLKDATFVYGTVDPTAADQISVYTLVDNRPRFLESL +GMKQAPVVAENSPKDQAFFFTWSPERADELESDVLVSWALDASVADAIEADPLLSALPAV +QKDGLVLQVDQQEVLSVSAISPLSIPFALERIVPPIAEAAARSRG +>PROKKA_00504 +MPQSPSRRSVLAAGGSGLALLLAACSTGPAGSSVPSSSPASSAGSAAASSSASGSAAYPL +TVEHVYGTTEIPARPERVATVSWVNQDVALALGVVPVGVPAVEFGGNADKSTDWFDAKLK +ELGGPTPVQWSEADGIDAEAIAAVKPDVILAVYSGLTREDYDRLSKIAPVVAYPKDVPAF +GTSWQQSTEVIGRVLGKEREAAALVADLERQIADAGAEEDGLAGASFIYGTLDPAAADQI +SIYTAADNRPKFLELLGMELAPVVAENAPEDGAFFFTWSPERADELESDVFVSWAASADV +ADAIEADPLLGAIPAVEKGGLVLQVDQQEVLSVSAISPLSIPYALEKVVPPIAEAARAAK +G +>PROKKA_02120 +MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSSAGASSSDAAGGDAAFPRSIEH +VYGTTEIPQRPARVATVSWVNQDVALALGVVPVGMAAVEFGGNAEKSTDWFDAKLAETEG +AQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVPAYGTS +WQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHAGLQGASFVYGTIDPAAADQISIY +TDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQDSVREA +IESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKTAQG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001702.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001702.fa new file mode 100644 index 0000000000000000000000000000000000000000..89f4e1b60451794dff50869049cb380f1e5e7304 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001702.fa @@ -0,0 +1,36 @@ +>PROKKA_02179 +MSADGMIVAHTRVVSVEQPCRGFRRIVLAGPDLEAASGDLLGLLPPGVADLHALYRGARP +RRDAYVKLLIPPPGGTSADPDLSAGFRAGFLAIPEEERGWMRTYTVRSAGLVRLDGRQVP +SLTVDVVLHGDPDDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSGWRQTGAHRVL +AVGDETAVPALVSVAEELADPFGGFDGEADLVLELPHDGQAADLIAERLAVPEPWDWRAV +TELTDRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPVAPPAASVEREWTVAA +LEADERPEAYVFLAGESAMVRALRRLSVGPGGVPKKHVSFMGYWREGQAES +>PROKKA_01893 +MSADGMIVAHTRVVSVEQPCRGLRRIVLAGPDLEAASGDLLGLLPPGVADLHALYRGARP +RRDAYVKLLIPPPGGTSADPDLSAGFRAGFLAIPEEERGWMRTYTVRSAGLVRLDGRQVP +SLTVDVVLHGDPDDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSGWRQTGAHRVL +AVGDETAVPALVSVAEELADPFGGFDGEADLVLELPHDGQAADLIAERLAVPEPWDWRAV +TELTDRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPVAPPAASVEREWTVAA +LEADERPEAYVFLAGESAMVRALRRLSVGPGGVPKKHVSFMGYWRQGQAES +>PROKKA_00573 +MSEGMFVAHTRVVSVEQPCRGFRRIVLAGPDLERASPDLMGLLPPGTADLHALYRGSRPR +RDAYVKVLIPPPGGVSADPDLSAGFRAGFLAIPEAERGWMRTYTVRSAGPVRLDGRPVPS +LTVDVVLHGDADDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSAWRQTGARRVLA +VGDETAVPALVSVAEELADPFGGFDGVADLVLELPHDGQVADLIAERLAVPEPWDWRQVT +ELADRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPVAPPAASADREWSVAAL +AEDERPEAYVFLAGESAMVRALRRLTVGPGGVPKAHVSFMGYWRQGQAES +>PROKKA_00500 +MSTEAMFVAHTRVVSTSQPCRGFRRIVLAGEDLEHASADLLGTLPPGVPDLHAIYRGSRP +RRDAYVKVLVPPPGGVSADPDLSAGFRAGFTAVPEDERGWMRTYTVRSAGRTRVDGREVP +ALTIDVVLHGDPDDAADPHQGPGLRWARTVAAGESVNVLVPTGEAPAWAGWRDTGARRVL +AVGDATAAPALLSVAEELADPFGGFDGEADLVLELPADAELADLIAERLAVPEPWDESRP +LDVAEHGRVRLHVGRTAPGRPVGAWAQARLGALLGLSGTARAGVVGVDGVVEAPPAEGAA +REWTLADLEPVTGVDRPDTYVFLAGESGMVRALRRLAVDGGDIPKKNVSFMGYWRQGQAE +S +>PROKKA_02124 +MSADGMFVAHTRVVSVEQPCRGFRRIVLAGPDLEAASRDLLGLLPPGVADLHALYRGARP +RRDAYVKLLIPPPGGTSADPDLSAGFRAGFLAIPEEERGWMRTYTVRSAGLVRLDGRQVP +SLTVDVVLHGDPDDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSGWRQTGAHRVL +AVGDETAVPALVSVAEELADPFGGFDGEADLVLELPHDGQAADLIAERLAVPEPWDWRAV +TELADRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPVAPPAASVEREWTVAA +LEADERPEAYVFLAGESAMVRALRRLSVGPGGVPKKHVSFMGYWREGQAES diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001703.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001703.fa new file mode 100644 index 0000000000000000000000000000000000000000..2301e045054f8fd6b14ef8b4c3348bd14d06ce48 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001703.fa @@ -0,0 +1,25 @@ +>PROKKA_02180 +MTRTVIIGGHGKVALLAAPLLAEAGHDVVSIIRNPDHAEDVRAAGAEPLVLDIEKADQEE +LLHALRDADNVVFSAGAGGGDAQRTRAVDHDAAVASMRAAEAAGVRRYVMVSYLGASLHH +DVPEDDPFYTYAQAKAEADEALRDSGLAWTILGPGALTDEEPSGRITVDPDLSDSDAPQR +GASRGNVARAIVAVLSEPGTVGRKIDFVDGDVPVAEAVRGD +>PROKKA_01894 +MTRTVIIGGHGKVALLAAPLLAEAGHDVVSIIRNPDHAEDVRAAGAEPLVLDIEKADQEE +LLHALRDADNVVFSAGAGGGDAQRTRAVDHDAAVASMRAAEAAGVRRYVMVSYLGASLHH +DVPEDDPFYAYAQAKAEADEALRDSGLAWTILGPGTLTDEEPSGRITVDPDLSDSDAPQR +GASRGNVARAIVAVLNEPGTVGRKIDFVDGDVPVAEAVRGD +>PROKKA_00572 +MTRTVIIGGHGKVALLAAPLLAEAGHDVTSIIRNPEHAAEVEAAGAAPLVLDVERAGEED +LVQAFRDADNVVFSAGAGGGDPARTRAVDHDAALATMRAAEAAGVRRYVMVSYLGASLHH +GVPEDDSFHAYAQAKAEADEALRDSGLAWTILGPAALTLEEPTGRITVDPDLDTPDAPKG +EVSRGNVARALVAVLADPTTVGRKIDFVDGDTPVAEAIRGA +>PROKKA_00499 +MDILIIGGHGKIALLTAPLLADAGHTVTSAIRNPEHADDVRTAGAEPLVLDVEHSSPAEL +EAAMRGRDVVVWSAGAGGGDPERTYAVDRDAAIASMDAARAAGVRRYVMVSYRGASVHHG +VPEDSSFFAYAEAKAAADEHLRGSHLDWTILGPGALTLDEPTGRVQVDPQGPSEELPGTS +RGNVARMIAAAVDSGASIGRQVEFVDGDTPVDDVFRR +>PROKKA_02125 +MTRTVIIGGHGKVALLAAPLLAEAGHDVVSLIRNPDHAEDVRAAGAEPLVLDIEKADQEE +LVHALRDADNVVFSAGAGGGDAQRTRAVDHDAAVASMRAAEAAGVRRYVMVSYLGASLHH +DVPEDDPFYTYAQAKAEADEALRDSGLAWTILGPGALTEEEASGRITVDPDLSGSDASQR +EASRGNVARAIVAVLSEPGTVGRKIDFVDGDVPVAEAVRGD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001704.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001704.fa new file mode 100644 index 0000000000000000000000000000000000000000..6c29f8345c6a79b675e77422a2d4813e727913a6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001704.fa @@ -0,0 +1,29 @@ +>PROKKA_02181 +MPLSTLRVSLPSVRRTRPAPQGVRGRIAHAVVSRLQPRPVPPVDRRSRLAWQVSGALPLI +GCLTSFPIGMSKDSMVIPGVGYQGGFPAGWSHALNQPAYFTWLSNALVAGTSLTLAARRE +APTSDAFWAVRTAGLGSVMVTGIVYNAVLRGREQDTFLYRFNDALQHIVNPVLAPAVWAL +CDPRGQITPRRAGLASVIPLMWAAATMARGPRIDWYPYPFLDVPRLGRRSVGVVLAGILA +GFTGLMGVLGTVDRRLGLA +>PROKKA_01895 +MPLSTLRVSLPSLRRTRPAPQGVRERIAHAVVSRLQPRPVPPVDRRSRLAWHVSGALPLI +GCLTSFPIGMSKDSMVIPGVGYQGGFPAGWSHALNQPAYFTWLSNALVAGTSLTLAARRE +APTSDAFWAVRTAGLGSVMVTGIVYNAVLRGREQDTFLYRFNDALQHIVNPVLAPAVWAL +FDPRGQITPRRAGLASVIPLMWAAATMARGPRIDWYPYPFLDVPRLGRRSVGVVLAGILA +GFTGLMGVLGTVDRRLGLA +>PROKKA_00569 +MLRLARPRSRRAPQGLGGRLVRAVAARPVPPVRPRARLAWHVSGALPLIGCLTSFPIGMS +KDSMVIPGVGYQGGFSAGWHHALNQPAYFTWLSNALVAGTSLTLATRRTAPTSDAFWAVR +TAGLGSVMVTGIVYNSVLRGREQDTVLYRFNDTLQHIVNPVLAPAVWALFDPRGQITPRR +AGLASVIPLAWAALTMARGPRIDWYPYPFLDVPRHGARTVGVVLAGILAGFTGLMGLLGG +LDRRLGGR +>PROKKA_00496 +MPAWLARFTRPRPAPRPSRAARAGWWAAGALPLVGCLTSFPIGASKPTMVIPGVGYHGGF +EAGWQHALNQPAYFTWLSNAMVAGTSLTLAARRDAPTSDAFWALRTAGLGSVMVTGIVYN +AVLRGMEQDTLLYRFNDAVQHVVNPVLAPLVWAAFDPRGQITYRRAGLAAVVPLMWATAT +LVRGARIDWYPYPFLDVPRLGWRGVGAAVSVVLAGFSAVLGLLGQVDRRLGTR +>PROKKA_02126 +MPLSTLRVSLPSVRRTRPAPQGVRERIAHAVVSRLQPRPVPPVDRRSRLAWQVSGALPLI +GCLTSFPIGMSKDSMVIPGVGYQGGFPAGWSHALNQPAYFTWLSNALVAGTSLTLAARRE +APTSDTFWAVRTAGLGSVMVTGIVYNAVLRGREQDTFLYRFNDALQHIVNPVLAPAVWAL +FDPRGQITPRRAGLASVIPLMWAAVTMARGPRIDWYPYPFLDVPRLGRRSVGVVLAGILA +GFTGLMGVLGTVDRRLGLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001705.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001705.fa new file mode 100644 index 0000000000000000000000000000000000000000..0a28b2063f6b9cbd8e7516e14c3102644318ef66 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001705.fa @@ -0,0 +1,45 @@ +>PROKKA_02182 +MRHPIPDYLASLITELGAVNPGETAQYIPVLAEADPDRFGIALATPTGRLHCAGDADVEF +TIQSASKPFTYAAALVDRGFAAVDRQVGLNPSGEAFNELSLEAESHRPDNAMINAGALAV +HQLLVGPEASREERLDRAVEIMSLLAGRRLSVDRETYESEMAVSDRNLALAHMLRSYGVL +QDSAEEIVAGYVAQCAVRVTVKDLAVMGACLATGGIHPMTGERVLPSIVVRRVVSVMTSS +GMYNAAGQWLADVGIPAKSGVAGGVLGALPGRVGIGVFSPRLDEVGNSARGVLACRRLSE +DFRLHLMDGDSLGGTAVRFVEREGDRVFLHLQGVIRFGGAEAVLDALTDLRTGAEKPGTG +WDAAVYPRWQEAAADRAALSAATGGGAVHEAAAVAARDENDGPIRTVVLNLTRVDWIDDV +GRRLIAEGVRRLQADGVRVEVEDPERILPLEEAGAH +>PROKKA_01896 +MRHPIPDYLASLITELGAVNPGETAQYIPVLAEADPDRLGIALATPTGRLHSAGDADVEF +TIQSASKPFTYAAALVDRGFAAVDRQVGLNPSGEAFNELSLEAESHRPDNAMINAGALAV +HQLLVGPEASRKERLDRAVEIMSLLAGRRLAVDRETYESEMAVSDRNLSLGHMLRSYGVL +QDSAEEIVAGYVAQCAVLVTAKDLAVMGACLATGGIHPMTGERVLPSIVARRVVSVMTSS +GMYDAAGQWLADVGIPAKSGVAGGVLGALPGRVGIGVFSPRLDEVGNSARGVLACRRLSE +DFRLHLMDGDSLGGTAVRFVEREGDRVFLHLQGVIRFGGAEAVLDALTDLRTGAEKPGTG +WDAAVYPRWQEAAADSAALAAATGGGAVYEAAAVAAQDENDGPIRTVVLNLTRVDRIDDV +GRRLIAEGVRRLQADGVRVEVEDPERILPLEEAGAH +>PROKKA_00568 +MRHPFVDYLEGLLGSLEHVTEGDVARYIPILAEADPSLSAVAVATTSGRVHTAGDADAEF +SIQSVSKPFTYAGALEDRGVELVDEYVALNPSGEAFNELSLEADSHRPDNAMINAGAIAV +HQLLVGPGATPAERTERAVSLMSTLAGRRLRVDERTFESEMATADRNLALGHMLRSHGIL +QDRAEDVVAGYIAQCSVMVTVRDLAVMGATLASGGLHPLTGERVLSSLVCRQVLSVMSSS +GMYDAAGQWMAHVGIPAKSGVSGAVLGALPGQVGIGTYSPRLDPFGNSVRGVEMCRIMSE +DLDLHIMEADVIGSTVVRSVRREGDTVHLHLQGVIRFGGGESVLAAMTELGTGADPDPVE +WAHCFYPFSEEPDTAAGRAAAQDEGRTAAEALEQEAPVRAVVVHLERVDRVAPVGRRLIE +DGLKRLRADGVQVRVEDPDGVLTGG +>PROKKA_00495 +MKHPVPDYLQHLVDSLREDRRGALADYIPVLAQADPERLGIALATVTGRLHSAGDDETEF +TIQSVSKPFAYAAALQDRGLDAVDARVGLNPSGEAFNELSLEAESKRPDNAMINAGALAV +HQLLVGPYAGRQERLDRLVGFMSTLAGRRLEIDRETFESEMATSDRNLSLAHMLRSHGII +QDRAEDVVAGYIAQCSVRVTVRDLALMGACLASGGVHPLTGERVLPSLVCRQVLSVMSSS +GMYDAAGQWLVNVGIPAKSGVSGAVLGALPGQVGLAVFSPRLDEVGNSVRGVEACRRMSE +DMDLHLMEGDSLGGTVVRFARREGDTVLLHLQGVIRFGGGEAVVTAMTDLGTGAAGGGRA +AWSEHDYPEWEDAPHGDVAAEAGDRRPVDAADPEAARAAATGDGSVHEAAACAVAEDGLP +IRTVVLNLERVDRVTAVGRRLIDEGVDRLRADGVAVEVVDPDGLLG +>PROKKA_02127 +MRHPIPDYLASLITDLGAVNPGETAQYIPVLAEADPDRFGIALATPTGRLHCAGDADVEF +TIQSASKPFTYAAALVDRGFAAVDRQVGLNPSGEAFNELSLEAESHRPDNAMINAGALAV +HQLLVGPEASRKERLDRAVEIMSLLAGRRLSVDWETYESEMAVSDRNLSLAHMLRSYGVL +QDSAEEIVAGYVAQCAVLVTAKDLAVMGACLATGGIHPMTGERMLPYIVARRVVSVMTSS +GMYDAAGQWLADVGIPAKSGVAGGVLGALPGRVGIGVFSPRLDEVGNSARGVLACRRLSE +DFRLHLMDGDSLGGTAVRFVEREGDRVFLHLQGVIRFGGAEAVLDALTDLRTGAEKPGTG +WDAAVYPRWQEAAADSAALSAATSGGAVHEAAAVAARDENDGPIRTVVLNLTRVDRIDDV +GRRLIAEGVRRLQADGVRVEVEDPERILPLEEAGAH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001706.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001706.fa new file mode 100644 index 0000000000000000000000000000000000000000..e563ba390bb6bfab18638ba350f2e3f497aaf15c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001706.fa @@ -0,0 +1,26 @@ +>PROKKA_02183 +MTSPDPAPPRPRVHVLTLRPDGAREDTARRVGIVLAEAFATDPYTLGLVPEDRREARLER +KFTAAVRHGLRTGADGAPLGAVDVAVDADDGTLLGAAVWTSPAAPRGVDVPGLLAGLPTA +VAVHGRHTLALKRIQAACERARPAGRHWYLEEVGAVPSARGRGAASALVRHGQRRASGLP +VHLEASVPATVPFYERLGFRATGHVPVPGGEPLTCLRWEA +>PROKKA_01897 +MTSPDPAAPRPRVHVLTLRPDGAREDTARRVGAVLAEAFATDPYTLGLVPEDRRGPRLER +KFTAAVRQGLRAGADGAPLGAVDVAVDAADGTLLGAAVWTSPAAPRGVDVPGLLAGLPTA +VAVHGRHTLALKRIQAACERARPAGRHWYLEEVGTVPSARGRGAASALVRHGQRRASGLP +VHLEASVPATVPFYERLGFRATGHVPVPGGEPLTCLRWEA +>PROKKA_00567 +MTSPDRAAPPAPPTPAFGPAPEAPAADNAAPARRRLQVVSLRPEGLSEDAVGRVAELLAE +AFAEDEFTLGLLPADRRAERLARMFALDVHDALRPARAAGGEAGPRGAVDVALDPEDGTL +LAAAVWDGPDAPRGTTVPGALAALPARLRVHGRRTWDAARTDAACERARPAAAHWHLTQL +GTAPAARGRGAASALVRLRQRRAARAGVGIHLEASSAEAVPFYARLGFRETGTVRAHGTR +DLTAMWWEAQA +>PROKKA_00492 +MSDAARRPRPLVTSLRPAAAADHPDAAAVAGMAGALAEAFAEDPYTTSFLPPDRREERLR +DYFDLLVRESLDAAARGHGAVDAAVDPRTGEVLGVALWERPGAPRPPAGLLGALRPAVPT +AARRWRAFGRHALDHVRTVAACQAVRPSEEHWYLLELGTVPSARGRGAGRALLERRRREA +RAAGVGIYLESSSAESTRFYEHVGFRPHGTATVHGADDLTTMWWKD +>PROKKA_02128 +MTSPDPAAPRPRVHVLTLRPGGAREDTARRVGAVLAEAFATDPYTLGLVPEDRREARLER +KFTAAVRHGLRAGADGAPLGAVDVAVDADDGTLLGAAVWTSPAAPRGVDVPGLLAGLPTA +VAVHGRHTLALKRIQAACERARPAGRHWYLEEVGTVPSARGRGAASALVRHGQRRAAGLP +VHLEASVPATVPFYERLGFRATGHVPVPGGEPLTCLRWEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001710.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001710.fa new file mode 100644 index 0000000000000000000000000000000000000000..e1bec1c450414d24a5c4f0b216f8331d239ee4ff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001710.fa @@ -0,0 +1,41 @@ +>PROKKA_02190 +MPPPVPQPTRRQMLLAGSALLGSGLLAACGQDGEDAASSSVPTSSAPTSAAPAGPPPAGE +PVAWPDVARVPHLFFHSLVVDPARAFDGDDKARGYLDFMVTVDEFDAVIRQVYERGYVLV +SPHELYEVGEDDVVRPKTLMVPEGRTPLILSLDDCSYYLYMDGDGFADRLIVAEDGRVRN +EYTDAQGTTHVGAFDVVPRLDDFLAEHPDFSLNGARGVLAMTGYDGVFGYRTSAREFGDS +PTFDADVAAATEVADALKDSGWEFASHTWGHRTVPKLTMEELEFDMGHWHEEVEPILGPT +DMLIYPFGADVTGPGKYTEDNERYRYLRELGYRSFFLVDGTSKAWGQLEPGYYRGSRINV +DGISLAAAVSGERPVLEEFFDPRSVLDPARPESIRGPKKPSPAPSSPAAAPRTPRP +>PROKKA_01904 +MPPPVPQPTRRQMLLAGSALLGSGLLAACGQDGEDAASSSVPTSSAPTSAAPAGPPPAGE +PVAWPDVARVPHLFFHSLVVDPARAFDGDDKAGGYLDFMVTVDEFDAVIRQVYERGYVLV +SPHELYEVGEDDVVRPKTLMVPEGRTPLILSLDDCSYYLYMDGDGFADRLIVAEDGRVRN +EYTDAEGTTHIGAFDVVPRLDDFLAEHPDFSLNGARGVLAMTGYDGVFGYRTSAREFGDS +PTFDADVAAATEVADALKDSGWEFASHTWGHRTVPKLTMEELEFDMRHWHEEVEPILGPT +DMLIYPFGADVTGPGKYTEDNERYRYFRELGYRSFFLVDGTSKAWGQLEPGYYRGSRINV +DGISLAAAVSGERPVLEEFFDPRSVLDPARPESIRGPKKPSPAPSSPAAAPRTPRP +>PROKKA_00554 +MAPSRRQILLTGSALLGSGLLAACSSEGGSAPASSSPAGTPAPAPSSSSAAPAGPGPAGE +PVAWPNTALVPHLFFHSLVVDPKRAFDGDHKEAGYLDFMVTMDEFAAILPQLYAKGYVLV +SPHELYEVGEDDVVRPKTLMVPENRTPLVFSLDDCSYYLYMEGDGFADRLIVDEDGRVRN +EYTDADGTTHVGSYDMVPMLDDFLEEHPDFSLNGARGVLAMTGYEGVFGYRTSAREFGDS +PTFDADVAAATEVADAMKATGWEFASHTWGHRTVPKLELDELQRDLELWHGEVEPILGPT +DMMIYPFGADVARTGKYEADNERYQYMRSLGYRSFFLVDGTAKAWGQLEPGYYRGSRINV +DGISLEAAISGKRPVLDEFFDSRSVLDPARPASIRGTQQSPAAPPGGQSGSASPSATG +>PROKKA_00483 +MEYSRRHVIFGGSALLGAGLLAACAPAQDGAAPSAGGGSSSEAASSSAAPSPSSTRPVIP +SAPEPAGKPVAWKDVAKVPHLFFHSLVVDPEKAFHVHGESDGYLNYMVTQAEFERILPQL +WALGYVLVSPHELYEVGRDDVVRARTLMVPENRTPLIISLDDCSYYEYMEGDGFATRLLV +DDSGRVRTEYTDQEGKTTIGANDLVPILDDFVRDHPDFTLNGAKGVLALTGYNGVLGYRS +SPTMYPEGPELDEAVATAKEVVAAMKETGWEFASHSWSHRSMAQMSLADLKEDCERWIED +VQPIVGPTDMLIYPFGADIAGIEKYSGPEYEHLRSLGFRSFFLVDGSSKAWGQLEPGYYR +GSRINVDGISLAGAKDGSRPVLDEFMDVDSVLDPARPESIHAPSYVPPEERAAASSGAPS +ASPSS +>PROKKA_02135 +MPPPVPQPTRRQLLLAGSALLGSGLLAACGQDGEDAASSSVPTSSAPTSAAPAGPPPAGE +PVAWSDVARVPHLFFHSLVVDPARAFDGDDKAGGYLDFMVTVDEFDAVIRQVYERGYVLV +SPHELYEVGEDDVVRPKTLMVPEGRTPLILSLDDCSYYLYMDGDGFADRLIVAEDGRVRN +EYTDAEGTTHIGAFDVVPRLDDFLAEHPDFSLNGARGVLAMTGYDGVFGYRTSAREFGDS +PTFDADVAAATEVADALKDSGWEFASHTWGHRTVPKLTMEELEFDMGHWHEEVEPILGPT +DMLIYPFGADVTGPGTYTEDNERYRYFRELGYRSFFLVDGTSKAWGQLEPGYYRGSRINV +DGISLAAAVSGERPVLEEFFDPRSVLDPARPESIRGPKKPSPAPSSPAAAPRSPRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001711.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001711.fa new file mode 100644 index 0000000000000000000000000000000000000000..1d8061cc6ae2053f013f6558eabd3afcc54447f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001711.fa @@ -0,0 +1,24 @@ +>PROKKA_02194 +MTSAPRAAVVRPARPEDAPAIAAIAAATFPDASPSSLPRAAVEAHIALHLSEAAVAAWIA +DPERIVLVGAAADAPETLLGYAMYETAATPEAPVTERLGDVPAGHLSKLYVLAEGRGTGL +AEALVHDGVERLRRLGFRHVWLGTNAQNTRANRFYERLGFATIGARQFVVGGERVEDDWV +RLLTVE +>PROKKA_01907 +MTSAPRAAVVRPARPEDAPAIAAIAAATFPDASPASLPRAAVEAHIALHLSEAAVAAWIA +DPERIVLVGAAADAPETLLGYAMYETAAAPEAPVTERLGDVPAGHLSKLYVLAEGRGTGL +AEALVHDGVERLRRLGFRHVWLGTNAQNARANRFYERLGFETVGARQFVVGGERVEDDWV +RLLTVA +>PROKKA_00546 +MIQAHIDEHLNERVVAAWIADPARIVLVGGTAPDEVLGYAMLETAATPEAPVVEHLGETP +AGHLSKVYVLAESRGTGLAETLVRDGVARLEALGFRHVWLGTNAQNARANAFYERLGFEK +IGARTFVVGGTRVEDDWVRLLSLG +>PROKKA_00482 +MPTSPTPRPVPAVIRPATPADVPALVRVAAETFPDACPPTTSQEAKDEHIASSLNAEVIG +GWVAGPGHAVHLAEAPAGRDDAGRLLGYVMAELAPEEEPAVTAVLGEGAAVGCLSKLYVV +REARGTGAAAALMAAGLDALRVRGLTHAWLGTSEENHRANAFYERVGFRTVGSRTFLVGG +RPERDNVRLITP +>PROKKA_02138 +MTSAPRAAVVRPARPEDAPAIAAIAAATFPDASPASLPRAAVEAHIALHLSEAAVAAWIA +DPERIVLVGAAADAPETLLGYAMYETAAAPEAPVTERLGDVPAGHLSKLYVLAEGRGTGL +AEALVHDGVERLRRLGFRHVWLGTNAQNARANRFYERLGFETVGARQFVVGGERVEDDWV +RLLTVE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001714.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001714.fa new file mode 100644 index 0000000000000000000000000000000000000000..1a09bc9d17a7974bacebf3bcf0fd82e0b9ee5f12 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001714.fa @@ -0,0 +1,25 @@ +>PROKKA_02197 +MATRPRREDVRAAILDHAARVFGREGYARSSLARIAAEAGYTKGAVYSGFAGKPDLFAAA +CTVQFERATTRAMDGVADALDDPDLPREDLVARVAEALADVVLETTGSWPLLLHEFQAVG +LREPAVGRAYRTLTVRRRDFLAGLLREHRVLADVPDEQVTHTAAMLLMLVHTLSVERHLA +PEDLTVDDVRDTLAAAVRSLLP +>PROKKA_01910 +MATRPRREDVRAAILDHAARVFGREGYARSSLARIAAEAGYTKGAVYSGFAGKPDLFAAA +CTVQFERATTRAMDGVADALDDPDLPREDLVARVAEALADVVLETTGSWPLLLHEFQAVG +LREPAVGRAYRTLTVRRRDFLAGLLREHRVLADVPDEQVTHTAAMLLMLVHTLSVERHLA +PEDLTVDDVRDTLAAAVRSLLP +>PROKKA_00547 +MATRPRREDVRAAILDHAAQVFGREGYARSSLTRIAAEAGYTKGAVYSGFAGKPDLFAAA +CTVQFERATTQAMDGVADALDDPDLPREDLVARVAEALADVVLEPTGSWPLLLHEFQSVG +LREPAVGRAYRVLTVRRRDFLAGLLREHRVLADVPDAQVTHTAAMLLMLVHTLTVERHLA +PEDLTVDDVRDTLAAAVRSLLP +>PROKKA_00480 +MGGLRGVRRFDTVGIQYHRYRKGKMASRPRHQDVRADLLQYATEAFERDGYGRASLAGIA +ADAGYTKGAVYSGFGSKAALFAEVCGAQFEALTRRTLDVVGRELAVEGGGRADLVARLAA +VLTSLTFDGDARWPLLLHEFQAVGLRDESVASEYRALTARRVRFLAEALGEHPRLAGLSA +ERLERTSSLTLVLVHTLAVEHRLSPEAMDRRGGELSFTALLDSALPD +>PROKKA_02141 +MATRPRREDVRAAILDHAARVFGREGYARSSLARIAAEAGYTKGAVYSGFAGKPDLFAAA +CTVQFERATTRAMDGVADALDDPDLPREDLVARVAEALADVVLETTGSWPLLLHEFQAVG +LREPAVGRAYRTLTVRRRDFLAGLLREHRVLADVPDEQVTHTAAMLLMLVHTLSVERHLA +PEDLTVDDVRDTLAAAVRSLLP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001715.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001715.fa new file mode 100644 index 0000000000000000000000000000000000000000..89e5b63e487db419e475f02260c25033d36ae605 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001715.fa @@ -0,0 +1,30 @@ +>PROKKA_02198 +MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA +VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL +QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL +TSLVTKSLFGAAVPAGLHVPWPVWVAVVVGGPLGVLLGSVVARRVDPAKARVLAICLAGV +GGTVALVRGVAGTLG +>PROKKA_01911 +MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA +VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL +QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL +TSLVTKSLFGAAVPAGLHVPWPVWVAVVVGGPLGVLPGSVVARRVDPAKARVLAICLAGV +GGTLALVRGVAGTLG +>PROKKA_00545 +MSVVVLTGADGGARLGHTAPMDMSLVMLVPALVALAALMVGGALQRVSGMGVGMIAGPTL +SLLLGPVAGVSLANVAAVVSAVLLFALLRRHVDWGRFLRLAPLLIVGSFAGAWAVRSLDV +HALEVLLGGSVLVAIAASLGLQRRFTASGSAPAALAGTAAGFMNTTAAVAGPALAVYAVA +SRWEQRSWAATLQPIFLLANLTSLATKSLFGTAVPASVDVHWTVWTAVVVGGPIGVLIGS +RIAPRVNPSRARLLAICVAGVGASVALLRGIVGLLA +>PROKKA_00481 +MAATAAAAVRTAERARSGGGVTVPVWHAPAVASRRRGARAHTAGVSISLAAVVFLCVAVG +GVLQRISGMGVGMVAAPTLSLLVGPVAGVTMSNAAASVSALILFWMLRRHVDWPRFLRLA +PLLVVGALAGAWTVRVMDHAWLEVVLGACVLVAIAAVLGLQDRLTLRGSAAVFGSGAVAG +FMNTTAGVAGPALAVYAVASKWEQRSWAATLQPIFLTANVTSIVLKASLGATAGAAAVPW +WAWAAAVAGAPAGIAVGSRLARRVDPGRARRVAVTLAGVGAAVTLVRGLASL +>PROKKA_02142 +MDPSLVWLPAVVALAAITVGGTLQRVSGMGVGMIAAPTLSLLLGPVAGVTLSNVAASVSA +VLLFAVLHRHVDWPRFVRLAPLLVAGSFAGAWAVRVLDAHALEILLGSSVLVAVAAVLGL +QQRFTAQGNGAVFASGAVAGFMNTTAGIAGPALAVYAVASRWDQRSWAATLQPVFLLANL +TSLVTKSLFGAAVPAGLHVPWPVWVAVVAGGPLGVLLGSVVARRVDPEKARVLAICLAGV +GGTVALVRGVAGTLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001716.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001716.fa new file mode 100644 index 0000000000000000000000000000000000000000..8798f59ab455cd69eaecba889cee85cdd20baae9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001716.fa @@ -0,0 +1,30 @@ +>PROKKA_02200 +MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF +TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT +PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG +VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR +>PROKKA_01913 +MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF +TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT +PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG +VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR +>PROKKA_00542 +MLAAVLAFALIGAVLWAALALGPDGVPGQQGSRRPAASTPAPPTVSAEGFAEPVRGRVTS +RFGPRPNPFGEGSAPPSTDTDALTDHTGVDLGGVPEGTPFHSVSDGRVLFVEAGEDAGGN +LLAVDSGDGHVWRYLHAAPDSTVVNAGQRVSAGDALAGVGQTGTATGVHLHLELRVDGTP +VDPEPYLRERGVELGSSWERPRRR +>PROKKA_01787 +MKKLAVIAAVLVLFSPALLLLGVGMIFSPGANASCTTSTTGPSVVGPVPDSLDVTTADGQ +TFTLNTTQLTHAATIIQTGSQIEGVTRDGLQIALMAALTESNLRMLANTSVYPDSGNHPN +DGDASDHDSLGLFQMRPQAGWGTVPDLMDPGYQARAFFGGPTGPNHPSPRGLLDIPGWQT +LSKGEAAQAVEVSAYPDRYANYEPVAEQILTTLTTPTADSPQLPETGRVVFPLPEGTWVA +TSPFGMRVHPITGENKLHTGADYSAPDGTPVLAAADGIVTHASMSGGYGGLIIIEHTTGG +QKIATAYAHLWETGIHVNVGDQVTAGQHIGDVGSAGYSTGAHLHFELRQGGSDGEFTDPQ +PWLDQHTSGNLPAPTTPVEQEGCNPVATQPAPPQGPDAGDPDRKVDDPTTDGQITARMLH +VYTQALTAYPDSSWACYSPRPGTKSEHPLGRACDVTFGNAIGSRPTPQQLEAGWALTNWL +QDNAETLGVEYLIWQGQIWSLARDAEGWRPYNGGGMHDPTDVTGGHYDHVHITVKEGS +>PROKKA_02144 +MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF +TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT +PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG +VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001717.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001717.fa new file mode 100644 index 0000000000000000000000000000000000000000..19550910410b0f3c8812dc2672551c52ee58c96e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001717.fa @@ -0,0 +1,20 @@ +>PROKKA_02201 +MPHSLSLRPLRVDDAEAMAAVLADPDLYTYTGGTPPGEEELRQRYAILARGRSEDGAEDW +ANWIVVLEPEGRPVGYVQATIPVDGGPTQIAWLIGTPWQGRGLAKEAAGLLKGELRDRGV +RRLVADVHPEHTASQRVAQAIGLAPTDEVVDGEVRWAGSVDDGGGPVTG +>PROKKA_01914 +MPHSLSLRPLRVDDAEAMAAVLADPDLYTYTGGTPPGEEELRQRYAILARGRSEDGAEDW +ANWIVVLEPEGRPVGYVQATIPVDGGPTQIAWLIGTPWQGRGLAKEAAGLLKGELRDRGV +RRLVADVHPEHTASQRVAQAIGLAPTDEVVDGEVRWAGSVDDGGGPVTG +>PROKKA_00496 +MPSRLHLRPLTVADAEEMSAVLADPALYAHTGGEPPSEELLTQQFRIQTRGESADGSERW +QNLIVVLEETGEAVGYVQATTPKDGGPTEVAWVIGVPWQGRGLGGEAAAQLVEHLAGQGV +RELIADIAPGHAASEAVARHIGLEPSDVVVDGEVRWTGTVADRER +>PROKKA_01297 +MTPPIHLRPLRPDDADEMVAVLADPALYTFTGGEPPTRGALSGQYAVQARGHSEDRSETW +LNHLVVLDDTGEAVGYVQATIPVAGGAAEIAWVIGVPWQGRGHATAAARLLLDELARRGV +SEVVADIHPGHAASAAVARRLGLRPTGHIVDGEQRWEGPVAVVDGAASAPGG +>PROKKA_02145 +MPHSLSLRPLRVDDAEAMAAVLADPDLYTYTGGTPPGEEELRQRYAILARGRSEDGAEDW +ANWIVVLEPEGRPVGYVQATIPVDGGPTQIAWLIGTPWQGRGLAKEAAGLLKGELRDRGV +RRLVADVHPEHTASQRVAQAIGLAPTDEVVDGEVRWAGSVDDGGGPVTG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001725.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001725.fa new file mode 100644 index 0000000000000000000000000000000000000000..1bae836008082144d93112c6688050bf3542d942 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001725.fa @@ -0,0 +1,40 @@ +>PROKKA_02240 +MSAAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPTAPGADVPFQYA +RWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLPADGYGPTRALA +AEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVAARAHANGRRDG +AGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASRDPQVMARVRGW +RTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRAVVYPGLADHPD +AEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAERRARWGDDVPD +GFVRLSVGVEPTAELLADLERAMTAAGGGPTA +>PROKKA_01942 +MSAAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPTAPGADVPFQYA +RWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLPADGYGATRALA +AEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVAARAHANGRRDG +AGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASRDPQVMARVRGW +RTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRAVVYPGLADHPD +AEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAERRARWGDDVPD +GFVRLSVGVEPTAELLADLERAMTAAGGGPTA +>PROKKA_00505 +MPDSAARHSAARHDVPAPPPFGPVLHHRAHGMAPGDAISPPLVHASAFHLPGAGPDGAPA +EPAAQGGFQYARWGTPTWAALEAALGVLEDADVAVVPSGMAAIASVLLSHLRPGDRALLP +SDGYGATRALAAEHLSPIGVHVDLVPTPALASADLSAYDLVFVETPSNPGLRVADLADVA +ARAHANGRRGGAGALVVVDNTSLTPLGQRPLDLGADVVVASDTKALNGHSDALGGHVASR +DADVLARVRGWRTLTGAILGTHEAWLIHRGLETLEVRFARMCASALAVAELAAGHSAVRA +VAYPGLPDHPDAEVVARQTTAAGSVVGLEFADAAAAERFLAAARLVVPQTSFGGTHTSAE +RRARWGDDVPAGFVRLSVGVEPTAELLADVERALEAAG +>PROKKA_00441 +MASPQPPAFGPVLHHRAHGMAPGDAISPPLVHASAFHLPGAGPDGAPVAPGADVAFQYAR +WGTPTWAALEAALGVLEDADVAVVPSGMAAIAAALLPVLRPGGRALLPSDGYGATRALAA +EHLVPAGVHVDFVSTPGLADAGFSAYDLVFVETPSNPGLRVADLADVAARAHANGRRDGK +GALVVVDNTSLTPLGQRPLDLGADVVVASDTKALNGHTDALGGHVASRDPELMTRVRGWR +TLAGGILGTHEAWLIHRGLETLEVRFARMCASALAVAELAAGHPAVRAVAYPGLPDHPDA +AIVARQMTAAGGVVGLEFADAAAAERFIGAAAYVVAQTSFGGTHTAAERRARWGDDVPAG +FVRLSVGVEPTAELLTDLARALDAAAGPA +>PROKKA_02172 +MSAAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPTAPGADVPFQYA +RWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLPADGYGPTRALA +AEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVAARAHANGRRDG +AGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASRDPQVMARVRGW +RTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRAVVYPGLADHPD +AEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAERRARWGDDVPD +GFVRLSVGVEPTAELLADLERAMTAAGGGPTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001727.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001727.fa new file mode 100644 index 0000000000000000000000000000000000000000..06e08cacf7aede4a2a8c80b10407587f2c9aa8e3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001727.fa @@ -0,0 +1,28 @@ +>PROKKA_02244 +MTEHTSEHTPENPHVVRRGSGVPLIEVHGNSVDHRLLLPLDDALAEAGEVERIYVDLPGF +GRTSALQDDGGLPELAAWLVDWIRAEVGERPFAVLGNSLGGLLARHVAAEFGAQVLGLGL +LAPVVDPDEDRRTRTDLVVRERDDAFMSTLDPDDAAPFLEMSPRLTRDTWERFREHALPG +VRAVDEEALKRLSARYVLDAVPEEAAPPFEGPALILTGREDHLVGYRDQAALLEHYPRAT +YAALDAAGHNVHLDQPEVAEALVRAWAVQVGRAASD +>PROKKA_01946 +MTEHTSEHTPENPHVVRRGSGVPLIAVHGNSVDHRLLLPLDDALAEAGEVERIYVDLPGF +GRTSALQDDGGLPELAAWLVDWIRAEVGERPFAVLGNSLGGLLARHVAAESGAQVLGLGL +LAPVVDPDEDRRTRTDLVVRERDDAFMSTLDPDDAAPFLEMSPRLTRDTWERFREHALPG +VRAVDEEALKRLSARYVLDAVPEEAAPPFEGPALILTGREDHLVGYRDQAALLEHYPRAT +YAALDAAGHNVHLDQPEVAEALVRAWAVQVGRAASD +>PROKKA_00502 +MSRGGCLSGGLQSKCGEFRLQFPDRHSPRTACRPHRASAPHLRTAPHVRTFLATLDPDDA +EPFLEMSPRLVPETWERFRDHALPGIRAVDEDAVERPSARYVLDPVPEEAGPRVEAPALI +LTGRSWGSGPPRRRGRRGTEAPVREARSAHPLATRPAGFPSATCRGALAPWPT +>PROKKA_02088 +MSQPAPHLVRRGSGAPLVLVHGMGVDHRLLLPLDAALEAAGGWERVYVDLPGFGGTPALP +APGGLPELADWLDGVVGEIAGEDRFALLGNSLGGLLVREVLARRPGQVAGLAMIAPVVDP +DPERRDVPERVVLEQDEALLAELDGDDAAPFVEMAVIQTRPVWEGFREHVLPGVLAVDED +AVDRLEDRYALDGPLPEERFGEFDRPTLIVTGRQDDKVGWRDQLALAEHFPRLTLAMLDR +TGHNAHLDQEAAVGAMVRNWAEDAAREL +>PROKKA_02176 +MTEHTSEHTPENPHVVRRGSGVPLIAVHGNSVDHRLLLPLDDALAEAGEVERIYVDLPGF +GRTSALQDDGGLPELAAWLVDWIRAEVGERPFAVLGNSLGGLLARHVAAEFGAQVLGLGL +LAPVVDPDEDRRTRTDLVVRERDDAFMSTLDPDDAAPFLEMSPRLTRDTWERFREHALPG +VRAVDEEALKRLSARYVLDAVPEEAAPPFEGPALILTGREDHLVGYRDQAALLEHYPRAT +YAALDAAGHNVHLDQPEVAEALVRAWAVQVGRAASD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001728.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001728.fa new file mode 100644 index 0000000000000000000000000000000000000000..1db4ac1f8410474f64b5720cce08380ab0533e8f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001728.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001735.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001735.fa new file mode 100644 index 0000000000000000000000000000000000000000..eb8773e2e547d380874a1723615b3c74f39e0383 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001735.fa @@ -0,0 +1,50 @@ +>PROKKA_02270 +MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV +IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVYNAIVWQDTRTDRLCERLAGDV +GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGEG +GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET +PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEEPVHSDNGLLTTVAYRIGDQ +KPVYALEGSIAVTGSLIQWLRDNLGMIASAPEVETLAAGVEDNGGVYFVPAFSGLFAPHW +DAAARGVMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE +LLMQFQADLLRVPVVRPKVIETTALGAAYAAGLAVGFWASQDELVANWEEDKRWEPTTDE +EEVERTLRLWKKAVERSRDWVDEDVESAQG +>PROKKA_01963 +MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV +IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVYNAIVWQDTRTDHLCERLAGDV +GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGEG +GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET +PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEEPVHSDNGLLTTVAYRIGDQ +KPVYALEGSIAVTGSLIQWLRDNLGMIGSAPEVETLAAGVEDNGGVYFVPAFSGLFAPHW +DAAARGAMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE +LLMQFQADLLRVPVVRPKVIETTALGAAYAAGLAVGFWASQDELVANWEEDKRWEPTMDE +EEVERALRLWKKAVERSRDWVDEDVESAQG +>PROKKA_00461 +MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV +IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVHNAIVWQDTRTDRLCERLAGDV +GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGAG +GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET +PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEKPVHSDNGLLTTVAYRIGDQ +KPVYALEGSIAVTGSLIQWLRDNLGMIGSAPEVETLAASVEDNGGVYFVPAFSGLFAPHW +DATARGAMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE +LLMQFQADLLRVPVVRPKVTETTALGAAYAAGLAVGFWSSQDELVANWEEDKRWEPTMDE +EEAERALRLWKKAVERSRDWVDEDVESAQG +>PROKKA_00494 +MSAPRYVMAIDQGTTSTRAILFDHAGDAVATGQLEHAQHFPRAGWVEHDPLEIWRNTREA +IGQALSRADATRDDVAAIGVTNQRETAVVWDRTTGRPVHPAIVWQDTRTQHLCERLGGDA +GPDRWRERTGLPLATYFAGPKVAWILEHVDGAREAAERGDLLFGTTDSWTVWNLTGGVLG +GQHVTDVTNASRTLLMDLETLEWDAEIAAEMGIPGGMLPRIVSSSAEVGHAAPTSLLGGV +PIAGILGDQQAALFGQACFEAGQAKNTYGTGNFLLVNTGARPVRSRHGLLTTVAHRIGDE +PPAYALEGSVAVTGSLVQWLRDNLGLIRDAAEVEELAAGAPDNGGVFVVPAFSGLFAPHW +DPTARGTIVGLTRYADRRHLARAVLEATAFQSREVLDAVLADVAEAEEGAGVVGGLTELK +VDGGMVANDLLMQFQADVLGVPVVRPEVTETTALGAAYAAGLAVGFWASTAELAAHWSED +RRWEPAMDPERAARLLRLWARAVARSRGWIDDDVEALAAETRTAPDATPAGRTP +>PROKKA_02202 +MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV +IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVYNAIVWQDTRTDHLCERLAGDV +GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGEG +GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET +PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEEPVHSDNGLLTTVAYRIGDQ +KPVYALEGSIAVTGSLIQWLRDNLGMIGSAPEVETLAAGVEDNGGVYFVPAFSGLFAPHW +DATARGAMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE +LLMQFQADLLRVPVVRPKVIETTALGAAYAAGLAVGFWASQDELVANWEEDKRWEPTMDE +EEVERTLRLWKKAVERSRDWVDEDVESAQG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001736.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001736.fa new file mode 100644 index 0000000000000000000000000000000000000000..35eea5378c4da7ea2ee269be75ca737af2f4900c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001736.fa @@ -0,0 +1,45 @@ +>PROKKA_02282 +MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH +EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI +VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH +AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA +IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF +FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL +AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA +GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGGGGF +>PROKKA_01973 +MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH +EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI +VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH +AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA +IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF +FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL +AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA +GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGSGGF +>PROKKA_00454 +MTEDYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH +EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQTVPTAANASFYAEI +VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLSEIMEH +AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLAIDFARAAA +IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF +FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL +AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA +GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLASDAGGGPGGF +>PROKKA_00406 +MTEDYGDSGSYGGDRTPERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH +EMIYEAIIDLYGRGEPADAVTVADLLNKRQELTKVGGPAVLHELIQTVPTAANASFYAEI +VAEKAVLRRLVSAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH +AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA +IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF +FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL +AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA +GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLAQDGGGSGGF +>PROKKA_02221 +MTENYGDSGSYDGGRSSERFLPPQDLEAERSVLGGMMLSKDAIADVVELLRGHDFYRPSH +EMIYEAIIDLYGRGEPADAVTVADLLNKRQELSRVGGPAVLHELIQSVPTAANASFYAEI +VAEKAVLRRLVTAGTKITQLGYQGDGEVEEIVNEAQSEIYKVAENRQSEDYVRLAEIMEH +AVDEIEAAGNQGEGLTGVPTDFYDFDELTQGLHGGQMIVIAARPAVGKSTLALDFARAAA +IHHNMATVFFSLEMGKNEIAMRLLSAEATIALQDLRKGTIRDDQWSKIAATVGRLNEAPF +FIDDSPNMTMMEIRAKCRRLKQKNNLKMVVLDYLQLMSSGKKVESRQQEVAEFSRALKLL +AKELDVPVIALSQLNRGSEQRTDKRPQVSDLRESGSIEQDADMVILLHREDVYDKESPRA +GEADLIVAKHRNGPTKTIVVGFQGHYSRFSNLASDAGGAGGF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001738.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001738.fa new file mode 100644 index 0000000000000000000000000000000000000000..353c52c89179dd237c00feb4c06d36489ee4054e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001738.fa @@ -0,0 +1,21 @@ +>PROKKA_02286 +MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG +IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVIVMPLTLAG +RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA +>PROKKA_01977 +MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG +IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVVVMPLTLAG +RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA +>PROKKA_00451 +MSESKHTATAPHGVPPIDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG +IERFTRDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGKAQERVVVVMPLTLAG +RTFEAEVTLTHRDEMGFRMLVGRTALAAGGFHVDPAASYVGGQPPRGVRRRNRGRA +>PROKKA_00404 +MGHVTESNHTPGRAAARPPHGDAHDAAPRPAQADADARPVREAATGVVVGWREWVGLPEA +MTPWIKAKIDTGARTSALHAFGIERYTGADGAARVWFEVHPWQASAADARTVDLPVADLR +AVRSSNGEVQERVVVMMPLRLAGRTVDAEVTLTHRDEMGFRMLVGRTALAKGFLVDPGAS +YLGGQPPRGVRRRNRGHA +>PROKKA_02225 +MSESKHTAPAPHGVPPTDDGAARPGLVGWREWVGLPAAHTPWIKAKIDTGARTSALHAFG +IERFARDGAAWVRFEVHPWQTSAADARTAELPVADLRTVRSSNGEAQERVVVVMPLTLAG +RTIEAEVTLTHRDEMGFRMLVGRTALAAGGLLVDPAASYVGGQPPRGVRRRNRGRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001739.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001739.fa new file mode 100644 index 0000000000000000000000000000000000000000..1775024667c2da4e4df1bc874d53f783be98d75e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001739.fa @@ -0,0 +1,41 @@ +>PROKKA_02287 +MSRRPARAPFAFGGVEVAAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI +HGDEVAGVEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR +GSLASRIAHLMMTEVIARCTVGIDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF +HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADVGL +TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST +WVRARADGLVHLHVALGERVSAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG +DALVHIGGWDA +>PROKKA_01978 +MSRRPARAPFAFGGVEVPAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI +HGDEVAGVEIVRRVLERLQPTQLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR +GSLASRIAHLMMTEVIGRCTVGIDLHTGADRRSNLPQIRCDLEDSQTRALAEAFGAPVLF +HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADIGL +TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST +WVRARADGLVHLDVALGERVNAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG +DALVHIGGWDA +>PROKKA_00450 +MSRRPARAPFAFGGVEVPAGRRHELSLPISQLVTGADVTLPVHVLHGREDGPTVWVSAAI +HGNEVAGIEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR +GSLASRIAHLMMTEVIGRCSVGVDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF +HARLRDGSLRAAAREAGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALGMVDPAEVGL +TEPGPAAVVDAPGPLPGEVPGDATTDVPEATDATGEDTEAVHADVVDGGQDAPHLVWHSS +WVRARADGLVHLDVSLGERVAAGDRIGALYNSFGRRVAHVKAELTGVVIGRTEAPLVHRG +DALVHIGGWDA +>PROKKA_00403 +MSAPQKDPDRGGRTGDEAAAEKATGRRRASRAPFELAGVEVRPGRRHEVSLPVSRLVTGA +EVTLPVHVLHGREDGPTVWVSAAVHGDEVAGIEIVRRVLERLKPSRMRGTLLALPIVNVL +GVMTGDRYLPDRRDLNRSFPGAARGSLAARIAHLMMSEVVRRCEVGIDLHTGADRRSNLP +QIRCDLEDPRTRALAESFGAPVLFHARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAI +SPGVEGVLRVLAALGMVAAEDVGLATPVDAPAPLPGEVPEDRTTEVPEALDATGRDTGGV +HADVVDGDLAAPHRVWHSRWVRARADGLVHLDVALGEQVTAGDRIGALYDSFGRRRSDVK +AELTGVVLGRTEAPLVHRGDALVHIGELDGRPAGTFPAPSPGRRTAPSVAEGDPEAEAPP +AATP +>PROKKA_02226 +MSPRPARAPFAFGGVEVAAGRRHELSLPISQLVTGADVTLPVHVLHGRDDGPTVWVSAAI +HGDEVAGVEIVRRVLERLQPKHLRGTLLAVPIVNVLGVMAGDRYLPDRRDLNRSFPGSAR +GSLASRIAHLMMTEVIARCTVGIDLHTGADRRSNLPQIRCDLEDPQTRALAEAFGAPVLF +HARLRDGSLRAAARETGARVLLYEAGEAWRFDEYAIAPGVDGVLRVLAALDMVDPADVGL +TEPGPDAVVDAPGPLPGEVPEERTTDVPEATDATGEDTAAVHPDVVDGEQDAPYLVWQST +WVRARADGLVHLDVSLGERVSAGDRIGALYNSFGRRLAHVKAELTGVVIGRTEAPLVHRG +DALVHIGGWDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001740.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001740.fa new file mode 100644 index 0000000000000000000000000000000000000000..324baf184e77b9ef7131377dc6c87d5b767e9d0e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001740.fa @@ -0,0 +1,20 @@ +>PROKKA_02289 +MAKLILTQEVAGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV +ANLEDAQAQAAQLQSATVQLERTAGAEGRLFGAVQTADVAEAIEAAGLGSVDKRSITLPA +HIKSVGNHEAQVRLHEDVIATVQLQVVAAKAKK +>PROKKA_01981 +MAKLILTQEVAGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV +ANLEDAQAQAAQLQSATVKLERTAGAEGRLFGAVQTADVAEAIEAAGLGSVDKRSITLPA +HIKSVGNHEAQVRLHEDVIATVQLQVVAAKAKK +>PROKKA_00449 +MAKLILTQEVTGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV +ANLEDAQAQAEKLQSATVKLERTAGAEGRLFGAVQAADVAEAIEAAGLGSVDKRAVTLPA +HIKSVGNHQAQVRLHEDVVAVVDLQVVAAKAKK +>PROKKA_00401 +MAKLILTQEVPGLGIDGDVVEVKNGYARNYLLPRGFATVWTQGGEKQVESLKAARAARAT +ANLEEAQALAAKLQSATVRIDRKAGAEGRLFGAVQAADVAEAIEAAGLGSVSKRSVTLPN +HIKTVGNHEAQVRLHDEVTATVALQVVAAKGSKK +>PROKKA_02229 +MAKLILTQEVAGLGTSGDVVEVKNGYARNYLLPRGFATVWTKGGEKQVESLQKARAARAV +ANLEDAQAQAAQLQSATVKLERTAGAEGRLFGAVQTADVAEAIEAAGLGSVDKRSITLPA +HIKSVGNHEAQVRLHEDVIATVQLQVVAAKAKK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001744.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001744.fa new file mode 100644 index 0000000000000000000000000000000000000000..2ae7d5200a031472c8c43494502e0fc37705baa3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001744.fa @@ -0,0 +1,50 @@ +>PROKKA_02293 +MTPVTRDTVAELHAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG +YVVVRDGAAVAWIVPMGARALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK +LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ +LAIHLDREVNEGLTLKRQRHTNPVVGALVPRGEGAGEAEADGLAARVPGDVLTALAAAAG +VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA +IAYEGTVAGGVAGVAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG +QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA +FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD +VEHLTAAVREFFRGV +>PROKKA_01986 +MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG +YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGPSAGVVPVFRVLGAHTDSPGFK +LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ +LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG +VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLAALEELAREHGGAEGA +IAYEGTVAGGVAGEAADAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG +QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA +FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD +VEHLAAAVREFFRGV +>PROKKA_00443 +MTAVTRDTAPAPEMSAHVQDLAAFVTASPSSYHAAAEVARRLVAVGFTCLDEAADFPAAP +GGYVVVRDGAALAWVVPTGAGSDVSDGAGAAGGSGAGAAVPVFRVLGAHTDSPGFKLKPN +PATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQLAIH +LDREVNDGLKLQRQRHTNPVVGALAPRGEGAGEAVADVSEGVDGRSAPLEQAAGAGAGVG +AGAGEGAGAREGDGAGLEARAPGDVLSALAAAAGVDPAAVRGHDVMVADAQAPGLFGLAG +EFFASGRLDNLSSVHAGLVALEELARANGGASGAIAYAGTVAEGVAGEAAGAPVIPVLAA +FDHEELGSASRSGAAGPLLEEVMGRVLEALGVAGQGRARAIAGSWLLSADAGHLVHPNYA +ERHDPVNHPRVNHGPLLKINANQRYATDAGGEAAFARWCGVAGVPFQEFVSNNDMPCGST +IGPISATRLGIRTVDVGLGLLSMHSAREMCGVRDVEHLTAAVREFFRGV +>PROKKA_00396 +MSTVTSESTVTAAVPGAPALSAHLQDLAAFVQASPSSFHAAAEVARRLEAVGFTRVDPAQ +DLPAAPGGYVSVTDGAVLAWILPEALAERAADAVPVFRLLGAHTDSPGFKLKPQHLTVTA +DGWVQAGVEVYGGPLLNSWLDRELRFAGRLALADGRQVLAATGPVGRIPQLAIHLDRSAN +DDLTLGRQRHTQPIVAAVAGAPDAAGTDAADGASADPVVRLTGDILELLAAQAGVDPAEV +RGADVVVADAQQGGAFGANGEFFACGRLDNLSSVHAGLRALESLAADADRAGRGVVVAEG +VAGEAAGAPVIPVLAAFDHEEVGSATRTGAGGPLLEELMGRLLSACGVTGQGAARSRAGS +WLLSADAGHLVHPNYTERHDPVNHPRVNHGPLLKINANQRYSTDAAGEAAFARWCAAAGV +PFQRFVSNNDVPCGSTIGPISATRLGVRTVDVGIGLLSMHSAREMCGADDPARLAAVARA +FFAGV +>PROKKA_02234 +MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG +YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK +LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ +LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG +VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA +IAYEGTVAGGVAGEAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG +QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA +FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD +VEHLAAAVREFFRGV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001746.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001746.fa new file mode 100644 index 0000000000000000000000000000000000000000..632f2969cbea42d1e31cb4677e402c04a6eee132 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001746.fa @@ -0,0 +1,51 @@ +>PROKKA_02295 +MRPAPAHAATPSEPPTHAADGAPSDAVTAPGAPAGRSADSAPSGTLPAPGERGGRFQLAG +GLAANGPGRGTGSWAGPVALTGLLVALAAVVTVLQKSPCLLHGWGAPDVYYAGCYSDWAA +LYGGRGFAADPWAPFRAGSTFEYPVLMSVVGSVAAWITQALPFSPEQGTVVFWLVNLGFV +VVLWAVVAVLTVRMAGRRWTDGLMVAVAPGIVLAGTINWDLWAVALLACGMYAWSRGRSL +TAGVLFGLGAAMKLYPLLILGPLLILAVRSRRWRPFLLAAGGTVAAWAAVNVPLMAVNFQ +AWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGTFAVCCLGIFVLGV +RVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVVWLIPLLALALPRWRDFWVWQTVEALHFF +AVWMYLAKGVAETPPQHSMDDSVYVAAILAHILAVLWLCGRVVWEMLHPAEDLVKRDHGG +HPDADPLAGAYAGPARGRSGRPAAVQA +>PROKKA_01988 +MRPAPAHAATPSEPPTHAADGAPCDAVADPGAPAGRSADSAPSGALPAPGERGGRFQLAG +GLAANGPGRGTGSWAGPVALTGLLVALAAVVTVLQKSPCLLHGWGAPDVYYAGCYSDWAA +LYGGRGFAADPWAPFRAGSTFEYPVLMSVVGSVAAWITQALPFSPEQGTVVFWLVNLGFV +VVLWAVVAVLTVRMAGRRWTDGLMVAVAPGIVLAGTINWDLWAVALLACGMYAWSRGRSL +TAGVLFGLGAAMKLYPLLILGPLLILAVRSRRWRPFLLAAGGTVAAWAAVNVPLMAVNFQ +AWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGTFAVCCLGIFVLGV +RVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVVWLIPLLALALPRWRDFWVWQTVEALHFF +AVWMYLAKGVAETPPQHSMDDSVYVAAILAHMLAVLWLCGRVVWEMLHPAEDLVKRDHGG +HPDADPLAGAYAGPARGRSGRPAAVQA +>PROKKA_00441 +MRPAPAHAATPSEPPTHAVDGPSWAGPDGRAEAGGSAVSAPPSRGPAAVPAPVPAPGDRG +GRFQLPGGLAANRFTLGGRGGTGSWASPAALAGVLVALAAVVTVLQKAPCLLHGWGAPNV +YYAGCYSDWAALYGGRGFAADPWAPFQAGSTFEYPVLMSLVGSVGAQLTQWLPFGAEHGT +LVFWLVNLLFVVGLWAAVAVLTVRMAGRRWSDGLMVAVAPGVILAGTINWDLWAVALLAL +GMYAWARERPLAAGVLIGLGAAMKIYPLLILGPLLILAVRSRRWRPFLLAAGGAVAAWAA +VNVPLMVANFEAWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGAFA +VCCLGIFVLGVRVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVIWLIPLVALALPRWRDFW +AWQTVEALHFFAVWMYLAKGASGSMPQHSMDDSVYVAAILAHMLAVLWLCGRVVWEMLHP +EDDLVRRDHTDLPGGDPLAGAYRSAQA +>PROKKA_00394 +MSSSPAPGAAPDDPPAPAPQARPDVPVGAHRAPRHALTTPPPGSAEGAPSAGSGAVESDE +ATPEGEVDPRVVPAPGDRGGRFAIPGGLAANGRGRGTGAWAGPVALTALLVALGAIATVL +QKSPCLLHGWGAPNVYYAGCYSDWAALYGGRGFAADPWAPFQAGSTFEYPVLMSLVASVG +AQLTQWLPFPASVGTVVFWCVNLLFVVGLWAATAVLTVRTAGRRWTDGLMVAVAPGIILA +GTVNWDLWAVALMAWGMWVWLRGRPGWAGVLFGLGAATKLYPLLILGPLLILAVRSRRFG +PFLKATGGAVAAWLAVNLPLMLTHFESWKVFFTFSAERGPGLSSVWHAWDVVAAQAGWAA +VPDERLGMYAYGAFAVCCLGIFVLGVVAKRPPRLAQLTFLVVAAFVLTNKVYSPQFVIWL +IPLMALALPRWKDFWVWQTVEALHFFAVWMYLAKGASGSMPQHSMDDSVYVAAILAHMLA +VLWLCARVVLEILDPDDDLVRGPGGDPARDPEDPSAGPADPGMTGVRPVREAVAAGVGAA +SAQA +>PROKKA_02236 +MRPAPAHAATPSEPPTHAADGAPCDAVADPGAPAGRSADSAPSGTLPAPGERGGRFQLAG +GLAANGPGRGTGSWAGPAALTGLLVALAAVVTVLQKSPCLLHGWGAPDVYYAGCYSDWAA +LYGGRGFAADPWAPFRAGSTFEYPVLMSVVGSVAAWITQALPFSPEQGTVVFWLVNLGFV +VVLWAVVAVLTVRMAGRRWTDGLMVAVAPGIVLAGTINWDLWAVALLACGMYAWSRGRSL +TAGMLFGLGAAMKLYPLLILGPLLILAVRSRRWRPFLLAAGGTVAAWAAVNVPLMAVNFQ +AWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGTFAVCCLGIFVLGV +RVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVVWLIPLLALALPRWRDFWVWQTVEALHFF +AVWMYLAKGVAETPPQHSMDDSVYVAAILAHMLAVLWLCGRVVWEMLHPAEDLVKRDHGG +HPDTDPLAGAYAGPARGRSGRPAAVQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001752.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001752.fa new file mode 100644 index 0000000000000000000000000000000000000000..5442d60895a18674bec8328c3edba8f21a1df39d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001752.fa @@ -0,0 +1,35 @@ +>PROKKA_02306 +MAQEQESRGGAWRALRQKWTGRTAEKGGADAEEPARLQRRRLTRPDRTRVFTTSNQKGGV +GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV +QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWRAEDGQERLDYVFID +CPPSLGLLTVNAFVAAQEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM +FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA +AAEIAGRGAPSVKG +>PROKKA_01999 +MAQEQESRGGAWRALRQKWTGRTAEKGGADVEEPARLQRRRLTRPDRTRVFTTSNQKGGV +GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV +QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREEDGQERLDYVFID +CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM +FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA +AAEIAGRGAPTALKS +>PROKKA_00430 +MAQEQESRGGAWRALRQKWSGRSAEQGAGEAEESSRLKARRLARPERTRVFTTSNQKGGV +GKTTTTVNLAAALARAGMRVMVIDIDPQGNASTALNIPHTGDVASVYDVLLGEMEMHDVV +QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREENGQERLDYVFID +CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPKLQVSTILLTM +FDARTNLAVQVAEEVRAHFPEQLLGTAIPRNVRISEAPSYQQTVLTYDPTSAGAVAYREA +AAEIAGRGAPAAKG +>PROKKA_00383 +MAKDQDSRGGTWKALKQRWSGRASDKASPEEAARLKARRLPVPDRTRVFTTSNQKGGVGK +TTTTVNLAAALARAGMRVLVIDIDPQGNASTALNVPHAGDVASVYDVLLDEMEIHEAVQD +APDVDGLQVVPATIDLAGAEIELVSMVAREQRLARALDRYMAWRADQGQERLDYVFIDCP +PSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPKLQVSTILLTMFD +ARMNLAVQVAEEVKAHFPEQLLETAIPRNVRISEAPSYQQTVVTYDPASAGAVAYREAAA +EIARRGAPQAR +>PROKKA_02247 +MAQEQESRGGAWRALRQKWTGRTAEKGGADAEEPARLQRRRLTRPDRTRVFTTSNQKGGV +GKTTTTVNLAAALARAGMRVMVVDIDPQGNASTALNIPHTGDVASVYDVLLGEMEIQDVV +QDAPDVDGLQVVPATIDLAGAEIELVSLVAREQRLSRALEAYTAWREEDGQERLDYVFID +CPPSLGLLTVNAFVAAEEVLIPIQAEYYALEGLSQLLKNVQMIQKHLNPRLQVSTILLTM +FDARTNLAVQVAEEVRTHFPEQLLNTAIPRNVRISEAPSYQQTVLTYDPASAGAVAYREA +AAEIAGRGAPAVKG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001755.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001755.fa new file mode 100644 index 0000000000000000000000000000000000000000..f73d67a18c32bfa52cfd800b88cc2463e8f28e05 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001755.fa @@ -0,0 +1,35 @@ +>PROKKA_02309 +MFEAILAPFRWLMSWLLGAFHTVLEFAGMPADSGWTWALSILLLVVLIRTLLIPLFVKQI +KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF +FFALYQVLIGARGASERGESMDALSADQIRSFEGSTIFGARMSDTFLNSFGDPGSAPVII +TAIVLIVLMSGSMFYMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV +LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEKELNERRAAKGLPPVGQKVTDSKAEPSSAH +TQAAGGGAVLNGEVVRQSGQRVQPQRKNRRRK +>PROKKA_02002 +MFEAILSPFRWLMSWLLGAFHSILEFAGLPADSGWTWALSILLLVVLIRTLLIPLFVKQI +KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF +FFALYQVLIGARGAAERGEAMDALSADQIRSFEGSTIFGARMSDTFMNSLGAPGSGPVIV +TAIVLILLMSGSMFFMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV +LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEKELNERRAAKGLPPVGQKVSNAEATPSSAH +TQAGRGGAVLNGEVVRQSGQRVQPQRKNRRRK +>PROKKA_00427 +MFEAILAPFRWLMSWLLGAFHTVLEFAGMPADSGWTWALSILLLVVLIRTLLIPLFVKQI +KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF +FFALYQVLIGARGASERGESMDALSADQIRSFEGSMIFGARMSDTFLNSFGDPGSAPLII +TAIVLIVLMSGSMFYMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV +LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEQELNERRAAKGLPPVGQKVTDSKAEPSSAH +TQAAGGGTATLNGEPVRDSGQRVQPQRKNRRRK +>PROKKA_00380 +MFDAILAPFRWIMSWLLGAFHTVLDTIGLPADSGWTWALAILLLVILIRTLLIPLFVKQI +NAQRAMQTMQPELQKLQAKYKGKKDQLSRQAMALEQQALMREHKANPFAACLPLLIQMPF +FFALYQVLVGARGAAERGESMDALSAETIRSFESSQIFGARMSDTLMGSIGQPGGAAVVV +VAIVLILLMTGSMFFMQKMLMTKNMTQTALEGPMMQTQQIMLYAMPLIFGIGGINFPIGV +LLYWTYSNFWAVGQQWWIIRHNPTPGSLAEQELNERRAAKGLPPVGKKVASSEAKPGSAH +TEAAQGAVVNGEVLREGGQRVQPQRKNRRKK +>PROKKA_02250 +MFEAILSPFRWLMSWLLGAFHSILEFAGLPVDSGWTWALSILLLVVLIRTLLIPLFVKQI +KAQRAMQAIQPELQKLQAKYKGKKDQLSRQAMAMEQQALMKEHKANPFAACLPLLIQMPF +FFALYQVLIGARGAAERGEAMDALSADQIRSFEGSTIFGARMSDTFMNSLGAPGSTPVIV +TAIVLILLMSGSMFFMQKMLMTKNMTQQALSGPMMQTQQIMLYAMPLIFGIGGINFPIGV +LLYWTYSNFWAVGQQWWIIRNNPTPGSLAEKELNERRAAKGLPPVGQKVSNAEATPSSAH +TQAGRGGAVLNGEVVRQSGQRVQPQRKNRRRK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001756.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001756.fa new file mode 100644 index 0000000000000000000000000000000000000000..2796db03d9f5d51de22077a2e0e0f940f9dc49d9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001756.fa @@ -0,0 +1,20 @@ +>PROKKA_02310 +MTVTPSPFVVLEPSREWGPLRALPSALLAGLLTVYRAVVSPLYGPVCRFFPSCSAYGLEA +VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILTLNHPPIPPDLPQ +ED +>PROKKA_02003 +MTVTPSPFVVLEPSREWGPLRALPSALLAGLLTVYRAVVSPLYGPVCRFFPSCSAYGLEA +VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILTLNHPPIPPDLPQ +ED +>PROKKA_00426 +MAVTPSPFTVLEPSREWGPVRALPSALLAGLLTVYRAVVSPLYGQVCRFFPSCSAYGLEA +VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILTLNHPPIPPDLPQ +ED +>PROKKA_00379 +MPASSPYTVLEPSHEWGPLRALPSTLLAWLLTAYRAVVSPLYGPVCRFFPSCSAYGLEAV +HVHGAVRGSWLTARRLLRCHPWNDGGVDPVPPGRRRWPPGREPRIFALNHPPIPPDPSQE +D +>PROKKA_02251 +MTVTPSPFVVLEPSREWGPLRALPSALLAGLLTVYRAVVSPLYGPVCRFFPSCSAYGLEA +VHVHGAVKGSWLAARRIGRCHPWNDGGVDPVPPGHRRWPPGRQPRILALNHPPIPPDLPQ +ED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001758.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001758.fa new file mode 100644 index 0000000000000000000000000000000000000000..5ee6503c0d9a1a9b446cdb708bf89e9e992c6b6a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001758.fa @@ -0,0 +1,12 @@ +>PROKKA_02312 +MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSARRGKNRAELSA + +>PROKKA_02005 +MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSARRGKNRAELSA +>PROKKA_00424 +MTKRTFQPNNRRRARKHGFRARMRTRAGRAILAARRGKGRAELSA +>PROKKA_00377 +MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSTRRGKGRAELSA +>PROKKA_02253 +MTKRTFQPNNRRRARKHGFRARMRTRAGRAILSARRGKNRAELSA +