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Beyond_Prompt-based_Retrieval

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  1. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000002_tree.txt +1 -0
  2. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000019_tree.txt +1 -0
  3. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000030_tree.txt +1 -0
  4. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000038_tree.txt +1 -0
  5. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000039_tree.txt +1 -0
  6. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000055_tree.txt +1 -0
  7. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000073_tree.txt +1 -0
  8. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000075_tree.txt +1 -0
  9. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000078_tree.txt +1 -0
  10. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000085_tree.txt +1 -0
  11. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000086_tree.txt +1 -0
  12. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000101_tree.txt +1 -0
  13. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000102_tree.txt +1 -0
  14. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000121_tree.txt +1 -0
  15. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000122_tree.txt +1 -0
  16. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000125_tree.txt +1 -0
  17. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000127_tree.txt +1 -0
  18. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000137_tree.txt +1 -0
  19. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000154_tree.txt +1 -0
  20. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000158_tree.txt +1 -0
  21. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000167_tree.txt +1 -0
  22. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000172_tree.txt +1 -0
  23. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000179_tree.txt +1 -0
  24. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000182_tree.txt +1 -0
  25. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000194_tree.txt +1 -0
  26. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000197_tree.txt +1 -0
  27. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000198_tree.txt +1 -0
  28. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000210_tree.txt +1 -0
  29. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000211_tree.txt +1 -0
  30. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000213_tree.txt +1 -0
  31. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000225_tree.txt +1 -0
  32. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000226_tree.txt +1 -0
  33. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000243_tree.txt +1 -0
  34. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000245_tree.txt +1 -0
  35. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000257_tree.txt +1 -0
  36. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000264_tree.txt +1 -0
  37. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000267_tree.txt +1 -0
  38. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000270_tree.txt +1 -0
  39. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000274_tree.txt +1 -0
  40. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000276_tree.txt +1 -0
  41. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000280_tree.txt +1 -0
  42. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000287_tree.txt +1 -0
  43. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000289_tree.txt +1 -0
  44. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000298_tree.txt +1 -0
  45. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000305_tree.txt +1 -0
  46. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000312_tree.txt +1 -0
  47. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000313_tree.txt +1 -0
  48. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000321_tree.txt +1 -0
  49. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000323_tree.txt +1 -0
  50. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000329_tree.txt +1 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000002_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (((GCF_005280335_PROKKA_02348:0,GCF_005280335_PROKKA_02630:0)n2:0.0233998,(GCF_023573625_PROKKA_01019:5e-09,((GCF_002008305_PROKKA_01387:0,GCF_003691675_PROKKA_00320:0,GCF_003691675_PROKKA_01328:0,GCF_003691675_PROKKA_02266:0)n5:5e-09,((GCF_020097155_PROKKA_00316:0.0567134,(GCF_003691675_PROKKA_00787:5e-09,GCF_003691675_PROKKA_01659:0.0136713)n8:0.00151904)n7:0.00815592,(GCF_003691675_PROKKA_00332:0,GCF_020097155_PROKKA_02231:0)n9:0.0140067)n6:0.00140067)n4:0.00015563)n3:0.0233965)n1:0.0038409,((GCF_002008305_PROKKA_01069:0.0155085,((GCF_003691675_PROKKA_01117:0.0153727,(GCF_020097155_PROKKA_01795:0,GCF_020097155_PROKKA_01837:0,GCF_020097155_PROKKA_02208:0)n14:5e-09)n13:0.00768729,(GCF_005280335_PROKKA_01280:5e-09,(GCF_005280335_PROKKA_01313:0,GCF_005280335_PROKKA_01318:0)n16:0.0075694)n15:0.0469002)n12:5e-09)n11:5e-09,((GCF_005280335_PROKKA_00757:0,GCF_005280335_PROKKA_01303:0,GCF_005280335_PROKKA_02332:0)n18:5e-09,(GCF_023573625_PROKKA_01540:5e-09,((GCF_020097155_PROKKA_00621:0,GCF_020097155_PROKKA_00626:0)n21:0.015475,(GCF_023573625_PROKKA_00113:0,GCF_023573625_PROKKA_01883:0)n22:6e-09)n20:0.00776783)n19:0.00690848)n17:0.000767609)n10:0.0038409)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000019_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_01886:0.013508,(((GCF_005280335_PROKKA_02497:0,GCF_005280335_PROKKA_02616:0)n3:5e-09,(GCF_005280335_PROKKA_02275:0.0102694,GCF_005280335_PROKKA_02634:5e-09)n4:0.0102682)n2:0.0226592,((GCF_003691675_PROKKA_00342:0.0961499,GCF_023573625_PROKKA_01543:0.288029)n6:0.0685307,(GCF_023573625_PROKKA_00899:0.0372964,GCF_003691675_PROKKA_01766:0.038296)n7:0.00425511)n5:0.207353)n1:0.0230392)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000030_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_005280335_PROKKA_02334:5e-09,(GCF_005280335_PROKKA_00171:0.589658,(GCF_005280335_PROKKA_00191:1.12225,GCF_005280335_PROKKA_02217:0.747883)n3:0.326334)n2:0.628863)n1:0.00198673,(GCF_002008305_PROKKA_00169:0.00603084,(GCF_003691675_PROKKA_00360:5e-09,GCF_023573625_PROKKA_02010:0.00199069)n5:0.00400144)n4:0.00198673)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000038_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_01023:0.0453106,((GCF_005280335_PROKKA_01099:0.0624218,(GCF_002008305_PROKKA_01778:0.00213185,(GCF_002008305_PROKKA_00836:0.127971,GCF_002008305_PROKKA_00837:0.0590392)n4:0.474128)n3:0.0526808)n2:0.0456872,(GCF_003691675_PROKKA_01485:0.00975291,GCF_023573625_PROKKA_01707:0.00414833)n5:0.00347634)n1:0.0453106)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000039_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_01944:0.302987,((GCF_005280335_PROKKA_02045:0.691889,((GCF_002008305_PROKKA_00894:0.0271898,GCF_003691675_PROKKA_00616:0.0302301)n4:0.644884,(GCF_002008305_PROKKA_00884:0.00825059,GCF_003691675_PROKKA_00606:0.00961045)n5:0.524179)n3:0.0582421)n2:0.561111,GCF_023573625_PROKKA_00845:0.742872)n1:0.0951319)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000055_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_023573625_PROKKA_00735:0.225294,((GCF_020097155_PROKKA_00792:0.0836997,(GCF_003691675_PROKKA_01696:0.0139572,GCF_005280335_PROKKA_00855:0.00623493)n3:0.122743)n2:0.115924,(GCF_005280335_PROKKA_01010:0.469059,(GCF_020097155_PROKKA_00943:0.492378,GCF_020097155_PROKKA_00870:0.646041)n5:0.0717824)n4:0.0950986)n1:0.0105665)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000073_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_020097155_PROKKA_00079:0.126939,GCF_020097155_PROKKA_00526:0.889959)n1:0.0522248,(GCF_005280335_PROKKA_00111:0.0515937,(GCF_003691675_PROKKA_02272:0.0107424,(GCF_002008305_PROKKA_00258:0.00411397,GCF_023573625_PROKKA_00257:5e-09)n4:0.014808)n3:0.0609834)n2:0.0522248)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000075_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_020097155_PROKKA_00057:0.26398,GCF_020097155_PROKKA_00450:1.72894)n1:0.0354745,(GCF_005280335_PROKKA_00071:0.0172183,(GCF_003691675_PROKKA_02297:5e-09,(GCF_002008305_PROKKA_00282:0.0100593,GCF_023573625_PROKKA_00281:0.00499956)n4:0.0101127)n3:0.0723531)n2:0.0354745)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000078_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_005280335_PROKKA_00027:0.24417,(GCF_020097155_PROKKA_00654:1.32246,GCF_020097155_PROKKA_00023:0.174907)n2:0.0194342)n1:0.0365071,(GCF_002008305_PROKKA_00310:0.00291069,(GCF_003691675_PROKKA_00025:0.00559649,GCF_023573625_PROKKA_00317:5e-09)n4:0.0112438)n3:0.103671)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000085_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_02405:0.0525143,((GCF_002008305_PROKKA_00423:0.0165947,(GCF_003691675_PROKKA_00144:0.0118738,GCF_023573625_PROKKA_00426:0.0062224)n3:0.011001)n2:0.0782166,(GCF_005280335_PROKKA_02535:0.101283,GCF_005280335_PROKKA_02534:0.0872366)n4:0.00969295)n1:0.0184057)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000086_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (((GCF_005280335_PROKKA_02509:0.0347178,(GCF_020097155_PROKKA_00683:0.97028,GCF_020097155_PROKKA_02380:0.0591297)n3:0.00656997)n2:0.0384262,GCF_023573625_PROKKA_00451:0.00232437)n1:2.5e-09,(GCF_002008305_PROKKA_00448:5e-09,GCF_003691675_PROKKA_00169:0.00233114)n4:2.5e-09)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000101_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_02170:0.0617663,(GCF_005280335_PROKKA_02313:0.0673918,((GCF_003691675_PROKKA_00387:0.007385,GCF_023573625_PROKKA_00620:0.0048582)n3:0.0270805,(GCF_002008305_PROKKA_00841:1.91988,GCF_002008305_PROKKA_00650:0.0148699)n4:0.00165221)n2:0.0393187)n1:0.150212)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000102_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_02164:0.122944,((GCF_005280335_PROKKA_00162:1.39379,GCF_005280335_PROKKA_02307:0.0572831)n2:0.0435128,(GCF_003691675_PROKKA_00393:5e-09,(GCF_002008305_PROKKA_00656:5e-09,GCF_023573625_PROKKA_00626:0.00354992)n4:0.00354882)n3:0.0215804)n1:0.122944)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000121_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_01639:0.0439273,((GCF_002008305_PROKKA_01147:0.00374438,(GCF_003691675_PROKKA_00866:0,GCF_023573625_PROKKA_01097:0)n3:0.00386493)n2:0.0425685,(GCF_005280335_PROKKA_01745:0.0110625,GCF_005280335_PROKKA_00771:1.43435)n4:0.00775569)n1:0.0439273)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000122_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_005280335_PROKKA_01740:6e-09,(GCF_020097155_PROKKA_01634:0.154248,GCF_020097155_PROKKA_00545:1.33084)n2:0.147871)n1:0.0245682,(GCF_002008305_PROKKA_01152:0.00620805,(GCF_003691675_PROKKA_00871:0,GCF_023573625_PROKKA_01102:0)n4:0.00484693)n3:0.0470658)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000125_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_020097155_PROKKA_00131:1.36414,GCF_020097155_PROKKA_01453:0.1415)n1:0.0629249,(GCF_005280335_PROKKA_01557:0.0475667,((GCF_002008305_PROKKA_01334:0,GCF_023573625_PROKKA_01290:0)n4:5e-09,GCF_003691675_PROKKA_01055:0.0028761)n3:0.0403515)n2:0.0629249)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000127_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_01419:0.179044,(GCF_005280335_PROKKA_01524:0.0821859,(GCF_023573625_PROKKA_01324:0.00400482,(GCF_003691675_PROKKA_01089:0.0280004,(GCF_002008305_PROKKA_01953:1.50914,GCF_002008305_PROKKA_01369:0.00817524)n4:0.000908361)n3:0.0114932)n2:0.0343099)n1:0.179044)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000137_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00456:0.0674171,((GCF_005280335_PROKKA_01337:0.0207395,GCF_023573625_PROKKA_01512:0.00693389)n2:5e-09,(GCF_003691675_PROKKA_01296:0.00691918,(GCF_002008305_PROKKA_02251:0.0762475,GCF_002008305_PROKKA_01585:0.00749909)n4:0.000833232)n3:0.00302958)n1:0.709677)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000154_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_005280335_PROKKA_00875:0.142041,(GCF_020097155_PROKKA_00810:0.0159145,GCF_020097155_PROKKA_00823:0.177426)n2:0.0197139)n1:0.103096,((GCF_002008305_PROKKA_01983:0,GCF_023573625_PROKKA_01909:0)n4:5e-09,GCF_003691675_PROKKA_01677:0.00624049)n3:0.00917423)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000158_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00750:0.154272,(((GCF_005280335_PROKKA_00789:0.0273817,GCF_023573625_PROKKA_01966:0.00209429)n3:0.0423828,(GCF_002008305_PROKKA_02031:0.0221068,GCF_002008305_PROKKA_02029:0.0170158)n4:0.00189064)n2:0.11949,GCF_003691675_PROKKA_01738:5e-09)n1:0.154272)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000167_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00491:0.0966885,(GCF_005280335_PROKKA_00566:0.0703984,(GCF_003691675_PROKKA_01898:0.00634878,(GCF_023573625_PROKKA_00166:1.46154,(GCF_002008305_PROKKA_02184:5e-09,GCF_023573625_PROKKA_02129:0.00371049)n4:0.00448949)n3:0.000498833)n2:0.0359085)n1:0.0422593)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000172_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_023573625_PROKKA_00111:0.0984241,((GCF_005280335_PROKKA_01501:0.727312,(GCF_020097155_PROKKA_00694:0.197338,GCF_020097155_PROKKA_00288:0.397796)n4:0.0441996)n3:0.33429,GCF_020097155_PROKKA_00347:0.0722297)n2:0.00802553)n1:0.143819,GCF_003691675_PROKKA_02019:1.11717)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000179_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00370:0.0434789,(GCF_005280335_PROKKA_00418:0.0215076,(GCF_003691675_PROKKA_02011:0.00110173,(GCF_002008305_PROKKA_00006:0.00229181,GCF_023573625_PROKKA_00006:5e-09)n3:5e-09)n2:0.0245563)n1:0.0434789)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000182_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_02181:0.149491,(GCF_005280335_PROKKA_00386:0.0685417,(GCF_023573625_PROKKA_00011:5e-09,(GCF_003691675_PROKKA_02029:0.0115118,GCF_002008305_PROKKA_00011:0.00384383)n3:0.00377888)n2:0.0525377)n1:0.149491)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000194_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00304:0.0664401,(GCF_005280335_PROKKA_00366:0.020539,(GCF_002008305_PROKKA_00032:5e-09,(GCF_003691675_PROKKA_02049:0.0030909,GCF_023573625_PROKKA_00031:0.00615684)n3:0.00306956)n2:0.0112394)n1:0.0664401)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000197_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_005280335_PROKKA_00209:0.0101908,(GCF_023573625_PROKKA_00190:0.0059304,(GCF_003691675_PROKKA_02020:1.45261,(GCF_002008305_PROKKA_00190:6e-09,GCF_002008305_PROKKA_00035:0.803399)n3:0.0892666)n2:0.608316)n1:0.0101908)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000198_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00302:0.0272878,(GCF_005280335_PROKKA_00361:0.0959516,(GCF_023573625_PROKKA_00034:0.00862329,(GCF_002008305_PROKKA_00039:5e-09,GCF_003691675_PROKKA_02052:0.00423473)n3:5e-09)n2:0.0502468)n1:0.0272878)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000210_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00278:0.192732,(GCF_003691675_PROKKA_02070:0.00298778,(GCF_005280335_PROKKA_00338:0.135539,(GCF_002008305_PROKKA_00057:0.0026836,GCF_023573625_PROKKA_00052:0.00267826)n3:5e-09)n2:0.00248432)n1:0.192732)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000211_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00277:0.16741,(GCF_005280335_PROKKA_00337:0.0575252,(GCF_002008305_PROKKA_00058:0.00780026,(GCF_003691675_PROKKA_02071:0.0056242,GCF_023573625_PROKKA_00053:0.00140212)n3:0.00203306)n2:0.0795924)n1:0.16741)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000213_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00275:0.0349221,(GCF_005280335_PROKKA_00334:0.0187596,((GCF_002008305_PROKKA_00061:0,GCF_023573625_PROKKA_00056:0)n3:5e-09,GCF_003691675_PROKKA_02074:0.00932753)n2:0.0292382)n1:0.0349221)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000225_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00256:0.181184,(GCF_005280335_PROKKA_00315:0.0720153,(GCF_002008305_PROKKA_00078:0.0161606,(GCF_003691675_PROKKA_02091:0,GCF_023573625_PROKKA_00072:0)n3:0.016553)n2:0.102898)n1:0.181184)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000226_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00255:0.194519,(GCF_005280335_PROKKA_00314:0.101092,(GCF_002008305_PROKKA_00079:0.0287554,(GCF_003691675_PROKKA_02092:0,GCF_023573625_PROKKA_00073:0)n3:0.00728075)n2:0.0999786)n1:0.194519)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000243_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00238:0.0853837,(GCF_005280335_PROKKA_00293:0.207122,((GCF_002008305_PROKKA_00098:0,GCF_023573625_PROKKA_00093:0)n3:5e-09,GCF_003691675_PROKKA_02111:0.0131183)n2:0.193888)n1:0.0853837)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000245_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00235:0.192437,(GCF_005280335_PROKKA_00289:5e-09,(GCF_003691675_PROKKA_02114:5e-09,(GCF_002008305_PROKKA_00101:5e-09,GCF_023573625_PROKKA_00096:0.0162854)n3:0.01619)n2:0.0498763)n1:0.192437)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000257_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00204:0.0798111,(GCF_005280335_PROKKA_00272:0.0974807,((GCF_002008305_PROKKA_00115:0,GCF_003691675_PROKKA_02128:0)n3:0.00426828,GCF_023573625_PROKKA_00120:0.00400912)n2:0.089999)n1:0.0798111)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000264_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00193:0.119622,(GCF_005280335_PROKKA_00259:0.0690494,(GCF_002008305_PROKKA_00126:0.008145,(GCF_003691675_PROKKA_02140:0.00306198,GCF_023573625_PROKKA_00134:5e-09)n3:0.0104122)n2:0.0778492)n1:0.119622)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000267_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00188:0.0623438,(GCF_005280335_PROKKA_00252:0.108645,(GCF_023573625_PROKKA_00141:0.0219943,(GCF_002008305_PROKKA_00133:0.0062645,GCF_003691675_PROKKA_02147:0.00188606)n3:0.0122163)n2:0.104837)n1:0.0623438)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000270_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00181:0.00929656,((GCF_002008305_PROKKA_00137:0.00372642,GCF_005280335_PROKKA_00247:0.0715891)n2:0.00370741,(GCF_003691675_PROKKA_02151:5e-09,GCF_023573625_PROKKA_00145:0.00370457)n3:5e-09)n1:0.00929656)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000274_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00177:0.168865,(GCF_005280335_PROKKA_00243:0.107545,(GCF_002008305_PROKKA_00141:0.00311403,(GCF_003691675_PROKKA_02155:0,GCF_023573625_PROKKA_00149:0)n3:0.00515727)n2:0.0764295)n1:0.168865)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000276_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00175:0.0371212,(GCF_005280335_PROKKA_00241:0.0865828,(GCF_023573625_PROKKA_00151:0.00593509,(GCF_003691675_PROKKA_02157:0.0130984,GCF_002008305_PROKKA_00143:0.00681703)n3:0.000281041)n2:0.0592956)n1:0.0371212)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000280_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00820:0.0609395,((GCF_002008305_PROKKA_00148:0,GCF_003691675_PROKKA_02162:0,GCF_023573625_PROKKA_00156:0)n2:0.00629425,GCF_005280335_PROKKA_00235:0.0140518)n1:0.0609395)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000287_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00169:0.650968,(GCF_005280335_PROKKA_00223:0.0149304,(GCF_003691675_PROKKA_02174:0.0251951,(GCF_002008305_PROKKA_00178:0.00601323,GCF_023573625_PROKKA_00175:0.0510235)n3:0.0144957)n2:0.0428155)n1:0.650968)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000289_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00166:0.052807,(GCF_005280335_PROKKA_00221:0.0202464,(GCF_003691675_PROKKA_02176:0.00269585,(GCF_023573625_PROKKA_00177:0.0054009,GCF_002008305_PROKKA_00180:0.00269069)n3:0.00132241)n2:0.0171959)n1:0.052807)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000298_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00154:2.5e-09,(GCF_005280335_PROKKA_00207:0.0288614,(GCF_002008305_PROKKA_00193:0.00571307,(GCF_003691675_PROKKA_02189:0,GCF_023573625_PROKKA_00193:0)n3:5e-09)n2:0.00569246)n1:2.5e-09)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000305_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00140:0.00306697,(GCF_002008305_PROKKA_00204:0.00461133,((GCF_003691675_PROKKA_02199:0,GCF_023573625_PROKKA_00206:0)n3:0.00788612,GCF_005280335_PROKKA_00198:0.21002)n2:0.00453874)n1:0.00306697)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000312_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00120:0.128342,(GCF_005280335_PROKKA_00169:0.202063,(GCF_023573625_PROKKA_00214:0.0168546,(GCF_002008305_PROKKA_00214:0.0364367,GCF_003691675_PROKKA_02207:0.0280191)n3:0.0110104)n2:0.0750789)n1:0.128342)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000313_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00119:0.605644,(GCF_005280335_PROKKA_00166:0.357479,((GCF_002008305_PROKKA_00215:0,GCF_003691675_PROKKA_02208:0)n3:5e-09,GCF_023573625_PROKKA_00215:0.0202792)n2:0.218365)n1:0.605644)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000321_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00108:0.0335028,(GCF_005280335_PROKKA_00151:0.135636,(GCF_023573625_PROKKA_00231:0.00229916,(GCF_002008305_PROKKA_00230:0.00195798,GCF_003691675_PROKKA_02243:0.00188003)n3:0.00930367)n2:0.0585)n1:0.0335028)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000323_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00105:0.0563272,(GCF_005280335_PROKKA_00147:0.111509,(GCF_023573625_PROKKA_00233:0.00630314,(GCF_002008305_PROKKA_00232:0.00325259,GCF_003691675_PROKKA_02245:0.0033612)n3:0.0205365)n2:0.160375)n1:0.0563272)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000329_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00097:0.205511,(GCF_005280335_PROKKA_00132:0.0525527,(GCF_002008305_PROKKA_00239:0.00550086,(GCF_003691675_PROKKA_02252:0,GCF_023573625_PROKKA_00240:0)n3:0.00554103)n2:0.0527197)n1:0.205511)n0;