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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/OG0000003_tree.txt +1 -0
  2. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000004_tree.txt +1 -0
  3. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000005_tree.txt +1 -0
  4. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000006_tree.txt +1 -0
  5. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000008_tree.txt +1 -0
  6. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000009_tree.txt +1 -0
  7. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000011_tree.txt +1 -0
  8. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000013_tree.txt +1 -0
  9. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000015_tree.txt +1 -0
  10. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000016_tree.txt +1 -0
  11. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000018_tree.txt +1 -0
  12. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000021_tree.txt +1 -0
  13. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000022_tree.txt +1 -0
  14. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000023_tree.txt +1 -0
  15. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000028_tree.txt +1 -0
  16. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000029_tree.txt +1 -0
  17. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000032_tree.txt +1 -0
  18. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000034_tree.txt +1 -0
  19. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000035_tree.txt +1 -0
  20. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000036_tree.txt +1 -0
  21. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000037_tree.txt +1 -0
  22. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000045_tree.txt +1 -0
  23. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000047_tree.txt +1 -0
  24. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000048_tree.txt +1 -0
  25. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000049_tree.txt +1 -0
  26. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000050_tree.txt +1 -0
  27. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000053_tree.txt +1 -0
  28. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000054_tree.txt +1 -0
  29. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000056_tree.txt +1 -0
  30. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000057_tree.txt +1 -0
  31. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000059_tree.txt +1 -0
  32. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000060_tree.txt +1 -0
  33. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000061_tree.txt +1 -0
  34. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000062_tree.txt +1 -0
  35. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000063_tree.txt +1 -0
  36. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000064_tree.txt +1 -0
  37. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000066_tree.txt +1 -0
  38. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000068_tree.txt +1 -0
  39. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000069_tree.txt +1 -0
  40. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000070_tree.txt +1 -0
  41. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000071_tree.txt +1 -0
  42. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000074_tree.txt +1 -0
  43. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000077_tree.txt +1 -0
  44. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000079_tree.txt +1 -0
  45. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000082_tree.txt +1 -0
  46. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000083_tree.txt +1 -0
  47. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000088_tree.txt +1 -0
  48. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000090_tree.txt +1 -0
  49. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000093_tree.txt +1 -0
  50. Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000095_tree.txt +1 -0
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000003_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (((GCF_003691675_PROKKA_01116:5e-09,GCF_023573625_PROKKA_01884:0.00642897)n2:0.00642558,(GCF_023573625_PROKKA_00114:6e-09,((((GCF_002008305_PROKKA_02280:0.135022,GCF_020097155_PROKKA_00317:0.0497284)n7:0.0472623,((GCF_005280335_PROKKA_02347:6e-09,GCF_005280335_PROKKA_02631:0.0150545)n9:0.0150917,GCF_005280335_PROKKA_01304:4.5e-09)n8:5e-10)n6:0.00757128,((GCF_005280335_PROKKA_01281:0,GCF_005280335_PROKKA_01312:0)n11:0.00752593,GCF_020097155_PROKKA_00625:0.00671021)n10:0.000745579)n5:5e-09,(GCF_002008305_PROKKA_01068:0.0149832,(GCF_005280335_PROKKA_01317:0.0074632,(GCF_003691675_PROKKA_01658:0.00646513,((GCF_003691675_PROKKA_00319:0,GCF_003691675_PROKKA_02267:0)n16:0.00740272,GCF_003691675_PROKKA_00788:5e-09)n15:0.00664702)n14:0.000738558)n13:6e-09)n12:0.00655117)n4:0.00583393)n3:0.000648215)n1:2.5e-09,(GCF_005280335_PROKKA_02614:0.00795341,(GCF_002008305_PROKKA_01386:5e-09,((GCF_003691675_PROKKA_01327:0,GCF_005280335_PROKKA_00758:0,GCF_005280335_PROKKA_02331:0,GCF_023573625_PROKKA_01539:0)n20:5e-09,(GCF_020097155_PROKKA_01796:0,GCF_020097155_PROKKA_01836:0,GCF_020097155_PROKKA_02207:0)n21:0.00738984)n19:5e-09)n18:5e-09)n17:2.5e-09)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000004_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_01829:0.202887,(GCF_005280335_PROKKA_00899:0.362442,((((GCF_005280335_PROKKA_00643:0,GCF_005280335_PROKKA_01506:0)n5:5e-09,GCF_005280335_PROKKA_00229:5e-09)n4:5e-09,(GCF_003691675_PROKKA_01015:0.0260674,(GCF_002008305_PROKKA_02069:0.0235031,((GCF_023573625_PROKKA_01547:0,GCF_023573625_PROKKA_01549:0,GCF_023573625_PROKKA_01880:0)n9:5e-09,(GCF_002008305_PROKKA_00376:0,GCF_002008305_PROKKA_01393:0,GCF_002008305_PROKKA_02112:0,GCF_002008305_PROKKA_02277:0,GCF_003691675_PROKKA_00355:0,GCF_003691675_PROKKA_01125:0,GCF_003691675_PROKKA_01746:0,GCF_003691675_PROKKA_01819:0,GCF_003691675_PROKKA_02016:0,GCF_023573625_PROKKA_00116:0,GCF_023573625_PROKKA_01974:0)n10:6.8931e-07)n8:7.659e-08)n7:8.51e-08)n6:1.7e-08)n3:5e-09,(GCF_003691675_PROKKA_01012:0.00879715,((GCF_005280335_PROKKA_00228:0,GCF_005280335_PROKKA_00895:0)n13:5e-09,GCF_005280335_PROKKA_02100:0.00800633)n12:0.000889592)n11:1.7795e-05)n2:0.491081)n1:0.202887)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000005_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_005280335_PROKKA_01282:0.0471932,(GCF_020097155_PROKKA_00652:0.0408064,GCF_020097155_PROKKA_01820:0.0487728)n2:0.0350243)n1:0.0504201,((GCF_020097155_PROKKA_01361:0.0664936,(GCF_020097155_PROKKA_00641:0.0713213,GCF_020097155_PROKKA_01832:0.0347426)n5:0.0143019)n4:0.0587383,(GCF_020097155_PROKKA_00227:0.736291,((GCF_003691675_PROKKA_01778:1.08339,GCF_020097155_PROKKA_00678:0.747437)n8:1.026,(GCF_005280335_PROKKA_02274:0.0102952,((GCF_020097155_PROKKA_00315:0,GCF_020097155_PROKKA_00645:0)n11:0.020801,((GCF_020097155_PROKKA_00631:0,GCF_020097155_PROKKA_02162:0)n13:0.00290493,((GCF_020097155_PROKKA_00751:0,GCF_020097155_PROKKA_01794:0)n15:5e-09,(GCF_020097155_PROKKA_01890:0.011673,(GCF_020097155_PROKKA_00627:5e-09,(((GCF_020097155_PROKKA_00226:5e-09,GCF_020097155_PROKKA_01835:0.0028778)n20:5e-09,(GCF_020097155_PROKKA_00448:5e-09,GCF_020097155_PROKKA_02206:5e-09)n21:0.00342437)n19:0.00576261,GCF_020097155_PROKKA_00312:6e-09)n18:0.00580175)n17:5e-09)n16:0.00290432)n14:5e-09)n12:0.0129056)n10:0.00948523)n9:0.161534)n7:0.154764)n6:0.178416)n3:0.0504201)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000006_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_005280335_PROKKA_01214:0.00128355,(GCF_003691675_PROKKA_01011:0.00464154,(GCF_003691675_PROKKA_01114:0.00747385,((GCF_002008305_PROKKA_00157:0,GCF_002008305_PROKKA_01034:0,GCF_002008305_PROKKA_01292:0,GCF_002008305_PROKKA_02077:0,GCF_003691675_PROKKA_01104:0,GCF_023573625_PROKKA_01250:0)n4:5e-09,(GCF_023573625_PROKKA_01339:5e-09,((GCF_023573625_PROKKA_00588:0,GCF_023573625_PROKKA_02205:0)n7:0.00371775,((GCF_002008305_PROKKA_01384:5e-09,(GCF_003691675_PROKKA_02023:0.00278449,GCF_023573625_PROKKA_01885:0.0166207)n10:0.000941071)n9:5e-09,(GCF_023573625_PROKKA_00590:0.0335204,GCF_003691675_PROKKA_01112:4.5e-09)n11:5e-10)n8:0.00372693)n6:5e-09)n5:5e-09)n3:5e-09)n2:0.00114838)n1:0.00128355)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000008_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_002008305_PROKKA_02227:0.026191,(GCF_023573625_PROKKA_01016:0,GCF_023573625_PROKKA_01158:0)n2:0.00373267)n1:2.5e-09,(GCF_003691675_PROKKA_00092:0,GCF_003691675_PROKKA_00343:0,GCF_003691675_PROKKA_01013:0,GCF_003691675_PROKKA_01394:0,GCF_003691675_PROKKA_02284:0,GCF_023573625_PROKKA_00606:0,GCF_023573625_PROKKA_01349:0,GCF_023573625_PROKKA_02164:0,((GCF_002008305_PROKKA_01398:0.0719037,(GCF_002008305_PROKKA_01502:0.00443704,GCF_002008305_PROKKA_02225:0.46793)n6:0.00244087)n5:0.0621436,GCF_002008305_PROKKA_00711:0)n4:0)n3:5e-09)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000009_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_002008305_PROKKA_00712:0,GCF_002008305_PROKKA_01400:0,GCF_003691675_PROKKA_00091:0,GCF_003691675_PROKKA_00344:0,GCF_003691675_PROKKA_01014:0,GCF_003691675_PROKKA_01393:0,GCF_003691675_PROKKA_02283:0,GCF_023573625_PROKKA_00607:0,GCF_023573625_PROKKA_01017:0,GCF_023573625_PROKKA_01157:0,GCF_023573625_PROKKA_01350:0,GCF_023573625_PROKKA_02163:0)n1:2.5e-09,(GCF_002008305_PROKKA_01503:0.0796831,GCF_002008305_PROKKA_02228:0.00244825)n2:2.5e-09)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000011_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_023573625_PROKKA_02002:0.0199231,((GCF_003691675_PROKKA_00339:0,GCF_003691675_PROKKA_01779:0,(GCF_002008305_PROKKA_02074:5e-09,GCF_002008305_PROKKA_00616:0)n4:0)n3:0.0173983,GCF_005280335_PROKKA_00719:0.0143496)n2:0.141217)n1:0.0226881,((GCF_005280335_PROKKA_00727:0.0183933,(GCF_003691675_PROKKA_00350:0.0149387,GCF_003691675_PROKKA_00789:5e-09)n7:0.0432446)n6:0.0328139,(GCF_005280335_PROKKA_02366:0.0896787,(GCF_023573625_PROKKA_02005:0.893599,(GCF_002008305_PROKKA_00609:0.00206281,GCF_003691675_PROKKA_01769:0.0551862)n10:0.105956)n9:0.0679877)n8:0.00755419)n5:0.0226881)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000013_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_01887:0.0140417,((GCF_023573625_PROKKA_01544:0.406222,(GCF_003691675_PROKKA_01765:0.0218988,(GCF_005280335_PROKKA_00706:0.38075,((GCF_005280335_PROKKA_02276:0.00125225,GCF_005280335_PROKKA_02636:0.0115439)n6:0.012746,(GCF_005280335_PROKKA_02496:0.211792,(GCF_005280335_PROKKA_02495:0.00541976,GCF_005280335_PROKKA_02615:5e-09)n8:5e-09)n7:0.00349261)n5:0.0184091)n4:0.00204545)n3:0.16121)n2:0.0616112,(GCF_003691675_PROKKA_00341:0.124098,GCF_023573625_PROKKA_00898:0.0141744)n9:0.00157493)n1:0.0140417)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000015_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_020097155_PROKKA_01149:0.0283035,(GCF_005280335_PROKKA_01238:0.0173285,(GCF_002008305_PROKKA_01656:0.00831215,(GCF_003691675_PROKKA_01361:0.00453286,GCF_023573625_PROKKA_01586:0.0026178)n4:0.0035327)n3:0.00840392)n2:0.0137265)n1:0.239249,(GCF_020097155_PROKKA_02465:5e-09,(GCF_005280335_PROKKA_02606:0.0125999,(GCF_002008305_PROKKA_00355:0.00179295,(GCF_003691675_PROKKA_00071:0.00179101,GCF_023573625_PROKKA_00362:5e-09)n8:0.00178836)n7:0.00257201)n6:0.0229549)n5:0.239249)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000016_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((((GCF_002008305_PROKKA_01771:0,GCF_003691675_PROKKA_01478:0)n3:0.00640386,GCF_023573625_PROKKA_01700:0.00630266)n2:0.00346542,(GCF_005280335_PROKKA_01106:0.0334911,GCF_020097155_PROKKA_01032:0.109175)n4:0.0194111)n1:0.0112761,((GCF_003691675_PROKKA_00706:0.00583165,GCF_023573625_PROKKA_00935:0.00254211)n6:0.00401193,(GCF_005280335_PROKKA_01897:0.0411368,(GCF_002008305_PROKKA_00992:0.0145508,GCF_020097155_PROKKA_01844:0.0149575)n8:0.00218125)n7:0.00277314)n5:0.0112761)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000018_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_01147:0.131714,(GCF_005280335_PROKKA_01236:0.163345,(GCF_002008305_PROKKA_01845:0.679573,((GCF_002008305_PROKKA_01658:5e-09,(GCF_003691675_PROKKA_01363:5e-09,GCF_023573625_PROKKA_01588:0.00305814)n5:0.00924601)n4:0.392252,(GCF_002008305_PROKKA_01559:0.00979198,(GCF_003691675_PROKKA_01269:0.0122266,GCF_023573625_PROKKA_01486:0.00911241)n7:0.0116984)n6:0.35765)n3:0.20453)n2:0.252316)n1:0.131714)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000021_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_02254:0.139388,(((GCF_003691675_PROKKA_00295:0.00642524,(GCF_023573625_PROKKA_00572:0.00675958,GCF_002008305_PROKKA_00571:0.00644994)n4:5e-09)n3:0.0151776,(GCF_003691675_PROKKA_00294:0.00377234,GCF_002008305_PROKKA_00570:0.00530612)n5:0.000589569)n2:0.277528,(GCF_005280335_PROKKA_02375:0.250904,GCF_005280335_PROKKA_02374:0.265984)n6:0.0295538)n1:0.0376122)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000022_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_020097155_PROKKA_00711:0.105881,((GCF_002008305_PROKKA_01289:0,GCF_003691675_PROKKA_01008:0)n3:0.00125694,GCF_023573625_PROKKA_01247:0.00151652)n2:0.0511899)n1:0.256589,(GCF_002008305_PROKKA_00633:5e-09,((GCF_005280335_PROKKA_00405:0.00648903,GCF_020097155_PROKKA_02196:0.00124746)n6:0.0103637,GCF_023573625_PROKKA_00598:5e-09)n5:0.00256113)n4:0.256589)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000023_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_005280335_PROKKA_00513:0.113678,((GCF_020097155_PROKKA_01865:0.494812,(GCF_020097155_PROKKA_00440:0.75221,GCF_020097155_PROKKA_00650:1.0005)n4:0.363807)n3:0.342567,GCF_020097155_PROKKA_00454:0.0401095)n2:0.00445661)n1:0.00463707,(GCF_002008305_PROKKA_02238:0.00333617,(GCF_003691675_PROKKA_01940:0.0263141,GCF_023573625_PROKKA_02170:0.00645885)n6:0.00646765)n5:0.0276298)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000028_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_005280335_PROKKA_00725:0.00160657,((GCF_002008305_PROKKA_01072:0,GCF_003691675_PROKKA_00335:0,GCF_003691675_PROKKA_00348:0,GCF_023573625_PROKKA_01021:0)n2:5e-09,(GCF_002008305_PROKKA_00162:5e-09,GCF_003691675_PROKKA_00791:0.00289328)n3:0.000321476)n1:0.00160657)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000029_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_005280335_PROKKA_00726:0.00402188,((GCF_023573625_PROKKA_01020:0,((GCF_003691675_PROKKA_00349:0.00806332,GCF_003691675_PROKKA_00334:0)n4:0,GCF_003691675_PROKKA_00790:0)n3:0)n2:5e-09,(GCF_002008305_PROKKA_00163:0,GCF_002008305_PROKKA_01071:0)n5:5e-09)n1:0.00402188)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000032_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00093:0.106919,(GCF_002008305_PROKKA_00245:5e-09,((GCF_005280335_PROKKA_00124:0.0119858,GCF_023573625_PROKKA_00245:0.0104521)n3:0.0146913,((GCF_003691675_PROKKA_00096:0.753052,GCF_003691675_PROKKA_00100:0.999711)n5:0.423025,GCF_003691675_PROKKA_02257:4.5e-09)n4:5e-10)n2:0.00366845)n1:0.172288)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000034_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_02214:0,(GCF_023573625_PROKKA_02003:0.198198,(GCF_005280335_PROKKA_00718:0.00848374,(GCF_003691675_PROKKA_00340:0,((GCF_002008305_PROKKA_00617:0,GCF_002008305_PROKKA_02075:0)n5:0.00507506,GCF_003691675_PROKKA_01780:5e-09)n4:0.00635949)n3:0.000706611)n2:5e-09)n1:0.0154271)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000035_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_02189:0.0259167,((GCF_005280335_PROKKA_00410:5e-09,(GCF_005280335_PROKKA_00389:5e-09,GCF_005280335_PROKKA_00393:0.0302627)n3:0.0101513)n2:0.0101082,(GCF_002008305_PROKKA_00627:0.0101356,(GCF_003691675_PROKKA_00372:0,GCF_023573625_PROKKA_00604:0)n5:5e-09)n4:5e-09)n1:0.0259167)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000036_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_020097155_PROKKA_00451:1.08588,(GCF_005280335_PROKKA_01253:0.820278,GCF_005280335_PROKKA_01330:1.08257)n2:0.273357)n1:0.332923,(GCF_005280335_PROKKA_00403:5e-09,(GCF_020097155_PROKKA_02198:0.0127561,(GCF_002008305_PROKKA_00631:0,GCF_023573625_PROKKA_00600:0)n5:0.00776946)n4:0.00959987)n3:0.332923)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000037_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_020097155_PROKKA_02076:0.375524,(GCF_020097155_PROKKA_00685:0.591129,GCF_020097155_PROKKA_00686:0.887975)n2:0.508038)n1:0.132238,(GCF_005280335_PROKKA_02181:0.346323,(GCF_023573625_PROKKA_00713:0.00776034,(GCF_003691675_PROKKA_00479:0.0261668,GCF_002008305_PROKKA_00749:0.010459)n5:0.00784635)n4:0.168814)n3:0.132238)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000045_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_020097155_PROKKA_01240:0.199431,(GCF_020097155_PROKKA_01828:1.16549,(GCF_020097155_PROKKA_00714:1.59757,GCF_020097155_PROKKA_00643:0.664171)n3:0.128768)n2:0.427507)n1:0.078349,(GCF_023573625_PROKKA_01517:0.00179652,(GCF_002008305_PROKKA_01590:0.010479,GCF_003691675_PROKKA_01302:5e-09)n5:0.00660547)n4:0.078349)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000047_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_01003:0.0529808,((GCF_003691675_PROKKA_01503:0.0383186,(GCF_002008305_PROKKA_01806:0.00665126,GCF_023573625_PROKKA_01727:5e-09)n3:0.0173372)n2:0.0457164,((GCF_005280335_PROKKA_00397:0.217563,GCF_005280335_PROKKA_02641:0.804782)n5:0.171489,GCF_005280335_PROKKA_01068:0.0506263)n4:0.00562515)n1:0.101922)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000048_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_01001:0.083454,((GCF_002008305_PROKKA_01808:0,GCF_003691675_PROKKA_01505:0)n2:0.0207031,(GCF_023573625_PROKKA_01729:5e-09,((GCF_005280335_PROKKA_00398:0.156203,GCF_005280335_PROKKA_02643:0.809193)n5:0.146632,GCF_005280335_PROKKA_01066:0.00834272)n4:0.000926969)n3:0.0178622)n1:0.108492)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000049_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00774:0.0178715,(GCF_005280335_PROKKA_00837:0.0460029,((GCF_003691675_PROKKA_01715:0.00786137,GCF_002008305_PROKKA_02005:0.0125602)n3:0.0028999,((GCF_023573625_PROKKA_00173:0.527292,GCF_023573625_PROKKA_00174:0.595234)n5:0.277659,GCF_023573625_PROKKA_01943:0.00299376)n4:0.00033264)n2:0.0533522)n1:0.0585172)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000050_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_005280335_PROKKA_01308:0.0105914,GCF_020097155_PROKKA_02237:0.0127592)n1:0.12808,(GCF_020097155_PROKKA_00662:1.78369,(GCF_005280335_PROKKA_00694:0.0183283,(GCF_003691675_PROKKA_01794:5e-09,(GCF_023573625_PROKKA_02028:0.0207894,GCF_002008305_PROKKA_02089:5e-09)n5:0.0094745)n4:0.0143074)n3:0.0908522)n2:0.12808)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000053_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_020097155_PROKKA_00418:0.0325663,(GCF_002008305_PROKKA_02261:0.0261664,GCF_023573625_PROKKA_02192:0.0150979)n2:0.00921526)n1:0.115781,(GCF_020097155_PROKKA_00422:1.58451,(GCF_003691675_PROKKA_01948:0.0107584,(GCF_002008305_PROKKA_02246:5e-09,GCF_023573625_PROKKA_02178:0.00537302)n5:2.422e-06)n4:0.119768)n3:0.115781)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000054_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00434:0.00303817,(GCF_023573625_PROKKA_02184:0.00403191,(GCF_003691675_PROKKA_01952:0.00300307,((GCF_002008305_PROKKA_02275:0.28969,GCF_005280335_PROKKA_00493:0.173257)n4:0.157487,(GCF_005280335_PROKKA_00488:0.0161824,GCF_002008305_PROKKA_02253:0.00641504)n5:0.000712782)n3:0.00549399)n2:0.000610443)n1:0.00303817)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000056_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00353:0.221286,((GCF_002008305_PROKKA_00025:0.0157216,(GCF_023573625_PROKKA_00025:0.00957219,GCF_003691675_PROKKA_02043:0.00638713)n3:0.00717563)n2:0.000664308,(GCF_005280335_PROKKA_00370:0.0256665,GCF_005280335_PROKKA_00371:0.0160344)n4:0.0017816)n1:0.0198962)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000057_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00427:0.509673,(GCF_005280335_PROKKA_00464:0.960635,(GCF_023573625_PROKKA_02208:0.250534,(GCF_002008305_PROKKA_00568:1.40758,(GCF_002008305_PROKKA_00037:0.850779,GCF_002008305_PROKKA_02274:0.171758)n4:0.0171758)n3:0.00190842)n2:0.772146)n1:0.509673)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000059_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_005280335_PROKKA_00346:0.00709262,(GCF_020097155_PROKKA_00293:0.178921,GCF_020097155_PROKKA_00284:0.030938)n2:0.00343756)n1:0.0713523,(GCF_023573625_PROKKA_00048:0.00716124,(GCF_003691675_PROKKA_02066:0.0110657,GCF_002008305_PROKKA_00053:0.00947044)n4:0.013023)n3:0.15895)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000060_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00273:0.0641015,((GCF_023573625_PROKKA_00058:0.0165505,(GCF_002008305_PROKKA_00063:0.00342973,GCF_003691675_PROKKA_02076:0.0271495)n3:0.00805598)n2:0.138072,(GCF_005280335_PROKKA_00332:0.101313,GCF_005280335_PROKKA_00201:1.60376)n4:0.178196)n1:5e-09)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000061_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_020097155_PROKKA_00266:0.0507778,GCF_020097155_PROKKA_00684:0.781922)n1:0.0146412,(GCF_005280335_PROKKA_00326:0.0759528,(GCF_023573625_PROKKA_00062:0.00531867,(GCF_002008305_PROKKA_00068:6e-09,GCF_003691675_PROKKA_02081:0.0106655)n4:0.0065055)n3:0.0343515)n2:0.0146412)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000062_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00258:0.0828191,((GCF_002008305_PROKKA_00076:0,GCF_023573625_PROKKA_00070:0)n2:5e-09,(GCF_003691675_PROKKA_02089:0.00645918,(GCF_005280335_PROKKA_02338:1.30606,GCF_005280335_PROKKA_00317:0.0203714)n4:0.00226349)n3:0.00318119)n1:0.209305)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000063_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00231:0.0464833,((GCF_005280335_PROKKA_00038:1.65423,GCF_005280335_PROKKA_00285:5e-09)n2:0.00623731,(GCF_023573625_PROKKA_00100:0.00411274,(GCF_002008305_PROKKA_00105:0.00205499,GCF_003691675_PROKKA_02118:5e-09)n4:5e-09)n3:0.01531)n1:0.0464833)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000064_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00137:0.231945,(GCF_002008305_PROKKA_00119:5e-09,((GCF_003691675_PROKKA_02135:0,GCF_023573625_PROKKA_00127:0)n3:5e-09,(GCF_005280335_PROKKA_00088:0.61229,GCF_005280335_PROKKA_00265:0.0518959)n4:0.00576621)n2:0.00940129)n1:0.450584)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000066_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00149:3e-09,(GCF_002008305_PROKKA_00198:0.00331156,(GCF_023573625_PROKKA_00198:0.0166215,(GCF_005280335_PROKKA_00197:0.150655,(GCF_003691675_PROKKA_02194:0.0101568,GCF_003691675_PROKKA_02026:1.289)n4:0.143223)n3:0.217831)n2:5e-09)n1:3e-09)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000068_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00321:0.424257,((GCF_002008305_PROKKA_00216:0,GCF_003691675_PROKKA_02209:0,GCF_023573625_PROKKA_00216:0)n2:0.153734,(GCF_005280335_PROKKA_02206:0.722161,GCF_005280335_PROKKA_00167:0.0438055)n3:0.00486727)n1:0.845508)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000069_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00117:0.103974,((GCF_023573625_PROKKA_00222:0.000901637,(GCF_002008305_PROKKA_00221:0.00658315,GCF_003691675_PROKKA_02234:0.00564873)n3:0.00571932)n2:0.0879877,(GCF_005280335_PROKKA_00086:1.0168,GCF_005280335_PROKKA_00159:0.0891042)n4:0.00990047)n1:0.0931407)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000070_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00115:0.0627229,(((GCF_002008305_PROKKA_00223:0,GCF_003691675_PROKKA_02236:0)n3:0.00866475,GCF_023573625_PROKKA_00224:5e-09)n2:0.0793393,(GCF_005280335_PROKKA_00588:1.46708,GCF_005280335_PROKKA_00157:0.119192)n4:0.0132435)n1:0.0929253)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000071_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00100:0.0792224,(GCF_005280335_PROKKA_00135:0.030695,(GCF_002008305_PROKKA_00236:0.0052112,(GCF_003691675_PROKKA_00102:0.474068,(GCF_003691675_PROKKA_02249:0.00210409,GCF_023573625_PROKKA_00237:0.00210936)n4:0.00488264)n3:0.000542516)n2:0.0556894)n1:0.0878221)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000074_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_02346:0.129278,(GCF_002008305_PROKKA_00279:0.00519361,(GCF_005280335_PROKKA_00074:0.00533227,(GCF_003691675_PROKKA_00203:0.0521876,(GCF_003691675_PROKKA_02294:6e-09,GCF_023573625_PROKKA_00278:0.00799105)n4:5.4e-09)n3:6e-10)n2:0.00545202)n1:1.43336)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000077_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_020097155_PROKKA_00035:0.0908422,GCF_020097155_PROKKA_01222:2.01679)n1:0.0580221,(GCF_005280335_PROKKA_00057:0.0860688,(GCF_003691675_PROKKA_00005:0.0338802,(GCF_002008305_PROKKA_00297:0.013001,GCF_023573625_PROKKA_00304:0.00871193)n4:0.0296028)n3:0.0594053)n2:0.0580221)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000079_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_020097155_PROKKA_00015:0.0965629,GCF_020097155_PROKKA_00687:1.09006)n1:0.0108903,(GCF_005280335_PROKKA_00019:0.0617126,(GCF_003691675_PROKKA_00033:5e-09,(GCF_002008305_PROKKA_00318:0.00802572,GCF_023573625_PROKKA_00325:0.00404751)n4:0.00797851)n3:0.0325911)n2:0.0108903)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000082_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ ((GCF_005280335_PROKKA_02569:0.0292659,(GCF_020097155_PROKKA_02444:0.0341839,GCF_020097155_PROKKA_01756:0.0865893)n2:0.00962103)n1:0.00286866,(GCF_023573625_PROKKA_00392:0.00663066,(GCF_002008305_PROKKA_00386:5e-09,GCF_003691675_PROKKA_00110:0.00346887)n4:0.00379943)n3:0.00361157)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000083_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_02415:0.0161681,(((GCF_002008305_PROKKA_00412:0,GCF_023573625_PROKKA_00415:0)n3:5e-09,GCF_003691675_PROKKA_00132:0.00311154)n2:0.0202945,(GCF_005280335_PROKKA_02646:1.81989,GCF_005280335_PROKKA_02547:0.00729931)n4:0.000811034)n1:0.0436164)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000088_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_02336:0.0514642,(GCF_003691675_PROKKA_00216:5e-09,(GCF_002008305_PROKKA_00495:0.00917144,(GCF_005280335_PROKKA_01221:1.41679,(GCF_005280335_PROKKA_02452:0.0303728,GCF_023573625_PROKKA_00494:0.0202532)n4:0.00445337)n3:0.000494819)n2:0.0112162)n1:0.185651)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000090_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_02311:0.00444868,((GCF_023573625_PROKKA_00521:5e-09,(GCF_005280335_PROKKA_02428:0.00892789,GCF_005280335_PROKKA_01219:1.61464)n3:0.179404)n2:0.0301173,(GCF_003691675_PROKKA_00243:0.00592033,GCF_002008305_PROKKA_00521:0.0118539)n4:5e-09)n1:0.00296109)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000093_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_00505:0.0292453,((GCF_003691675_PROKKA_01888:0,GCF_023573625_PROKKA_02119:0,(GCF_002008305_PROKKA_00604:1.54478,GCF_002008305_PROKKA_02174:0)n3:0)n2:0.107953,GCF_005280335_PROKKA_00578:0.115182)n1:0.0977326)n0;
Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000095_tree.txt ADDED
@@ -0,0 +1 @@
 
 
1
+ (GCF_020097155_PROKKA_01190:0.697411,((GCF_005280335_PROKKA_02344:0.102409,((GCF_003691675_PROKKA_00327:0,GCF_023573625_PROKKA_02008:0)n4:0.0682043,GCF_003691675_PROKKA_01771:0.2608)n3:0.0289778)n2:0.0352008,GCF_002008305_PROKKA_00611:0.133729)n1:0.697411)n0;