diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000003_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000003_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..672f122eede9d6bc295403734a3ae8a7e406bd8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000003_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000004_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000004_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc2af9a7314aaeaf6614f2b84c0b45d9340073ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000004_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000005_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000005_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..76f406b9eba8602d3ca9dbf1bc22331dfeac607a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000005_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000006_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000006_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eee9ddd6d216fc31ceb59fb7e58aea402cfbce9f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000006_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000008_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000008_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a5b8119c76e5afad116bca6661f73310853ed1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000008_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000009_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000009_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05e3b0ebe38aab1b8f774d3be4e2c5c6e0711c09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000009_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000011_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000011_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..095c0a8767f0f8f9f1bf6252a1fc36ad42010595
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000011_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000013_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000013_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4b05d0b4462dc6305b7242f5be5be23691ac782
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000013_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000015_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000015_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22e1ecac158eb2f75cf4329bf842d35d8074e1e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000015_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000016_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000016_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43daf4a34621cd6914d601ce98c85ab9e0109303
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000016_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000018_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000018_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6ebbb022d61dfb94744926c6d096ba85cccf41f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000018_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000021_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000021_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a686cabc373b753b7886925d238d437284256bec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000021_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000022_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000022_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec7e2dc109188eea9d37d51ef0238fcad421f4fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000022_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000023_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000023_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a99728f2c0c2a0c52348fdacbd677f6ca24d5cd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000023_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000028_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000028_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a80395e73c23a84106e2240dbcd60a81fa70163
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000028_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000029_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000029_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..803f544c0c401ca7b8a0f66fe4dbe8e598cdbeef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000029_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000032_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000032_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b820d40d390dd30f9b32c55f640a5a4328a72488
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000032_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000034_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000034_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b67d402cf15f7da412779b2d0348d9b3435fb4bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000034_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000035_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000035_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8bf7b875e688d34547b34b5f38c92c24b6bb2ddc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000035_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000036_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000036_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..29db91cce9311543eae301c6bc3da0d1d7d37dab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000036_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000037_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000037_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0455ec0abab586ee6b93c6f5cb42dae7eb0b1452
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000037_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000045_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000045_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5eef25bab193253c7066643742450603232b8247
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000045_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000047_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000047_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7bef2e27d613b58f69587cffa16284dd1320e713
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000047_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000048_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000048_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fdbb701d76aedf6e96a6a824f8b4f5d1d6b09330
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000048_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000049_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000049_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a05a07073e00466beb5672d7a472587e7fc70310
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000049_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000050_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000050_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b40a0f0ba5c1f537c2bfe591778d1d1b012d3b23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000050_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000053_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000053_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16486a7dacb384a715057bcf7252e06ca9eb1804
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000053_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000054_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000054_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbbace16c85668d1651718b5cf1c8983565eefbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000054_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000056_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000056_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f8a9ab54aedfbf8ee284a8c4f182ffe91372f4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000056_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000057_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000057_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7dc23a7a81570ef588c66599ef7b41bfe883dc9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000057_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000059_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000059_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f304ce11abf6804e13ef55af46bdc075c23d9a86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000059_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000060_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000060_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15ebfd06fe796696ef7767c67be562b85e1db8bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000060_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000061_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000061_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1c9da7dac2007d7383518a7b42df761b5eba44f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000061_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000062_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000062_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5fe56fc15865b5f890fe7b1474405d96381ba71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000062_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000063_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000063_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ae746b23c609ddf6400e48559a5308333b10f3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000063_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000064_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000064_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b40d100dcc9b418930ede3b363d26a49fab8166
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000064_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000066_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000066_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4e5bff32a235c6106914dcfefe819c2958b56b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000066_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000068_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000068_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c7198c2699c79293710b20561feb46f20b1ef7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000068_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000069_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000069_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2051a1112e4423fc2fa3d13c6cf97c15722ceebf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000069_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000070_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000070_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78bacd085f7d90b9afc5139fecdae74358082d4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000070_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000071_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000071_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e91ba7de1f1a77cd66b6df2b72fc3f0da3542893
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000071_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000074_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000074_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb0524d759d6692690e433adc2faf84412c983dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000074_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000077_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000077_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e506669b9954e56942134d6a8572d930a9a3bfa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000077_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000079_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000079_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c83c4fc8b62007a8d0533fc62d6403d335308182
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000079_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000082_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000082_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7567ed9a8af36741a67828d1983c31cd5280e3b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000082_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000083_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000083_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb41d3c74d7c62d90caa426bfb305c8e4b330852
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000083_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000088_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000088_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41cd68ed14c4d25c8fa344884717f0c597d2198a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000088_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000090_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000090_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e01056e408a8f909fc4a1a4c09d979e3951992b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000090_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000093_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000093_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f3b4b39e27bb8acf9dc6202fb676feec91e01813
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000093_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000095_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000095_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60ab21e86c3bf6474c8f949915c770dee94e0b56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000095_tree.txt
@@ -0,0 +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;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000096_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000096_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5fdca62ad536d54f850c1f725227870a0106c9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000096_tree.txt
@@ -0,0 +1 @@
+(((GCF_023573625_PROKKA_02007:5e-09,(GCF_003691675_PROKKA_01774:0.0842955,GCF_003691675_PROKKA_00326:0.00616023)n3:0.00068447)n2:0.358886,GCF_002008305_PROKKA_00614:0.0274874)n1:0.0739174,(GCF_020097155_PROKKA_00544:0.256101,GCF_020097155_PROKKA_00702:0.272871)n4:0.0739174)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000097_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000097_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..986ca9f532a0feca6b5735380f2caeb2cd654c8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000097_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_00620:0.0278938,(GCF_020097155_PROKKA_02211:0.0443013,(GCF_020097155_PROKKA_00689:0.0504549,GCF_020097155_PROKKA_02215:1.2686)n3:4.5e-09)n2:5e-10)n1:0.00239562,(GCF_003691675_PROKKA_00361:0.036354,GCF_005280335_PROKKA_01310:0.0605429)n4:0.0161986)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000098_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000098_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e608f4b9ef49fcc7d8392d725f4ba07c4eb2a1f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000098_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02188:0.0183117,(GCF_002008305_PROKKA_00626:0.126624,((GCF_005280335_PROKKA_00392:5e-09,GCF_005280335_PROKKA_00411:0.0477376)n3:0.0136526,(GCF_003691675_PROKKA_00371:0.00338791,GCF_023573625_PROKKA_00605:0.00682011)n4:5e-09)n2:0.00865701)n1:0.0183117)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000099_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000099_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89d1bb998bb91855bc30ff60d7eaf83fbc744ff9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000099_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_PROKKA_00601:5e-09,((GCF_005280335_PROKKA_00402:0.00407998,GCF_020097155_PROKKA_02199:0.00409972)n3:0.00409701,(GCF_020097155_PROKKA_00452:0.916914,GCF_020097155_PROKKA_01060:1.10629)n4:0.445699)n2:0.0495221)n1:0.00204117,GCF_002008305_PROKKA_00630:5e-09)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000103_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000103_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52f5b2f11ce41bed3230a650547c18233326589f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000103_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02443:0.682159,((GCF_023573625_PROKKA_00662:0.00795867,(GCF_002008305_PROKKA_00692:5e-09,GCF_003691675_PROKKA_00429:0.00479587)n3:0.0212603)n2:0.0892214,(GCF_005280335_PROKKA_02262:0.292904,GCF_005280335_PROKKA_02263:0.25358)n4:0.0281755)n1:0.0480509)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000105_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000105_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b8f1fb39c4b184a5a576c1e031457ca83eaa0dd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000105_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02077:0.4101,(GCF_005280335_PROKKA_02182:0.355195,(GCF_023573625_PROKKA_00712:6e-09,(GCF_003691675_PROKKA_00478:5e-09,(GCF_002008305_PROKKA_00748:0.0143762,GCF_002008305_PROKKA_00747:0.034165)n4:0.00379611)n3:0.0633809)n2:0.341552)n1:0.4101)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000106_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000106_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37bd0366fa3f1a2ea0589dd378aee97b58edcc42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000106_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00528:1.67612,GCF_020097155_PROKKA_02063:0.0856185)n1:0.0526844,(GCF_005280335_PROKKA_02168:0.19968,(GCF_023573625_PROKKA_00726:5e-09,(GCF_002008305_PROKKA_00762:0.00731715,GCF_003691675_PROKKA_00492:0.00360066)n4:0.014716)n3:0.208996)n2:0.0526844)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000108_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000108_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc718c6ffdbb0415a0514410bd894b2adf9db598
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000108_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01711:0.0406012,(GCF_005280335_PROKKA_01822:0.0750625,((GCF_003691675_PROKKA_00784:0,GCF_023573625_PROKKA_01012:0)n3:5e-09,(GCF_002008305_PROKKA_00838:0.715086,GCF_002008305_PROKKA_01065:0.00764836)n4:0.000849817)n2:0.0519126)n1:0.102233)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000113_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000113_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ef4b9d78fb636cd6582115a8aac16282692753f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000113_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01744:1.8335e-05,((GCF_002008305_PROKKA_01028:0,GCF_003691675_PROKKA_00743:0,GCF_023573625_PROKKA_00972:0)n2:0.0591364,(GCF_005280335_PROKKA_00185:1.03623,GCF_005280335_PROKKA_01852:0.802572)n3:0.942112)n1:1.8335e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000120_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000120_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67fb541363e2e458c8ece2491658a7d0ea51b517
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000120_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01668:0.106192,((GCF_002008305_PROKKA_01118:0.00434856,(GCF_003691675_PROKKA_00837:0,GCF_023573625_PROKKA_01068:0)n3:5e-09)n2:5e-09,(GCF_005280335_PROKKA_01775:0.0388122,GCF_005280335_PROKKA_00163:1.38093)n4:0.153437)n1:0.0344813)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000123_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000123_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2e64d7e086b94b13813e8516bf0fae1040ff539
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000123_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01510:0.0199705,((GCF_002008305_PROKKA_01272:0,GCF_003691675_PROKKA_00991:0,(GCF_023573625_PROKKA_01882:1.52538,GCF_023573625_PROKKA_01230:0)n3:0)n2:0.0448732,GCF_005280335_PROKKA_01615:0.0327305)n1:0.0464907)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000124_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000124_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53955120a9ef4e53dd55993c91f7fb082750cf46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000124_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_01600:0.0509287,(GCF_020097155_PROKKA_02080:1.30636,GCF_020097155_PROKKA_01496:0.0996785)n2:0.0110754)n1:0.0119617,(GCF_002008305_PROKKA_01285:0.00623214,(GCF_003691675_PROKKA_01004:0,GCF_023573625_PROKKA_01243:0)n4:5e-09)n3:0.0157839)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000126_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000126_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f4bb4bf12d2d31537840137adbe814496861303d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000126_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_01415:1.22889,GCF_020097155_PROKKA_01447:0.0508999)n1:0.101791,(GCF_005280335_PROKKA_01551:0.0622696,(GCF_002008305_PROKKA_01341:0.00708199,(GCF_003691675_PROKKA_01061:0,GCF_023573625_PROKKA_01296:0)n4:0.00339804)n3:0.0401779)n2:0.101791)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000129_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000129_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac50a25b159b840d4c9d2ed614258f45af7caf88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000129_tree.txt
@@ -0,0 +1 @@
+(((GCF_002008305_PROKKA_01450:0.00784136,GCF_023573625_PROKKA_01400:0.00642993)n2:0.0295322,(GCF_020097155_PROKKA_01775:1.68553,GCF_020097155_PROKKA_01353:0.20896)n3:0.0232178)n1:0.0117258,(GCF_005280335_PROKKA_01449:0.114845,GCF_003691675_PROKKA_01182:0.0562135)n4:0.0106706)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000131_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000131_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06cf35a65d455b930fd8193b518bc0f0dd18deb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000131_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_01267:0.00863428,GCF_020097155_PROKKA_01296:1.47263)n1:0.0571502,(GCF_005280335_PROKKA_01376:0.0343491,(GCF_023573625_PROKKA_01476:5e-09,(GCF_003691675_PROKKA_01259:0.00437517,GCF_002008305_PROKKA_01549:5e-09)n4:0.00435445)n3:0.0481655)n2:0.0571502)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000132_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000132_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47715af8b6b1903fcc1c2dbf4df0955047a68fa2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000132_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01254:0.0804966,((GCF_002008305_PROKKA_01563:0.0181877,(GCF_003691675_PROKKA_01273:0.0226528,GCF_023573625_PROKKA_01490:5e-09)n3:0.0282172)n2:0.0528568,(GCF_005280335_PROKKA_02268:1.5525,GCF_005280335_PROKKA_01363:0.0340998)n4:0.00378886)n1:0.544263)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000133_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000133_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ba7b2c6b4fdee8fc5b0ee3adabe00544a56973bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000133_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01248:0.060227,((GCF_023573625_PROKKA_01496:0.00765813,(GCF_002008305_PROKKA_01569:5e-09,GCF_003691675_PROKKA_01279:0.00414549)n3:0.00708532)n2:0.112051,(GCF_005280335_PROKKA_02577:0.292769,GCF_005280335_PROKKA_01355:0.0631262)n4:0.00701402)n1:0.0797216)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000134_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000134_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..719c0bab4c64dd2396f9ae214738892aa71a81e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000134_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01581:0.00505921,(GCF_020097155_PROKKA_01235:0.00716569,(GCF_005280335_PROKKA_01342:0.0136529,GCF_020097155_PROKKA_01767:1.58933)n3:0.0200856)n2:0.00223173)n1:0.000634585,(GCF_003691675_PROKKA_01291:0.00247269,GCF_023573625_PROKKA_01508:5e-09)n4:0.00137153)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000136_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000136_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c56d4cdad469d11969f4de9eecd4609a9c09c4fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000136_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00458:0.0796873,((GCF_005280335_PROKKA_01338:0,GCF_023573625_PROKKA_01511:0,(GCF_002008305_PROKKA_02249:0.0799541,GCF_002008305_PROKKA_01584:0)n3:0)n2:0.00405034,GCF_003691675_PROKKA_01295:6e-09)n1:1.3278)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000139_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000139_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa82aaf8fba475418c26199c0139b6ec0d481713
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000139_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01198:0.013121,((GCF_005280335_PROKKA_01275:0.849017,GCF_005280335_PROKKA_01290:0.0418183)n2:0.0265374,(GCF_023573625_PROKKA_01531:0.00540258,(GCF_002008305_PROKKA_01604:0.0017942,GCF_003691675_PROKKA_01316:5e-09)n4:0.00179762)n3:0.0110508)n1:0.013121)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000140_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000140_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be2c7c72fd687332fda9f4149fa9f2c1e72378fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000140_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_PROKKA_01273:5e-09,(GCF_020097155_PROKKA_01182:5e-09,GCF_020097155_PROKKA_00781:1.52715)n3:0.169684)n2:0.00518613,GCF_023573625_PROKKA_01551:0.0174343)n1:0.00135223,(GCF_002008305_PROKKA_01624:5e-09,GCF_003691675_PROKKA_01330:0.00493305)n4:0.00135223)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000142_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000142_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dff4b52a98eb37fe186077bb8a113dbb0cc8c5bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000142_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01126:0.0878436,((GCF_003691675_PROKKA_01385:0.00272092,(GCF_002008305_PROKKA_01681:0.00848626,GCF_023573625_PROKKA_01610:0.00281284)n3:0.00290541)n2:0.103973,(GCF_005280335_PROKKA_01209:0.218086,GCF_005280335_PROKKA_01197:0.104299)n4:0.0115888)n1:0.110621)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000144_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000144_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75deaf064b86f977fb3664975462a2bc0bc24a88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000144_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_01022:0.163286,GCF_020097155_PROKKA_01806:1.46328)n1:0.00820567,(GCF_005280335_PROKKA_01098:0.0916714,(GCF_023573625_PROKKA_01708:0.0135036,(GCF_002008305_PROKKA_01779:0.0138398,GCF_003691675_PROKKA_01486:0.014148)n4:0.0116171)n3:0.0901985)n2:0.00820567)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000146_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000146_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..418e41a38c98aa02b033e26db3c0e58e6627dea2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000146_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00730:0.0722288,((GCF_005280335_PROKKA_01081:0,(GCF_002008305_PROKKA_02050:0.00581132,GCF_002008305_PROKKA_01795:0)n3:0)n2:0.701311,(GCF_003691675_PROKKA_01756:0.00180269,GCF_023573625_PROKKA_01984:0.00541202)n4:0.00506352)n1:0.0722288)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000147_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000147_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5fcc44e603b97b45116730ac09241b0290a03d45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000147_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01000:0.0619796,(((GCF_002008305_PROKKA_01809:0,GCF_003691675_PROKKA_01506:0)n3:0.00737441,GCF_023573625_PROKKA_01730:0.0156063)n2:0.0714646,(GCF_005280335_PROKKA_02644:0.967376,GCF_005280335_PROKKA_01065:0.0451231)n4:0.00501368)n1:0.0529771)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000152_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000152_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5c5348bdcfb4e678f9e26f9f3bae5a0b304e8b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000152_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00854:0.0917662,GCF_020097155_PROKKA_02134:1.23738)n1:0.0356679,(GCF_005280335_PROKKA_00920:0.0331897,((GCF_002008305_PROKKA_01939:0,GCF_023573625_PROKKA_01858:0)n4:0.0121581,GCF_003691675_PROKKA_01635:5e-09)n3:0.0681954)n2:0.0356679)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000153_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000153_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef1973bc2ffbc72f0562c3346747f7233fe1822b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000153_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00817:0.0308704,((GCF_005280335_PROKKA_00882:0.11307,((GCF_002008305_PROKKA_01976:0.0085242,GCF_023573625_PROKKA_01901:0.00407248)n4:0.00821689,GCF_002008305_PROKKA_01975:5.4e-09)n3:6e-10)n2:0.00857515,GCF_003691675_PROKKA_01669:5e-09)n1:0.0308704)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000156_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000156_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..876398052a52bc58970ea46d360341869201f017
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000156_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00765:0.0138985,((GCF_005280335_PROKKA_00129:1.40824,GCF_005280335_PROKKA_00826:0.101623)n2:0.12162,(GCF_023573625_PROKKA_01952:0.00729428,(GCF_003691675_PROKKA_01724:0.0169255,GCF_002008305_PROKKA_02014:0.00826595)n4:0.00419015)n3:0.059043)n1:0.0138985)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000160_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000160_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18a3094d4f6c96ae25dcdf52d4af875d77242850
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000160_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00488:0.0965002,((GCF_002008305_PROKKA_02072:0.0527864,GCF_023573625_PROKKA_02000:5e-09)n2:0.20781,(GCF_005280335_PROKKA_00740:0.197834,(GCF_005280335_PROKKA_00736:0.400109,GCF_005280335_PROKKA_00741:0.149667)n4:0.0149667)n3:0.00166297)n1:0.578076)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000161_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000161_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bd79cf89b6be81a1e4bdda3e966a564827aa0e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000161_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_PROKKA_01783:0.0245408,((GCF_005280335_PROKKA_00705:0.0173652,GCF_020097155_PROKKA_00619:0.358047)n3:0.00506514,(GCF_002008305_PROKKA_02079:0.00771655,GCF_020097155_PROKKA_00615:0.0116018)n4:0.00247878)n2:0.00027542)n1:0.00168376,GCF_023573625_PROKKA_02017:0.0139116)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000162_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000162_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..287ed45b9fce16ca3c4f7d22260d89e450dd4662
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000162_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00555:1.17161,(GCF_002008305_PROKKA_02093:0.0263871,GCF_003691675_PROKKA_01801:0.042273)n2:0.0699416)n1:0.0609639,(GCF_003691675_PROKKA_01800:0.0650793,(GCF_005280335_PROKKA_00685:0.0318044,GCF_020097155_PROKKA_00601:0.0321214)n4:0.294598)n3:0.0609639)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000164_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000164_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb8821a5f340cef2d8d23d38962ce0820dcf7db2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000164_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00658:0.103516,(GCF_020097155_PROKKA_00575:0.0166268,GCF_020097155_PROKKA_00718:0.566658)n2:0.0629619)n1:0.0386993,(GCF_003691675_PROKKA_01830:0.00241851,(GCF_002008305_PROKKA_02122:0.00361238,GCF_023573625_PROKKA_02060:0.00698486)n4:0.00588296)n3:0.0123145)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000169_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000169_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..328d5194e72743c2678c747e8b1742d26b5f3067
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000169_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00419:0.0355731,((GCF_023573625_PROKKA_02198:0.00936818,(GCF_002008305_PROKKA_02265:0.00257922,GCF_003691675_PROKKA_01960:0.0077685)n3:0.00344861)n2:0.00667517,(GCF_005280335_PROKKA_00641:0.112115,GCF_005280335_PROKKA_00469:0.00511444)n4:0.000568271)n1:0.0654001)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000171_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000171_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f84fc4466f83f32ae0db896c658dfd192bff985b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000171_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00384:0.0553472,(((GCF_002008305_PROKKA_02305:0,GCF_003691675_PROKKA_01998:0)n3:0.00305769,GCF_023573625_PROKKA_02246:5e-09)n2:0.00840558,(GCF_005280335_PROKKA_01948:1.89173,GCF_005280335_PROKKA_00432:0.147129)n4:0.0163476)n1:0.174569)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000174_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000174_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..adc04f4c05ca4a36d4546f5c8e33678fafa1668d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000174_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00376:0.0629483,(GCF_005280335_PROKKA_00423:0.0406022,(GCF_023573625_PROKKA_00001:0.00280295,(GCF_002008305_PROKKA_00001:0.00563271,GCF_003691675_PROKKA_02006:5e-09)n3:0.00471924)n2:0.026155)n1:0.0629483)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000175_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000175_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6ccc65256af060cace46a4a3964f40f387a5f33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000175_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00375:0.0572724,((GCF_002008305_PROKKA_00002:0,GCF_003691675_PROKKA_02007:0,GCF_023573625_PROKKA_00002:0)n2:0.0241473,GCF_005280335_PROKKA_00422:0.0171679)n1:0.0572724)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000180_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000180_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b8b0b4dac256950ec6d87136eaa43a83e319777
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000180_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00369:0.124459,(GCF_005280335_PROKKA_00417:0.0593308,(GCF_002008305_PROKKA_00007:5e-09,(GCF_003691675_PROKKA_02012:0,GCF_023573625_PROKKA_00007:0)n3:0.00571276)n2:0.0982439)n1:0.124459)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000183_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000183_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..38698727308cb8cefd90c6e8e2eae98d94f6dafd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000183_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00364:0.299747,(GCF_005280335_PROKKA_00383:0.131603,(GCF_003691675_PROKKA_02032:0.0116936,(GCF_002008305_PROKKA_00014:0.00242322,GCF_023573625_PROKKA_00014:0.00236226)n3:0.0131167)n2:0.131453)n1:0.299747)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000184_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000184_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee96582d64e5616244c4833b96d92b9b7dad8102
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000184_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00363:0.0124187,((GCF_002008305_PROKKA_00015:0,GCF_003691675_PROKKA_02033:0,GCF_023573625_PROKKA_00015:0)n2:0.0456502,GCF_005280335_PROKKA_00382:0.0331805)n1:0.0124187)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000187_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000187_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b5bba4db341e895cd0084513a727adfeddc067c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000187_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00360:0.0511346,(GCF_005280335_PROKKA_00379:0.0516466,(GCF_003691675_PROKKA_02036:0.00453493,(GCF_002008305_PROKKA_00018:0.00453666,GCF_023573625_PROKKA_00018:0.00454608)n3:6e-09)n2:0.0418007)n1:0.0511346)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000188_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000188_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69e9491964a9469f585ac1c781c261512146f402
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000188_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00359:0.302809,(GCF_005280335_PROKKA_00377:0.220339,(GCF_003691675_PROKKA_02037:0.0263684,(GCF_002008305_PROKKA_00019:0.0100885,GCF_023573625_PROKKA_00019:0.0261258)n3:0.00666336)n2:0.15711)n1:0.302809)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000189_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000189_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..972be69e430f46d25116ad37d6480588dd9a1fd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000189_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00358:0.171511,(GCF_005280335_PROKKA_00376:0.116401,(GCF_002008305_PROKKA_00020:0.00653245,(GCF_003691675_PROKKA_02038:0.0114431,GCF_023573625_PROKKA_00020:0.0107823)n3:0.0180848)n2:0.0716335)n1:0.171511)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000190_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000190_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c91d9ef6880d197da94cad6abb58634fd859cf93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000190_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00357:0.205248,((GCF_002008305_PROKKA_00021:0.00197384,GCF_003691675_PROKKA_02039:5e-09)n2:0.00248704,(GCF_023573625_PROKKA_00021:0.0113186,GCF_005280335_PROKKA_00375:0.0257106)n3:0.00455451)n1:0.205248)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000191_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000191_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13833c38a67970b4d6f5046bb757fa4c628534e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000191_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00356:0.0861282,(GCF_005280335_PROKKA_00374:0.0137495,(GCF_023573625_PROKKA_00022:0.00199727,(GCF_002008305_PROKKA_00022:0.00217986,GCF_003691675_PROKKA_02040:0.00217033)n3:0.00453288)n2:0.0063618)n1:0.0861282)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000193_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000193_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ffc535c588dff9d2ca01a28990e2d7587782186
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000193_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00354:0.119758,(GCF_023573625_PROKKA_00024:5e-09,(GCF_005280335_PROKKA_00372:0.00523846,(GCF_002008305_PROKKA_00024:0.00522453,GCF_003691675_PROKKA_02042:5e-09)n3:0.00523565)n2:0.00523569)n1:0.119758)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000195_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000195_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00c919d87041e3fcf2f1a2f84ec9ea1b2105b36c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000195_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00463:0.0965653,(GCF_005280335_PROKKA_00365:0.0947443,(GCF_002008305_PROKKA_00033:5e-09,(GCF_023573625_PROKKA_00032:0.00456754,GCF_003691675_PROKKA_02050:5e-09)n3:0.00455617)n2:0.116082)n1:0.0965653)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000196_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000196_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce4eea92d0493734039d577713623b73b7bbec04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000196_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00303:0.0398141,(GCF_005280335_PROKKA_00362:0.0638475,(GCF_023573625_PROKKA_00033:0.00533612,(GCF_002008305_PROKKA_00034:0.00529539,GCF_003691675_PROKKA_02051:5e-09)n3:0.00529036)n2:0.0445062)n1:0.0398141)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000200_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000200_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d1a852cac018f38f29b933928e2375f96382bf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000200_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00300:0.0435366,(GCF_005280335_PROKKA_00358:0.0411812,(GCF_002008305_PROKKA_00042:0.00602161,(GCF_003691675_PROKKA_02055:6e-09,GCF_023573625_PROKKA_00037:0.00222799)n3:0.00742121)n2:0.0551322)n1:0.0435366)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000201_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000201_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4723dd1194853f331809a2cbc309285058fc952
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000201_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00299:0.086447,(GCF_005280335_PROKKA_00357:0.048045,(GCF_002008305_PROKKA_00043:0.00304685,(GCF_003691675_PROKKA_02056:0,GCF_023573625_PROKKA_00038:0)n3:5e-09)n2:0.0703473)n1:0.086447)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000203_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000203_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcd855ed73ee237aa901230474ff0f6763a77f71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000203_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00297:0.124886,(GCF_005280335_PROKKA_00355:0.140269,(GCF_002008305_PROKKA_00045:0.0123964,(GCF_003691675_PROKKA_02058:0,GCF_023573625_PROKKA_00040:0)n3:0.0122852)n2:0.181312)n1:0.124886)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000205_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000205_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b5bb2ba12be18bb1f2014d5fb7bd4dfea3e47dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000205_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00295:0.242476,(GCF_005280335_PROKKA_00348:0.193746,(GCF_002008305_PROKKA_00047:0.0108019,(GCF_003691675_PROKKA_02060:0.0104044,GCF_023573625_PROKKA_00042:0.017401)n3:0.0105924)n2:0.195259)n1:0.242476)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000208_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000208_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..caa62fa7a8596b57747a7857bc77f1e92e14eb1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000208_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00281:0.0521174,(GCF_005280335_PROKKA_00342:0.0265246,(GCF_003691675_PROKKA_02068:5e-09,(GCF_002008305_PROKKA_00055:0.00692975,GCF_023573625_PROKKA_00050:5e-09)n3:0.00345597)n2:0.0476009)n1:0.0521174)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000212_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000212_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..233bc76dd15dee5bb58f76888798f9f41d06d720
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000212_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00276:0.157102,(GCF_005280335_PROKKA_00335:0.0883084,(GCF_002008305_PROKKA_00060:5e-09,(GCF_003691675_PROKKA_02073:0.0195094,GCF_023573625_PROKKA_00055:0.00383826)n3:0.00388011)n2:0.083192)n1:0.157102)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000214_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000214_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62935c59a2738eb2bc2c9965f7dc3adcbd9ef3d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000214_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00274:0.0378614,(GCF_005280335_PROKKA_00333:0.20336,(GCF_002008305_PROKKA_00062:0.00312099,(GCF_003691675_PROKKA_02075:0.00947628,GCF_023573625_PROKKA_00057:0.00314765)n3:0.00318142)n2:0.255438)n1:0.0378614)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000216_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000216_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0055689ca97d5d4ede9c04e028b8a5ebbe02995
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000216_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00268:0.0417756,(GCF_005280335_PROKKA_00329:0.0925282,(GCF_003691675_PROKKA_02079:0.00724765,(GCF_002008305_PROKKA_00066:5e-09,GCF_023573625_PROKKA_00060:0.0109235)n3:0.00368295)n2:0.0565247)n1:0.0417756)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000217_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000217_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df643c02d75e9196f81f6ac4cf243478bc0726ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000217_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00267:0.0697169,(GCF_005280335_PROKKA_00327:0.1524,((GCF_002008305_PROKKA_00067:0,GCF_003691675_PROKKA_02080:0)n3:0.00467595,GCF_023573625_PROKKA_00061:5e-09)n2:0.0415797)n1:0.0697169)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000218_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000218_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db2fdffed9671ba5c55a2e68455df47b6113d372
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000218_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00265:0.147106,(GCF_005280335_PROKKA_00323:0.339084,(GCF_003691675_PROKKA_02082:0.0172604,(GCF_002008305_PROKKA_00069:0.0160863,GCF_023573625_PROKKA_00063:0.00996742)n3:0.00924649)n2:0.207267)n1:0.147106)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000219_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000219_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a912e5a12d900f543620f0427458ee928d9291b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000219_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00264:0.0694759,(GCF_005280335_PROKKA_00322:0.149361,(GCF_002008305_PROKKA_00070:5e-09,(GCF_003691675_PROKKA_02083:0.0167829,GCF_023573625_PROKKA_00064:0.00716334)n3:0.00713443)n2:0.0880708)n1:0.0694759)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000220_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000220_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07e66234f1a48ceb1ea4634a4e844b90aed59c9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000220_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00263:0.0983498,(GCF_005280335_PROKKA_00321:0.291632,(GCF_023573625_PROKKA_00065:0.0198372,(GCF_003691675_PROKKA_02084:0.0293046,GCF_002008305_PROKKA_00071:0.0142987)n3:0.00857201)n2:0.152309)n1:0.0983498)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000221_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000221_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a58ea4b44f20df8d96eed56492e86509692ab76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000221_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00262:0.0132092,(GCF_005280335_PROKKA_00320:0.0459298,((GCF_002008305_PROKKA_00072:0,GCF_003691675_PROKKA_02085:0)n3:5e-09,GCF_023573625_PROKKA_00066:0.00530634)n2:0.0374047)n1:0.0132092)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000223_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000223_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64154639145534e47f49087d3b1986a8fbed0384
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000223_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00259:0.0595857,(GCF_005280335_PROKKA_00318:0.0268488,((GCF_002008305_PROKKA_00075:0,GCF_003691675_PROKKA_02088:0)n3:5e-09,GCF_023573625_PROKKA_00069:0.00478556)n2:0.038506)n1:0.0595857)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000224_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000224_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd8be5fee4178b75b8bfd800d1e869407a58a7f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000224_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00257:0.0879547,(GCF_005280335_PROKKA_00316:0.0343331,(GCF_002008305_PROKKA_00077:5e-09,(GCF_003691675_PROKKA_02090:0.00757203,GCF_023573625_PROKKA_00071:0.00753228)n3:0.00751618)n2:0.0218153)n1:0.0879547)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000230_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000230_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78598c7a7aaca031debefaecbc12bcd21fda44c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000230_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00251:0.257663,(GCF_005280335_PROKKA_00307:0.112752,(GCF_002008305_PROKKA_00084:0.020486,(GCF_003691675_PROKKA_02097:0,GCF_023573625_PROKKA_00079:0)n3:0.00712058)n2:0.0494506)n1:0.257663)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000232_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000232_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d378ba80eb407a550804397ded1a6d042979dc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000232_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00249:0.288556,(GCF_005280335_PROKKA_00304:0.0471547,(GCF_002008305_PROKKA_00087:0.0126349,(GCF_003691675_PROKKA_02100:5e-09,GCF_023573625_PROKKA_00082:0.00354246)n3:0.0128206)n2:0.0192963)n1:0.288556)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000233_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000233_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92f9322928fd7dc17ff1c059f64efe06a71b61b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000233_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00248:0.0823186,(GCF_005280335_PROKKA_00303:0.0869428,(GCF_002008305_PROKKA_00088:5e-09,(GCF_003691675_PROKKA_02101:0,GCF_023573625_PROKKA_00083:0)n3:0.00640458)n2:0.0757881)n1:0.0823186)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000234_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000234_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3958177d3b61f72e613badb33034b2199fcf4d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000234_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00247:0.155647,(GCF_005280335_PROKKA_00302:0.0817186,(GCF_023573625_PROKKA_00084:0.00464224,(GCF_002008305_PROKKA_00089:0.00826212,GCF_003691675_PROKKA_02102:5e-09)n3:0.0161242)n2:0.134773)n1:0.155647)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000235_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000235_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a0868430aa496dd68ea736227fad954b9984c64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000235_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00246:0.0391169,((GCF_002008305_PROKKA_00090:0,GCF_003691675_PROKKA_02103:0,GCF_023573625_PROKKA_00085:0)n2:0.0838676,GCF_005280335_PROKKA_00301:0.204798)n1:0.0391169)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000236_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000236_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9cf58af8940517f7c5a1ce242389d4315fcc34e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000236_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00245:0.00675224,(GCF_005280335_PROKKA_00300:0.00896867,((GCF_002008305_PROKKA_00091:0,GCF_023573625_PROKKA_00086:0)n3:0.00441605,GCF_003691675_PROKKA_02104:0.0044352)n2:0.00903542)n1:0.00675224)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000237_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000237_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1093822de46b27bf7ed2d4e7f5c46dcd2cf68bd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000237_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00244:2.5e-09,(GCF_003691675_PROKKA_02105:0.0185177,((GCF_002008305_PROKKA_00092:0,GCF_023573625_PROKKA_00087:0)n3:0.0122994,GCF_005280335_PROKKA_00299:0.0184459)n2:0.00613077)n1:2.5e-09)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000241_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000241_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c93f6fa8258be101605ac49f9a810a40f74d4586
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000241_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00240:0.056131,(GCF_005280335_PROKKA_00295:0.118441,(GCF_002008305_PROKKA_00096:0.00534235,(GCF_003691675_PROKKA_02109:5e-09,GCF_023573625_PROKKA_00091:0.00299448)n3:0.00965796)n2:0.077794)n1:0.056131)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000242_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000242_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..edeadfb99ab00e914ecfad94ae9527774b0b968a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000242_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00239:0.0499257,(GCF_005280335_PROKKA_00294:0.0288876,(GCF_003691675_PROKKA_02110:0.00195878,(GCF_002008305_PROKKA_00097:5e-09,GCF_023573625_PROKKA_00092:0.00583692)n3:0.00387418)n2:0.0183912)n1:0.0499257)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000244_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000244_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aacb00cef17c30ff96ed434b159c47d8e6612fb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000244_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00237:0.0255228,(GCF_005280335_PROKKA_00291:0.0171906,(GCF_003691675_PROKKA_02113:0.00234141,(GCF_002008305_PROKKA_00100:0.00116805,GCF_023573625_PROKKA_00095:5e-09)n3:0.0011666)n2:0.00977426)n1:0.0255228)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000247_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000247_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00b942aa07f860b21b4b944689dc526bd9afabb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000247_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00233:0.10112,(GCF_005280335_PROKKA_00287:0.0454889,(GCF_002008305_PROKKA_00103:0.010078,(GCF_003691675_PROKKA_02116:0.00324618,GCF_023573625_PROKKA_00098:0.0129354)n3:0.00606098)n2:0.104234)n1:0.10112)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000250_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000250_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..117fd7926f8d43097836ba017e7dd908f62ad501
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000250_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00224:0.157908,(GCF_005280335_PROKKA_00283:0.0701521,(GCF_023573625_PROKKA_00102:0.00750184,(GCF_002008305_PROKKA_00107:5e-09,GCF_003691675_PROKKA_02120:0.00252858)n3:0.00036094)n2:0.176122)n1:0.157908)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000251_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000251_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4c7ea716b7b340e47b76e356b02deaae0d659025
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000251_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00223:0.0283884,(GCF_005280335_PROKKA_00282:0.10202,((GCF_002008305_PROKKA_00108:0,GCF_003691675_PROKKA_02121:0)n3:0.0031016,GCF_023573625_PROKKA_00103:5e-09)n2:0.169611)n1:0.0283884)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000252_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000252_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b471eed2f020d40750ba2348f1c0e48dedc4ea62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000252_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00222:0.0585608,((GCF_002008305_PROKKA_00109:0,GCF_003691675_PROKKA_02122:0,GCF_023573625_PROKKA_00104:0)n2:0.229649,GCF_005280335_PROKKA_00281:0.128525)n1:0.0585608)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000253_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000253_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce62661be0c35b5dcfc92a230c8c788546367799
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000253_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00221:0.01176,(GCF_005280335_PROKKA_00280:0.0154063,((GCF_002008305_PROKKA_00110:0,GCF_003691675_PROKKA_02123:0)n3:5e-09,GCF_023573625_PROKKA_00105:0.00758386)n2:0.0593648)n1:0.01176)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000256_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000256_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62e1a7836b4f7ff8f0057042a788cbaf40f81543
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000256_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00218:0.0714123,((GCF_002008305_PROKKA_00113:0,GCF_003691675_PROKKA_02126:0,GCF_023573625_PROKKA_00108:0)n2:0.0974459,GCF_005280335_PROKKA_00277:0.0353566)n1:0.0714123)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000258_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000258_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf5b5beeed8997c23aabaaebb8f9b1cf1f401b98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000258_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00203:0.194908,(GCF_005280335_PROKKA_00271:0.0947221,(GCF_023573625_PROKKA_00121:0.0035663,(GCF_003691675_PROKKA_02129:0.00665947,GCF_002008305_PROKKA_00116:0.016738)n3:6e-09)n2:0.100537)n1:0.194908)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000259_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000259_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d98df8bbb5a7424fd28fc96edcbb7fc9a5e10041
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000259_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00201:0.0954326,(GCF_005280335_PROKKA_00270:0.0653448,(GCF_002008305_PROKKA_00117:0.00138645,(GCF_003691675_PROKKA_02130:0,GCF_023573625_PROKKA_00122:0)n3:0.00329267)n2:0.060479)n1:0.0954326)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000260_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000260_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce0d7aceea3a30c830a321704ce8ac262fe00602
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000260_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00197:0.0548041,(GCF_005280335_PROKKA_00263:0.0529838,(GCF_002008305_PROKKA_00122:0.0558762,(GCF_003691675_PROKKA_02136:0.0197224,GCF_023573625_PROKKA_00130:0.00379651)n3:0.0582516)n2:0.0268986)n1:0.0548041)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000261_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000261_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7a6e10aec7e426c7aa5a830002e233cff99fae6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000261_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00196:0.09257,(GCF_005280335_PROKKA_00262:0.0461994,(GCF_002008305_PROKKA_00123:0.0461355,(GCF_003691675_PROKKA_02137:5e-09,GCF_023573625_PROKKA_00131:0.062965)n3:0.0281348)n2:0.101598)n1:0.09257)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000262_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000262_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..191cd2981ef44558fe8c8a7b1e52c33844db2e02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000262_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00195:0.454165,(GCF_005280335_PROKKA_00261:0.203627,(GCF_002008305_PROKKA_00124:0.130889,(GCF_003691675_PROKKA_02138:0.0186811,GCF_023573625_PROKKA_00132:0.0189083)n3:0.0992326)n2:0.0685022)n1:0.454165)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000266_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000266_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91e192aefe14c2175cf86ad7a126fadf15796c7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000266_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00651:0.873897,(GCF_005280335_PROKKA_00254:0.234325,(GCF_023573625_PROKKA_00139:0.0240406,(GCF_002008305_PROKKA_00131:5e-09,GCF_003691675_PROKKA_02145:0.00478493)n3:5e-09)n2:5e-09)n1:0.873897)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000269_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000269_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da253972f2dd8edca5e21195a85b4d910b5c0372
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000269_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00182:0.169569,(GCF_005280335_PROKKA_00248:0.0924403,(GCF_002008305_PROKKA_00136:0.0131934,(GCF_003691675_PROKKA_02150:0.00672451,GCF_023573625_PROKKA_00144:5e-09)n3:0.0111677)n2:0.0528819)n1:0.169569)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000273_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000273_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3a8c83069f032806adde7f6735256e04f0137a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000273_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00178:0.0302064,(GCF_005280335_PROKKA_00244:0.0301191,((GCF_002008305_PROKKA_00140:0,GCF_023573625_PROKKA_00148:0)n3:0.0175469,GCF_003691675_PROKKA_02154:0.00771428)n2:0.0304354)n1:0.0302064)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000275_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000275_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b41d43407dd15769d5d2e8391db9eac57f6febe2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000275_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00176:0.119104,(GCF_005280335_PROKKA_00242:0.0399919,((GCF_002008305_PROKKA_00142:0,GCF_023573625_PROKKA_00150:0)n3:5e-09,GCF_003691675_PROKKA_02156:0.0167454)n2:0.0627288)n1:0.119104)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000278_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000278_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ea72ffe8154d103bb64a5e34a0a7b9a2830dc37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000278_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00173:0.0190152,(GCF_005280335_PROKKA_00238:0.0290484,(GCF_002008305_PROKKA_00146:0.00886671,(GCF_023573625_PROKKA_00154:0.00873807,GCF_003691675_PROKKA_02160:5e-09)n3:0.00273496)n2:0.0440574)n1:0.0190152)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000279_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000279_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..79e37695b0231b1ce177bb2e0307beaeea2613a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000279_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00821:0.259547,(GCF_005280335_PROKKA_00236:0.0482157,(GCF_002008305_PROKKA_00147:0.00200206,(GCF_003691675_PROKKA_02161:0,GCF_023573625_PROKKA_00155:0)n3:5e-09)n2:0.0256569)n1:0.259547)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000281_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000281_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7870fb4c74b745b7c4695fea51b3132f66094ce6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000281_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00819:0.159304,(GCF_005280335_PROKKA_00234:0.0905265,(GCF_003691675_PROKKA_02163:5e-09,(GCF_002008305_PROKKA_00149:0.00336875,GCF_023573625_PROKKA_00157:5e-09)n3:0.00168223)n2:0.0614105)n1:0.159304)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000282_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000282_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8afcdbb43299be090d70b969e8a7d36154503fe4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000282_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00172:0.208981,(GCF_005280335_PROKKA_00233:0.086044,(GCF_023573625_PROKKA_00158:0.00237268,(GCF_002008305_PROKKA_00150:5e-09,GCF_003691675_PROKKA_02164:5e-09)n3:5e-09)n2:0.0629937)n1:0.208981)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000283_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000283_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0279cd844e0a2a7ed46ddd39bcaa999ba26a1bd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000283_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00171:0.0463413,(GCF_005280335_PROKKA_00232:0.052447,(GCF_002008305_PROKKA_00151:5e-09,(GCF_023573625_PROKKA_00159:0.00697101,GCF_003691675_PROKKA_02165:0.00696276)n3:0.00697655)n2:0.0329464)n1:0.0463413)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000284_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000284_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f9d22ff09a0f1ee60538621fbf5916916418523
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000284_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00170:0.059487,((GCF_002008305_PROKKA_00152:0,GCF_003691675_PROKKA_02166:0,GCF_023573625_PROKKA_00160:0)n2:0.0286996,GCF_005280335_PROKKA_00231:0.0314605)n1:0.059487)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000286_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000286_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d695e70ec07fb59c04e14fcb0ee1bb43b1f3d32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000286_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00676:0.772205,(GCF_003691675_PROKKA_00359:5e-09,(GCF_002008305_PROKKA_00168:0.00999145,(GCF_005280335_PROKKA_02333:5e-09,GCF_023573625_PROKKA_02011:0.00500257)n3:5e-09)n2:0.00499533)n1:0.772205)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000292_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000292_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..550b87cabbf784a778efddc9bcd5d91f9a7d425e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000292_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00163:0.206787,(GCF_003691675_PROKKA_02179:0.00112337,((GCF_002008305_PROKKA_00183:0.00803938,GCF_023573625_PROKKA_00180:5e-09)n3:0.00329041,GCF_005280335_PROKKA_00218:0.00568151)n2:0.00212855)n1:0.206787)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000294_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000294_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..762b798165071c80aeb2a17bc94f7c2d64050718
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000294_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00161:0.0671427,(GCF_005280335_PROKKA_00216:0.0152399,(GCF_002008305_PROKKA_00185:0.00224517,(GCF_003691675_PROKKA_02181:0.0196056,GCF_023573625_PROKKA_00182:5e-09)n3:0.0219581)n2:0.0155477)n1:0.0671427)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000295_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000295_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b093add7e7ebb92aa054c771f40c1f4fd6257981
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000295_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00160:0.0312979,((GCF_002008305_PROKKA_00186:0.00242264,GCF_003691675_PROKKA_02182:0.00246236)n2:0.010961,(GCF_005280335_PROKKA_00215:0.00736985,GCF_023573625_PROKKA_00183:0.00991627)n3:0.00407918)n1:0.0312979)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000296_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000296_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03fd04a8f11fccdd9886571cfd3fc9af37bd411e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000296_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00159:0.00454226,(GCF_005280335_PROKKA_00214:0.00543334,((GCF_002008305_PROKKA_00187:0,GCF_023573625_PROKKA_00184:0)n3:0.00179029,GCF_003691675_PROKKA_02183:0.00180222)n2:5e-09)n1:0.00454226)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000297_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000297_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22e1730d2f88a76f0477d7886f6a78984c9d1205
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000297_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00155:0.0299185,(GCF_002008305_PROKKA_00192:0.00186133,(GCF_023573625_PROKKA_00192:5e-09,(GCF_003691675_PROKKA_02188:0.0027286,GCF_005280335_PROKKA_00208:0.0372386)n3:0.0056611)n2:0.00662965)n1:0.0299185)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000299_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000299_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e417d35771105675e1a689bd5e29c0479587efd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000299_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00153:2.5e-09,(GCF_005280335_PROKKA_00206:0.00433436,(GCF_023573625_PROKKA_00194:0.00588984,(GCF_002008305_PROKKA_00194:0.00665334,GCF_003691675_PROKKA_02190:0.00357765)n3:0.0216383)n2:0.00594396)n1:2.5e-09)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000300_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000300_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21b58447ed2524fd46cbcbd5e376ba7021d9a01d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000300_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00152:0.00197179,(GCF_005280335_PROKKA_00204:0.550495,((GCF_002008305_PROKKA_00195:0,GCF_003691675_PROKKA_02191:0)n3:0.0164235,GCF_023573625_PROKKA_00195:0.125915)n2:0.016169)n1:0.00197179)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000301_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000301_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c73aa2c4276e9fedfba1dbe7c347e44232f34c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000301_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00151:0.00718281,(GCF_005280335_PROKKA_00203:0.154052,(GCF_002008305_PROKKA_00196:0.0261374,(GCF_003691675_PROKKA_02192:0,GCF_023573625_PROKKA_00196:0)n3:0.0297379)n2:0.0193607)n1:0.00718281)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000302_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000302_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e651a204238274f24b0760564123e6aa437544f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000302_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00150:0.133361,(GCF_005280335_PROKKA_00202:0.249472,(GCF_023573625_PROKKA_00197:0.0471718,(GCF_002008305_PROKKA_00197:0.0290964,GCF_003691675_PROKKA_02193:0.0192318)n3:0.0109025)n2:0.249171)n1:0.133361)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000303_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000303_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45a8b36985f4c4c44ea3f51e047317febea9e62e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000303_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00144:0.00746657,(GCF_005280335_PROKKA_00190:0.200145,(GCF_023573625_PROKKA_00204:0.0065468,(GCF_002008305_PROKKA_00202:0.00392574,GCF_003691675_PROKKA_02197:0.00677438)n3:5e-09)n2:0.00736221)n1:0.00746657)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000309_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000309_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51d4d6eb681595bb6d3f9ff45ef9acef2fa6ebfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000309_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00124:0.0512453,(GCF_005280335_PROKKA_00175:0.0190121,((GCF_002008305_PROKKA_00211:0,GCF_003691675_PROKKA_02204:0)n3:0.00260106,GCF_023573625_PROKKA_00211:0.00258247)n2:0.0185329)n1:0.0512453)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000311_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000311_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..806b5f0f9f37ef4635190d1c46f60ea7dad61ef5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000311_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00122:0.0244466,(GCF_005280335_PROKKA_00173:0.0483772,((GCF_002008305_PROKKA_00213:0,GCF_023573625_PROKKA_00213:0)n3:5e-09,GCF_003691675_PROKKA_02206:0.0110794)n2:0.0092283)n1:0.0244466)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000314_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000314_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c08d5cc6854dc5b0fc54d6ae014528f58c659d82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000314_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00616:0.422354,(GCF_005280335_PROKKA_01604:0.22166,(GCF_002008305_PROKKA_00218:0.00858437,(GCF_003691675_PROKKA_02212:0,GCF_023573625_PROKKA_00219:0)n3:0.0278346)n2:0.447249)n1:0.422354)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000316_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000316_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d5bd77abcc2f421778a13814b82a3bcd4eb45f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000316_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00116:0.0544731,(GCF_005280335_PROKKA_00158:0.00679382,((GCF_002008305_PROKKA_00222:0,GCF_003691675_PROKKA_02235:0)n3:0.00440578,GCF_023573625_PROKKA_00223:5e-09)n2:0.0244694)n1:0.0544731)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000317_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000317_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..021340af4f273b7aec1ed43b8d595090e4058262
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000317_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00114:0.235028,(GCF_005280335_PROKKA_00156:0.186024,(GCF_003691675_PROKKA_02237:0.00124699,(GCF_023573625_PROKKA_00225:0.0199742,GCF_002008305_PROKKA_00224:0.00991736)n3:0.00624948)n2:0.185076)n1:0.235028)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000320_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000320_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..83bf312cdd09f110cb04afa917b1bceb6740454e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000320_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00110:0.0191545,(GCF_005280335_PROKKA_00153:0.14219,(GCF_003691675_PROKKA_02241:0.00690321,(GCF_002008305_PROKKA_00228:0.0221424,GCF_023573625_PROKKA_00229:0.0154469)n3:0.00537236)n2:0.00639687)n1:0.0191545)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000322_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000322_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99e9b316fb57b495049b074ea8a4aca00cfebb18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000322_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00107:0.0649343,(GCF_005280335_PROKKA_00150:0.051535,((GCF_002008305_PROKKA_00231:0,GCF_003691675_PROKKA_02244:0)n3:0.00347542,GCF_023573625_PROKKA_00232:0.0034832)n2:0.0357755)n1:0.0649343)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000324_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000324_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c093874769be715ef627650371961065aacad86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000324_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00103:0.162257,(GCF_005280335_PROKKA_00138:0.0556254,(GCF_023573625_PROKKA_00234:0.00889254,(GCF_002008305_PROKKA_00233:0.00327998,GCF_003691675_PROKKA_02246:5e-09)n3:0.00430671)n2:0.0891917)n1:0.162257)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000326_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000326_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a38b21cdc74685d7c4d7e56026eac79e37762fa6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000326_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00101:0.104431,(GCF_005280335_PROKKA_00136:0.0673638,(GCF_023573625_PROKKA_00236:0.00238759,(GCF_002008305_PROKKA_00235:0.0220865,GCF_003691675_PROKKA_02248:0.00269923)n3:0.00584761)n2:0.0900616)n1:0.104431)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000327_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000327_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e248a5a6d4ac75e86b51205410f486b904d8ca28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000327_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00099:0.384004,(GCF_005280335_PROKKA_00134:0.0712193,(GCF_003691675_PROKKA_02250:0.00458866,(GCF_002008305_PROKKA_00237:0.0166815,GCF_023573625_PROKKA_00238:0.0136141)n3:0.00911151)n2:0.0664826)n1:0.384004)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000330_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000330_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ba01ddbf78c06d7c3c89fb7127efd0310fd2fe4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000330_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00096:0.332179,(GCF_005280335_PROKKA_00131:0.203814,(GCF_003691675_PROKKA_02253:0.0120049,(GCF_002008305_PROKKA_00240:0.0184033,GCF_023573625_PROKKA_00241:0.00185324)n3:0.00748757)n2:0.0997616)n1:0.332179)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000331_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000331_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3975645fa9741788ac4322a2ac15786360ffe95c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000331_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00095:0.405255,(GCF_005280335_PROKKA_00128:0.127607,(GCF_002008305_PROKKA_00241:0.00866558,(GCF_003691675_PROKKA_02254:0.00871661,GCF_023573625_PROKKA_00242:0.00891529)n3:0.00960281)n2:0.0836151)n1:0.405255)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000335_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000335_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da5f9d6186c103444f5601fa0bacccdbac198fce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000335_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00089:0.0994527,(GCF_005280335_PROKKA_00121:0.0316347,(GCF_002008305_PROKKA_00249:0.0211894,(GCF_003691675_PROKKA_02261:0,GCF_023573625_PROKKA_00249:0)n3:5e-09)n2:0.0770112)n1:0.0994527)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000337_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000337_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..348b1b2bd53d058328f8a52097701f64f8c4ddbe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000337_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00082:0.0862458,(GCF_005280335_PROKKA_00114:0.00115302,(GCF_003691675_PROKKA_02269:6e-09,(GCF_023573625_PROKKA_00254:0.00401793,GCF_002008305_PROKKA_00255:0.00100191)n3:0.00100176)n2:0.00588922)n1:0.0862458)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000341_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000341_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..491a3012d24cd599515aebecb288695dbf93be95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000341_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00075:0.342472,(GCF_005280335_PROKKA_00105:0.296022,(GCF_023573625_PROKKA_00260:0.0151461,(GCF_002008305_PROKKA_00262:0.00536198,GCF_003691675_PROKKA_02275:0.00556994)n3:0.0213307)n2:0.174658)n1:0.342472)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000343_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000343_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..231ae0a674ad4134b52378da210c7674e179b73e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000343_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00070:0.190615,(GCF_005280335_PROKKA_00099:0.0263461,((GCF_002008305_PROKKA_00264:0,GCF_003691675_PROKKA_02277:0)n3:0.00644262,GCF_023573625_PROKKA_00262:0.0133719)n2:0.0366556)n1:0.190615)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000345_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000345_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae2c98648608a729d209bc06dc41d7b843cdee34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000345_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00068:0.0537833,(GCF_005280335_PROKKA_00097:0.0538067,(GCF_003691675_PROKKA_02279:0.00475919,(GCF_002008305_PROKKA_00266:0.0238532,GCF_023573625_PROKKA_00264:0.00943896)n3:0.004734)n2:0.077188)n1:0.0537833)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000347_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000347_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0b1fe11aba0028c0cd517d9f46f20494d7f22e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000347_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00066:0.164121,(GCF_005280335_PROKKA_00095:0.0204433,(GCF_002008305_PROKKA_00268:0.00241995,(GCF_003691675_PROKKA_02281:0,GCF_023573625_PROKKA_00266:0)n3:0.0024723)n2:0.0306006)n1:0.164121)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000348_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000348_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0bca558397f5713aab37aeef7815fe0a8be0d765
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000348_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00397:0.103089,(GCF_005280335_PROKKA_00444:0.603711,((GCF_002008305_PROKKA_00269:0,GCF_023573625_PROKKA_00267:0)n3:6e-09,GCF_003691675_PROKKA_02282:0.0129058)n2:0.6056)n1:0.103089)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000351_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000351_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b34c739bd747884aeb9e393e27ef20fd1310ca9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000351_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00061:0.0685134,(GCF_005280335_PROKKA_00076:0.0443408,(GCF_023573625_PROKKA_00276:5e-09,(GCF_002008305_PROKKA_00277:0.00663991,GCF_003691675_PROKKA_02292:5e-09)n3:0.00662514)n2:0.0417904)n1:0.0685134)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000353_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000353_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75cac6e00ccbb60cf54ebf24a457f20e78b9b6ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000353_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00059:0.108423,(GCF_005280335_PROKKA_00073:5e-09,((GCF_002008305_PROKKA_00280:5e-09,GCF_003691675_PROKKA_02295:0.00918736)n3:0.00931063,GCF_023573625_PROKKA_00279:0.0278368)n2:0.00916807)n1:0.108423)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000355_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000355_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a65e064b7ed74bad486387577c2f9de99aede5cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000355_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00056:0.0846097,(GCF_005280335_PROKKA_00070:0.0518247,(GCF_002008305_PROKKA_00283:0.0102843,(GCF_003691675_PROKKA_02298:0.0056559,GCF_023573625_PROKKA_00282:0.00880445)n3:0.0500678)n2:0.0354758)n1:0.0846097)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000357_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000357_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3fa4712580479ff667f988fe69a2f7cf005c4a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000357_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00045:0.120967,(GCF_005280335_PROKKA_00066:5e-09,(GCF_002008305_PROKKA_00288:5e-09,(GCF_003691675_PROKKA_02310:0,GCF_023573625_PROKKA_00294:0)n3:0.00652336)n2:0.0200393)n1:0.120967)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000358_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000358_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2fd8a6538f5a5573c4ce8762204569db0cffc189
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000358_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00044:0.248446,(GCF_005280335_PROKKA_00065:0.176711,(GCF_002008305_PROKKA_00289:0.0162821,(GCF_003691675_PROKKA_02311:0,GCF_023573625_PROKKA_00295:0)n3:0.0117195)n2:0.113053)n1:0.248446)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000359_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000359_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b12fbc2a8825a42a49345cdf9240bfc06d0a193
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000359_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00042:0.0524966,(GCF_005280335_PROKKA_00063:0.0211484,(GCF_023573625_PROKKA_00298:0.0179769,(GCF_002008305_PROKKA_00291:5e-09,GCF_003691675_PROKKA_02314:0.00666351)n3:0.0102029)n2:0.0858688)n1:0.0524966)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000363_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000363_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b61c82743ec2d5511dc7e596183e2dad01b2f2f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000363_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00036:0.0147426,(GCF_005280335_PROKKA_00058:0.0582378,(GCF_002008305_PROKKA_00296:0.00923586,(GCF_003691675_PROKKA_00004:0.0016439,GCF_023573625_PROKKA_00303:5e-09)n3:0.00398798)n2:0.0101523)n1:0.0147426)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000367_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000367_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6cf95b37be78c4c72b365cf4090f30df0021a250
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000367_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00031:0.139333,(GCF_005280335_PROKKA_00053:0.0456368,(GCF_002008305_PROKKA_00301:0.00484402,(GCF_003691675_PROKKA_00009:0.00713372,GCF_023573625_PROKKA_00308:0.00953361)n3:0.00955218)n2:0.0676239)n1:0.139333)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000369_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000369_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..079da14da4b7e0b3dd10bb35017b12f1dfb7092a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000369_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00028:0.0547392,(GCF_005280335_PROKKA_00032:0.0448057,(GCF_002008305_PROKKA_00305:0.00378801,(GCF_003691675_PROKKA_00020:0,GCF_023573625_PROKKA_00312:0)n3:0.00582216)n2:0.0553794)n1:0.0547392)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000373_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000373_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66760ac898f49a30a45a7ba525c19f57fde54adb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000373_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00022:0.148619,(GCF_005280335_PROKKA_00026:0.07103,(GCF_023573625_PROKKA_00318:5e-09,(GCF_002008305_PROKKA_00311:0.0137993,GCF_003691675_PROKKA_00026:0.00686942)n3:0.00689385)n2:0.0923485)n1:0.148619)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000375_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000375_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c6fc6756a9faac04b4b0af401a7615b176d56e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000375_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00019:0.0769854,(GCF_005280335_PROKKA_00023:0.0493202,(GCF_002008305_PROKKA_00314:0.00922261,(GCF_003691675_PROKKA_00029:0,GCF_023573625_PROKKA_00321:0)n3:0.00542315)n2:0.0253253)n1:0.0769854)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000376_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000376_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..356044a24d4fd8f3c49ab21a3e4886e6ae120bf7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000376_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00018:0.133939,(GCF_005280335_PROKKA_00022:0.068271,(GCF_002008305_PROKKA_00315:0.0158511,(GCF_003691675_PROKKA_00030:0.00877429,GCF_023573625_PROKKA_00322:5e-09)n3:0.0110515)n2:0.0707156)n1:0.133939)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000377_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000377_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6657707d97939b511120f3e6544f0581d9eaeb25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000377_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00017:0.319252,(GCF_005280335_PROKKA_00021:0.131125,(GCF_002008305_PROKKA_00316:5e-09,(GCF_003691675_PROKKA_00031:0,GCF_023573625_PROKKA_00323:0)n3:0.02193)n2:0.123467)n1:0.319252)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000378_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000378_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cac019343c443048f94a20fd58ee2353a17e7e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000378_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00016:0.142127,(GCF_005280335_PROKKA_00020:0.0541091,(GCF_002008305_PROKKA_00317:0.0219101,(GCF_003691675_PROKKA_00032:0.00727174,GCF_023573625_PROKKA_00324:5e-09)n3:5e-09)n2:0.0595201)n1:0.142127)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000380_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000380_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4725c6c2cc257a5c7e8e1233ef693d59b200487e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000380_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00013:0.0897262,(GCF_005280335_PROKKA_00017:0.0501894,((GCF_002008305_PROKKA_00320:0,GCF_003691675_PROKKA_00035:0)n3:5e-09,GCF_023573625_PROKKA_00327:0.00235154)n2:0.0256753)n1:0.0897262)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000382_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000382_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88a481de6e9c21c8bae41f6ef37e291e106b9e8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000382_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00011:0.281983,((GCF_002008305_PROKKA_00322:0,GCF_003691675_PROKKA_00037:0,GCF_023573625_PROKKA_00329:0)n2:0.0894851,GCF_005280335_PROKKA_00015:0.140622)n1:0.281983)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000383_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000383_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05cadffc30f1bfa48255d8cc966cb03884556986
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000383_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00010:0.0187213,(GCF_005280335_PROKKA_00014:0.0298683,((GCF_002008305_PROKKA_00323:0,GCF_003691675_PROKKA_00038:0)n3:0.00615218,GCF_023573625_PROKKA_00330:5e-09)n2:0.0212699)n1:0.0187213)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000386_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000386_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..652ee0c38a184c184ebecd8c10c2b786cfd098d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000386_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00007:0.0385114,(GCF_005280335_PROKKA_00009:0.0288009,((GCF_002008305_PROKKA_00326:0,GCF_003691675_PROKKA_00042:0)n3:5e-09,GCF_023573625_PROKKA_00333:0.00603977)n2:0.0388034)n1:0.0385114)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000387_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000387_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c4d3d613ba7b3d23e2c7719167fbf2de1019051
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000387_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00006:0.102831,(GCF_005280335_PROKKA_00005:0.0765754,(GCF_002008305_PROKKA_00330:0.0014775,(GCF_003691675_PROKKA_00046:0.00570615,GCF_023573625_PROKKA_00337:0.0100905)n3:0.00142712)n2:0.0554375)n1:0.102831)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000388_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000388_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c07b60190c85e8da41d5914f6d9b7a4616aa7535
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000388_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00005:0.0836295,(GCF_005280335_PROKKA_00004:0.0659427,(GCF_003691675_PROKKA_00047:0.00442161,(GCF_002008305_PROKKA_00331:0.013263,GCF_023573625_PROKKA_00338:0.00643579)n3:0.00389058)n2:0.0296639)n1:0.0836295)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000389_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000389_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..267577d80c6898dd26cf804fbeb88f0a25aa7c4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000389_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02492:0.674034,(GCF_005280335_PROKKA_02680:0.304755,(GCF_002008305_PROKKA_00335:0.0347382,(GCF_003691675_PROKKA_00051:5e-09,GCF_023573625_PROKKA_00342:0.0142856)n3:0.0244372)n2:0.305267)n1:0.674034)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000395_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000395_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2de2316432f2fb732195d97ace07a3e03fd7fb00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000395_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02479:0.153362,(GCF_005280335_PROKKA_02627:0.0815032,(GCF_023573625_PROKKA_00349:0.00886836,(GCF_002008305_PROKKA_00342:0.0174236,GCF_003691675_PROKKA_00058:0.00569138)n3:0.00582207)n2:0.110348)n1:0.153362)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000396_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000396_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eba44b318e45e25cf9968950e8bcc3bcb5430c94
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000396_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02478:0.431408,(GCF_005280335_PROKKA_02626:0.0991737,(GCF_002008305_PROKKA_00343:5e-09,(GCF_003691675_PROKKA_00059:0.0127002,GCF_023573625_PROKKA_00350:0.0127511)n3:0.00633589)n2:0.120803)n1:0.431408)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000398_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000398_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a841de5f5aceab0f2aec6a28562490b39e621cb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000398_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02475:0.0748785,(GCF_005280335_PROKKA_02623:0.0714567,(GCF_023573625_PROKKA_00353:5e-09,(GCF_002008305_PROKKA_00346:0.00462917,GCF_003691675_PROKKA_00062:5e-09)n3:0.0023102)n2:0.0381849)n1:0.0748785)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000400_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000400_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c8691ee74b82a4d4ab9b8693af448c7e5c64573
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000400_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02471:0.160577,(GCF_005280335_PROKKA_02612:0.137911,(GCF_023573625_PROKKA_00356:0.020416,(GCF_002008305_PROKKA_00349:0.0248212,GCF_003691675_PROKKA_00065:0.0235509)n3:0.00262184)n2:0.106985)n1:0.160577)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000402_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000402_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1156a65930aef9523d5071af28b6aaf50092a3c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000402_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02468:0.0738626,(GCF_005280335_PROKKA_02609:0.0660878,(GCF_003691675_PROKKA_00068:0.00474973,(GCF_002008305_PROKKA_00352:0.00934885,GCF_023573625_PROKKA_00359:0.00888975)n3:0.00461178)n2:0.024209)n1:0.0738626)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000403_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000403_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e29c4d20dbcccb64997eefdcfb4ac43d66739da5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000403_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02467:0.238864,(GCF_005280335_PROKKA_02608:0.0660314,(GCF_002008305_PROKKA_00353:5e-09,(GCF_003691675_PROKKA_00069:0,GCF_023573625_PROKKA_00360:0)n3:0.00886929)n2:0.0485253)n1:0.238864)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000405_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000405_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..129e59d58b5a85e420b8aa3366acc3dfda80256b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000405_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02464:0.178866,(GCF_005280335_PROKKA_02605:0.0902751,(GCF_002008305_PROKKA_00356:0.00642588,(GCF_003691675_PROKKA_00072:0.00311737,GCF_023573625_PROKKA_00363:5e-09)n3:0.00296811)n2:0.103189)n1:0.178866)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000408_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000408_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34b74514d648fde2150d24eb271ceeacec918378
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000408_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02460:0.269529,(GCF_005280335_PROKKA_02601:0.146072,(GCF_002008305_PROKKA_00360:5e-09,(GCF_003691675_PROKKA_00076:0,GCF_023573625_PROKKA_00367:0)n3:0.0109082)n2:0.180223)n1:0.269529)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000409_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000409_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb1e18ac4a437561b12cfcd44038658c627664d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000409_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02459:0.0711567,(GCF_005280335_PROKKA_02600:0.0843623,(GCF_002008305_PROKKA_00361:0.00764953,(GCF_003691675_PROKKA_00077:0,GCF_023573625_PROKKA_00368:0)n3:5e-09)n2:0.0261832)n1:0.0711567)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000411_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000411_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b57a9b52ca108765387617c8b98732c6854b67a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000411_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02457:0.058657,(GCF_005280335_PROKKA_02598:0.0377754,(GCF_023573625_PROKKA_00370:0.00607536,(GCF_002008305_PROKKA_00363:0.0107742,GCF_003691675_PROKKA_00079:0.00487052)n3:0.00526884)n2:0.0481287)n1:0.058657)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000412_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000412_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be3ff6a51dcd1407ea37f463509460fc905bb2e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000412_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02456:0.122424,(GCF_005280335_PROKKA_02597:0.0978696,(GCF_003691675_PROKKA_00080:0.00386633,(GCF_002008305_PROKKA_00364:0.0123537,GCF_023573625_PROKKA_00371:0.00748155)n3:0.00558137)n2:0.0470528)n1:0.122424)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000414_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000414_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8cc3436832fed4acf549e8d3ab7f7f2a84805d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000414_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02452:0.122908,(GCF_005280335_PROKKA_02593:0.0921362,(GCF_002008305_PROKKA_00368:0.0120762,(GCF_003691675_PROKKA_00084:0,GCF_023573625_PROKKA_00375:0)n3:0.0107823)n2:0.0963647)n1:0.122908)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000415_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000415_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6931dc1fab1f7094bb07c62bb43b0bacea08d2fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000415_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02451:0.0582252,(GCF_005280335_PROKKA_02592:0.0256818,(GCF_002008305_PROKKA_00370:0.00691714,(GCF_003691675_PROKKA_00086:0.0034462,GCF_023573625_PROKKA_00377:0.00345068)n3:5e-09)n2:0.0242029)n1:0.0582252)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000416_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000416_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cb6116f6cb9a7ef8e7caf8163352a21b2ab3096
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000416_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02450:0.0363576,(GCF_005280335_PROKKA_02591:0.0129079,(GCF_023573625_PROKKA_00378:0.00260443,(GCF_002008305_PROKKA_00371:0.00761285,GCF_003691675_PROKKA_00087:0.00254446)n3:0.00511714)n2:0.0102059)n1:0.0363576)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000418_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000418_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff9bde6c1bb6950b69d08957efb84db7c6509adc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000418_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01177:0.259676,((GCF_002008305_PROKKA_00373:0,GCF_023573625_PROKKA_00380:0)n2:0.0286009,(GCF_005280335_PROKKA_01002:0.367142,GCF_005280335_PROKKA_02589:5.4e-09)n3:6e-10)n1:0.511713)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000419_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000419_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77914431d4c57f4ff34f19ef1c5ebc0f8a27eb21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000419_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01178:0.560227,((GCF_002008305_PROKKA_00374:0,GCF_023573625_PROKKA_00381:0)n2:0.0404052,(GCF_005280335_PROKKA_01001:0.524485,GCF_005280335_PROKKA_02588:4.5e-09)n3:5e-10)n1:0.915025)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000420_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000420_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90634b4fb41d3585ef995c3744920758476ee077
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000420_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01180:0.465263,((GCF_002008305_PROKKA_00377:0,GCF_023573625_PROKKA_00383:0)n2:5e-09,(GCF_005280335_PROKKA_00011:1.22737,GCF_005280335_PROKKA_02586:0.0057084)n3:0.000634267)n1:0.323704)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000421_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000421_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c701bd7c4eb67fd0555f2c75e3f01b27492f6f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000421_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02448:0.0588615,(GCF_003691675_PROKKA_00103:0.0200856,((GCF_002008305_PROKKA_00379:0,GCF_023573625_PROKKA_00385:0)n3:0.00794812,GCF_005280335_PROKKA_02576:0.00278493)n2:0.00178142)n1:0.0588615)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000422_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000422_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7b9044703e8271b7bcf7363d374d5df45e5f57f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000422_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02447:2.5e-09,(GCF_005280335_PROKKA_02575:0.0226484,((GCF_002008305_PROKKA_00380:0,GCF_023573625_PROKKA_00386:0)n3:0.0151717,GCF_003691675_PROKKA_00104:5e-09)n2:0.0301849)n1:2.5e-09)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000425_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000425_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..047670d91ec2fcb721e37f51bf656a7f920ac022
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000425_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02572:0.00580348,(GCF_023573625_PROKKA_00389:0.0235684,(GCF_002008305_PROKKA_00383:0.0106297,(GCF_003691675_PROKKA_00098:1.71251,GCF_003691675_PROKKA_00107:0.0121568)n3:0.00135075)n2:5e-09)n1:0.00580348)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000426_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000426_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06b42ee6c5d8cb87129d9f330bb71ed48cf431ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000426_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01754:0.236417,(GCF_005280335_PROKKA_02571:0.0271769,((GCF_002008305_PROKKA_00384:0,GCF_023573625_PROKKA_00390:0)n3:0.00522413,GCF_003691675_PROKKA_00108:5e-09)n2:0.00460316)n1:0.236417)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000428_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000428_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c6d8dab779e2a06b6cf5adcfa775c268f6a1e67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000428_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02439:0.17723,(GCF_005280335_PROKKA_02568:0.00903184,((GCF_002008305_PROKKA_00388:0,GCF_023573625_PROKKA_00394:0)n3:0.0113854,GCF_003691675_PROKKA_00112:5e-09)n2:0.0141045)n1:0.17723)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000429_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000429_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..275cc379851d78a6b2ae0fc6cd7d33e62198b41a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000429_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02438:0.20037,(GCF_005280335_PROKKA_02567:0.0556574,(GCF_003691675_PROKKA_00113:6e-09,(GCF_023573625_PROKKA_00395:0.0163248,GCF_002008305_PROKKA_00389:5e-09)n3:0.00649164)n2:0.0895037)n1:0.20037)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000430_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000430_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e6f7c8d079f7c891be40bfd1f9721af4d027060
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000430_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02436:0.076323,(GCF_005280335_PROKKA_02565:0.0767101,(GCF_003691675_PROKKA_00115:0.00737419,(GCF_002008305_PROKKA_00391:0.00733823,GCF_023573625_PROKKA_00397:5e-09)n3:5e-09)n2:0.0913416)n1:0.076323)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000432_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000432_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e870f01c5ef340168ba6b0924c649262284f17c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000432_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00172:0.644016,GCF_005280335_PROKKA_02563:0.212973)n1:0.105561,(GCF_003691675_PROKKA_00117:0.0128809,(GCF_002008305_PROKKA_00393:0.0344105,GCF_023573625_PROKKA_00399:0.0142558)n3:0.00710731)n2:0.105561)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000435_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000435_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aeb6d1d724e775acd5a8617ae77dc2c50c560408
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000435_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02431:0.205567,(GCF_005280335_PROKKA_02560:0.123626,(GCF_023573625_PROKKA_00403:0.00239419,(GCF_002008305_PROKKA_00397:0.0112409,GCF_003691675_PROKKA_00121:0.0132977)n3:0.0088167)n2:0.101538)n1:0.205567)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000441_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000441_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fd6c10bb876be796653d5c403fbe371aa7398a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000441_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02420:0.141825,(GCF_005280335_PROKKA_02552:0.0273699,(GCF_003691675_PROKKA_00127:0.0102658,(GCF_002008305_PROKKA_00404:0.00499959,GCF_023573625_PROKKA_00410:0.00503133)n3:0.00479542)n2:0.0242162)n1:0.141825)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000444_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000444_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5912284e415ec697774e56a6885bb9312bcc418e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000444_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02417:0.0460942,(GCF_005280335_PROKKA_02549:0.0345054,(GCF_002008305_PROKKA_00410:0.0247858,(GCF_003691675_PROKKA_00130:0.0162919,GCF_023573625_PROKKA_00413:0.0113551)n3:0.0112262)n2:0.0169501)n1:0.0460942)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000445_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000445_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..695e744fd993d951c32e4590ff7f9b0ab6a52aa0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000445_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02416:0.00497999,(GCF_005280335_PROKKA_02548:0.00936668,((GCF_002008305_PROKKA_00411:0,GCF_003691675_PROKKA_00131:0)n3:0.0024596,GCF_023573625_PROKKA_00414:0.00992389)n2:0.0152176)n1:0.00497999)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000446_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000446_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8abb42b2cff03c809c926b140f1e41a0ac9f5018
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000446_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02414:0.066632,((GCF_003691675_PROKKA_00133:0,GCF_023573625_PROKKA_00416:0)n2:5e-09,(GCF_002008305_PROKKA_00413:5e-09,GCF_005280335_PROKKA_02546:0.010521)n3:0.00349347)n1:0.066632)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000447_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000447_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb326ebe4f480f68dffa8e1bf0c5b04ee4c901ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000447_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02413:0.0621583,(GCF_005280335_PROKKA_02545:0.0101107,(GCF_002008305_PROKKA_00414:5e-09,(GCF_003691675_PROKKA_00134:0,GCF_023573625_PROKKA_00417:0)n3:0.00694998)n2:0.0257116)n1:0.0621583)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000449_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000449_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7cc52c7ecab28ad925abcbab16ce7cd48f75d81f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000449_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02411:0.12021,(GCF_005280335_PROKKA_02543:0.046041,(GCF_003691675_PROKKA_00138:0.0064124,(GCF_002008305_PROKKA_00417:5e-09,GCF_023573625_PROKKA_00420:0.00321143)n3:0.0130622)n2:0.0395967)n1:0.12021)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000452_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000452_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ba8703827a506568c8aa6a631eac4d22715694c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000452_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02407:0.00835816,(GCF_023573625_PROKKA_00424:0.0164763,(GCF_003691675_PROKKA_00142:0.00985731,(GCF_002008305_PROKKA_00421:0.00327314,GCF_005280335_PROKKA_02538:0.0577379)n3:5e-09)n2:0.00328209)n1:0.00835816)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000453_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000453_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbc0050ff1f9f43a12b12c3ff34c956cb712117b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000453_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02406:0.0812052,(GCF_005280335_PROKKA_02536:0.0238784,(GCF_002008305_PROKKA_00422:0.00310088,(GCF_003691675_PROKKA_00143:5e-09,GCF_023573625_PROKKA_00425:0.00922647)n3:0.00302932)n2:0.0362143)n1:0.0812052)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000454_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000454_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09ce204b6933f187c633fd347dfa23e1a00f7cf4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000454_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02403:0.151936,(GCF_005280335_PROKKA_02533:0.0592178,(GCF_023573625_PROKKA_00427:0.00441127,(GCF_002008305_PROKKA_00424:0.00408943,GCF_003691675_PROKKA_00145:0.00197747)n3:0.00229004)n2:0.0288583)n1:0.151936)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000458_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000458_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b9963ba3e2ecbabbd2a76c806099746447f5718
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000458_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02399:0.0730217,(GCF_005280335_PROKKA_02529:0.127204,(GCF_002008305_PROKKA_00428:5e-09,(GCF_023573625_PROKKA_00431:0.0116014,GCF_003691675_PROKKA_00149:5e-09)n3:0.00769105)n2:0.100595)n1:0.0730217)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000460_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000460_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e3bd01db7e4ea2de35cca09a30ee2da6a505df2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000460_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02397:0.213988,(GCF_005280335_PROKKA_02527:0.449009,(GCF_003691675_PROKKA_00151:0.00675705,(GCF_023573625_PROKKA_00433:5e-09,GCF_002008305_PROKKA_00430:0.009698)n3:0.00313046)n2:0.352271)n1:0.213988)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000462_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000462_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70fb5f2c656b1836396b48ffd910779814285b33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000462_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02395:0.0321892,(GCF_005280335_PROKKA_02524:0.0171402,(GCF_002008305_PROKKA_00433:0.00379561,(GCF_003691675_PROKKA_00154:0,GCF_023573625_PROKKA_00436:0)n3:5e-09)n2:0.0338675)n1:0.0321892)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000463_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000463_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b6fe03c9c568e7824b9b54f63f988ee31c6a5f16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000463_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02394:0.0135784,(GCF_005280335_PROKKA_02523:0.0121653,((GCF_002008305_PROKKA_00434:0,GCF_023573625_PROKKA_00437:0)n3:5e-09,GCF_003691675_PROKKA_00155:0.00336282)n2:0.0085108)n1:0.0135784)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000465_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000465_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3d09c95c88a25d4c7ab4a46837f6b9b45413c7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000465_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02392:0.0455994,((GCF_002008305_PROKKA_00436:0,GCF_003691675_PROKKA_00157:0,GCF_023573625_PROKKA_00439:0)n2:0.0398004,GCF_005280335_PROKKA_02521:0.0231685)n1:0.0455994)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000466_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000466_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4ba473d605d3924325943f85899c6831c5d25d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000466_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02391:0.0852755,(GCF_005280335_PROKKA_02520:0.0330606,(GCF_023573625_PROKKA_00440:0.0029903,(GCF_002008305_PROKKA_00437:0.00505203,GCF_003691675_PROKKA_00158:0.00251426)n3:0.00467453)n2:0.0261105)n1:0.0852755)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000467_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000467_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4cef5940906895c591dedc2567eeb0ef8e7c0da4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000467_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02390:0.0678189,(GCF_005280335_PROKKA_02519:0.0691741,(GCF_002008305_PROKKA_00438:0.00230989,(GCF_003691675_PROKKA_00159:0,GCF_023573625_PROKKA_00441:0)n3:6e-09)n2:0.0498671)n1:0.0678189)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000468_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000468_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc1d9681f6dc2db7aa2c65b15f7bb53bc10b3cbd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000468_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02389:0.1043,(GCF_005280335_PROKKA_02518:0.282369,(GCF_003691675_PROKKA_00160:0.00788943,(GCF_002008305_PROKKA_00439:0.00254334,GCF_023573625_PROKKA_00442:0.00254943)n3:0.0260863)n2:0.0821424)n1:0.1043)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000470_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000470_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..789a0e282ee6c5646c246065b5b5644e3cf32500
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000470_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02387:0.0810846,(GCF_005280335_PROKKA_02516:0.267819,(GCF_002008305_PROKKA_00441:0.00640675,(GCF_003691675_PROKKA_00162:0.0105738,GCF_023573625_PROKKA_00444:0.00619498)n3:0.00204138)n2:0.142398)n1:0.0810846)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000471_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000471_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef74f16ef3651d9b8a70de11fcd3ed12e7cbffa0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000471_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02386:0.0610846,(GCF_005280335_PROKKA_02515:0.213253,(GCF_023573625_PROKKA_00445:5e-09,(GCF_003691675_PROKKA_00163:0.00455034,GCF_002008305_PROKKA_00442:0.00455542)n3:0.00227503)n2:0.131406)n1:0.0610846)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000472_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000472_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0bbe06c8d686bd274f15b2b461bacf8b2bde5688
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000472_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02385:0.179844,(GCF_005280335_PROKKA_02514:0.107597,(GCF_023573625_PROKKA_00446:5e-09,(GCF_002008305_PROKKA_00443:0.00715049,GCF_003691675_PROKKA_00164:0.00720083)n3:0.00727021)n2:0.0488971)n1:0.179844)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000475_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000475_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4c42d013c2363770bf3f269a18d41fc84876c446
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000475_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02382:0.079277,(GCF_005280335_PROKKA_02511:0.027571,(GCF_003691675_PROKKA_00167:0.00245314,(GCF_002008305_PROKKA_00446:0.00989557,GCF_023573625_PROKKA_00449:0.00245403)n3:5e-09)n2:0.028415)n1:0.079277)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000476_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000476_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb54ddd7080692d3562f2470a272aec1f6766827
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000476_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02381:0.154346,(GCF_005280335_PROKKA_02510:0.114092,(GCF_023573625_PROKKA_00450:0.0205002,(GCF_002008305_PROKKA_00447:0.00372925,GCF_003691675_PROKKA_00168:0.0112091)n3:0.00592164)n2:0.115361)n1:0.154346)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000477_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000477_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9130d539034673129aabcb40d50bc4993fc3681a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000477_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02379:0.25529,(GCF_005280335_PROKKA_02507:0.102416,(GCF_002008305_PROKKA_00449:0.0164214,(GCF_003691675_PROKKA_00170:0.0108052,GCF_023573625_PROKKA_00452:5e-09)n3:0.0352595)n2:0.163126)n1:0.25529)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000482_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000482_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd27bf7171c06d06c9a1130f01ee7397e7613205
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000482_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02373:0.270413,(GCF_005280335_PROKKA_02489:0.11606,(GCF_023573625_PROKKA_00458:0.00674939,(GCF_002008305_PROKKA_00458:0.00998323,GCF_003691675_PROKKA_00176:0.00471881)n3:0.0108103)n2:0.0938371)n1:0.270413)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000483_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000483_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3add3ad077443cc2dace986c9d91e0538f8cd1f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000483_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02372:0.0992653,(GCF_005280335_PROKKA_02488:0.0727241,(GCF_003691675_PROKKA_00177:0.00604814,(GCF_002008305_PROKKA_00459:0.00435615,GCF_023573625_PROKKA_00459:5e-09)n3:0.000515945)n2:0.0804881)n1:0.0992653)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000486_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000486_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b86b77f6e4d88cf4882dc7c3de8a0182d206d38f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000486_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02369:0.363812,(GCF_005280335_PROKKA_02485:0.124688,((GCF_002008305_PROKKA_00462:0,GCF_003691675_PROKKA_00180:0)n3:5e-09,GCF_023573625_PROKKA_00462:0.0132008)n2:0.0921965)n1:0.363812)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000488_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000488_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1dfa82ef0a29fca69ea0af0989089f5e177a2f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000488_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02366:0.11489,(GCF_005280335_PROKKA_02482:0.0465942,(GCF_023573625_PROKKA_00465:5e-09,(GCF_002008305_PROKKA_00465:5e-09,GCF_003691675_PROKKA_00183:0.00427259)n3:0.00858828)n2:0.0570658)n1:0.11489)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000489_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000489_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c46f4db988d35e452afe28abc91e0b349e8476a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000489_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02365:0.0943911,((GCF_002008305_PROKKA_00466:0,GCF_003691675_PROKKA_00184:0,GCF_023573625_PROKKA_00466:0)n2:0.0854434,GCF_005280335_PROKKA_02481:0.0890008)n1:0.0943911)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000490_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000490_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..145f87f9dba41cafba927e16b2c3632a27609c0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000490_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02364:0.168255,(GCF_005280335_PROKKA_02480:0.189278,((GCF_002008305_PROKKA_00467:0,GCF_023573625_PROKKA_00467:0)n3:0.014914,GCF_003691675_PROKKA_00185:5e-09)n2:0.159044)n1:0.168255)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000491_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000491_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26b9e036f8e28fb57b8983fc0af840c05e356795
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000491_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02363:0.0884787,(GCF_005280335_PROKKA_02479:0.0905815,(GCF_003691675_PROKKA_00186:5e-09,(GCF_002008305_PROKKA_00468:0.00411089,GCF_023573625_PROKKA_00468:0.00205169)n3:0.00205315)n2:0.0753633)n1:0.0884787)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000492_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000492_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..100b810a50f3d70870627bdeb5c162bf19e3f573
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000492_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02362:0.208476,(GCF_005280335_PROKKA_02478:0.191295,(GCF_002008305_PROKKA_00469:0.0141697,(GCF_003691675_PROKKA_00187:0,GCF_023573625_PROKKA_00469:0)n3:0.0245555)n2:0.106562)n1:0.208476)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000498_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000498_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7aef9192c27034a4640d9b6f628bbe24be6f7155
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000498_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02356:0.199281,(GCF_005280335_PROKKA_02471:0.112299,((GCF_002008305_PROKKA_00475:0,GCF_023573625_PROKKA_00475:0)n3:0.00653933,GCF_003691675_PROKKA_00193:0.00857647)n2:0.0965862)n1:0.199281)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000501_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000501_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7549f078f6bc7c5a27354273c925e0a846cdd25d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000501_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02352:0.163116,(GCF_005280335_PROKKA_02468:0.123153,((GCF_002008305_PROKKA_00479:0,GCF_023573625_PROKKA_00479:0)n3:0.00826953,GCF_003691675_PROKKA_00197:0.00652452)n2:0.110024)n1:0.163116)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000504_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000504_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f0aeb7d3592792ce0d3c6586fba200214692648
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000504_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02349:0.191751,((GCF_002008305_PROKKA_00482:0,GCF_003691675_PROKKA_00200:0,GCF_023573625_PROKKA_00482:0)n2:0.10431,GCF_005280335_PROKKA_02465:0.0331104)n1:0.191751)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000506_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000506_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c5e55b48111d8336dcf3232d2e81198c1ed3e6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000506_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02347:0.227056,(GCF_005280335_PROKKA_02463:0.0906436,(GCF_003691675_PROKKA_00202:0.0488694,(GCF_002008305_PROKKA_00484:0.0172518,GCF_023573625_PROKKA_00484:0.0127846)n3:0.0224093)n2:0.0643806)n1:0.227056)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000509_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000509_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4975151db2f0003704f08f2ea3659f1070da6e20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000509_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02343:0.115917,(GCF_005280335_PROKKA_02459:0.0164242,(GCF_003691675_PROKKA_00207:0.0124622,(GCF_002008305_PROKKA_00487:0.00339532,GCF_023573625_PROKKA_00487:5e-09)n3:0.0131568)n2:0.0313191)n1:0.115917)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000510_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000510_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5627bd08e9c4e5dddcc84afab127d5abc5b592a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000510_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02341:0.0892601,((GCF_005280335_PROKKA_02457:0.0125238,GCF_023573625_PROKKA_00489:5e-09)n2:0.00265935,(GCF_003691675_PROKKA_00211:0.0126338,GCF_002008305_PROKKA_00490:0.00619641)n3:0.00684401)n1:0.0892601)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000511_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000511_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05d9a649b13df6b715a012103eeaa67f061415a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000511_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02340:0.0824836,(GCF_005280335_PROKKA_02456:0.0334722,(GCF_003691675_PROKKA_00212:0.00651574,(GCF_002008305_PROKKA_00491:0.00325347,GCF_023573625_PROKKA_00490:0.00327194)n3:0.00166739)n2:0.035906)n1:0.0824836)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000513_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000513_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98cefb60cf35286f73d54a4d88fbc87c2fa734bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000513_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02338:0.106806,(GCF_005280335_PROKKA_02454:0.0816974,(GCF_002008305_PROKKA_00493:0.011065,(GCF_003691675_PROKKA_00214:0,GCF_023573625_PROKKA_00492:0)n3:0.00458767)n2:0.0805928)n1:0.106806)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000516_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000516_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8096d5f1b0899d4f8845d1feff4a46aebb072f27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000516_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02333:0.0165743,(GCF_005280335_PROKKA_02449:0.00903703,((GCF_002008305_PROKKA_00500:0,GCF_023573625_PROKKA_00499:0)n3:0.00296598,GCF_003691675_PROKKA_00221:5e-09)n2:0.0124013)n1:0.0165743)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000517_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000517_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b444764e85405d9bc26526abd95fad69228b683
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000517_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02332:0.164383,(GCF_005280335_PROKKA_02448:0.0730139,(GCF_003691675_PROKKA_00222:0.00391656,(GCF_002008305_PROKKA_00501:0.00389776,GCF_023573625_PROKKA_00500:0.0120186)n3:0.00414791)n2:0.109829)n1:0.164383)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000519_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000519_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..024cbf7332dc64fcfb3e0d66da1f3eb4ca02787f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000519_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02330:0.0834031,(GCF_005280335_PROKKA_02446:0.0456976,(GCF_023573625_PROKKA_00503:0.00953077,(GCF_002008305_PROKKA_00504:0.00910066,GCF_003691675_PROKKA_00224:0.00407739)n3:0.00949719)n2:0.0659686)n1:0.0834031)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000520_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000520_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4059907c5a503b1ef01999cb095c246fdb012fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000520_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02329:0.0603962,(GCF_005280335_PROKKA_02445:0.0781028,(GCF_003691675_PROKKA_00225:0.00938038,(GCF_002008305_PROKKA_00505:0.00364714,GCF_023573625_PROKKA_00504:0.0145221)n3:0.00755429)n2:0.074163)n1:0.0603962)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000521_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000521_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b9aa200ac120a9c3c7a0c98ff5e4d3be55a9984d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000521_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02328:0.137808,(GCF_005280335_PROKKA_02444:0.191417,(GCF_002008305_PROKKA_00506:0.00791746,(GCF_003691675_PROKKA_00226:0.0219779,GCF_023573625_PROKKA_00505:0.010844)n3:0.0167596)n2:0.209726)n1:0.137808)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000523_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000523_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4421e4e83aadd8ad1000c216e140f9a875c1c3e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000523_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02326:0.0406196,(GCF_005280335_PROKKA_02442:0.0391783,(GCF_002008305_PROKKA_00508:0.00991343,(GCF_003691675_PROKKA_00228:0.0107165,GCF_023573625_PROKKA_00507:0.00411626)n3:0.00210574)n2:0.0437146)n1:0.0406196)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000525_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000525_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..797a0b4ad7c530ddd5d38bff090be95d95ee7a97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000525_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02322:0.0735316,(GCF_003691675_PROKKA_00232:0.100319,(GCF_002008305_PROKKA_00512:0.00787466,(GCF_005280335_PROKKA_02439:0.0282092,GCF_023573625_PROKKA_00511:0.00932854)n3:0.0177787)n2:0.218919)n1:0.0735316)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000528_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000528_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d7818a7940c88ac1affcc96176ac542517d0aa84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000528_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02310:0.00589746,(GCF_005280335_PROKKA_02427:0.0387717,(GCF_003691675_PROKKA_00244:0.0148611,(GCF_002008305_PROKKA_00522:0.0104055,GCF_023573625_PROKKA_00522:0.0125755)n3:0.00837414)n2:0.00672034)n1:0.00589746)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000529_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000529_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4faf9c895b865ea4d5eb5ebf7e1d1198fbe04195
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000529_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02308:0.0528765,(GCF_005280335_PROKKA_02425:0.0447997,(GCF_003691675_PROKKA_00247:5e-09,(GCF_002008305_PROKKA_00526:0.0242862,GCF_023573625_PROKKA_00526:0.0286087)n3:0.00914733)n2:0.0373445)n1:0.0528765)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000531_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000531_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..386dfa72d7373d1ad2d8c1c0645d5fbdf6f86122
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000531_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02305:0.206968,(GCF_005280335_PROKKA_02423:0.0866012,(GCF_002008305_PROKKA_00529:5e-09,(GCF_023573625_PROKKA_00529:0.0165147,GCF_003691675_PROKKA_00250:0.0109464)n3:0.00542454)n2:0.0593411)n1:0.206968)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000532_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000532_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22a16f2eef83eb801c634cd4fbe1e3aa3cb719b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000532_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02304:0.214834,(GCF_005280335_PROKKA_02422:0.133452,(GCF_002008305_PROKKA_00530:0.0399068,(GCF_003691675_PROKKA_00251:0.0232747,GCF_023573625_PROKKA_00530:0.0175062)n3:0.00650606)n2:0.0584415)n1:0.214834)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000533_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000533_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..323a0893687ea8e1a4d5ee27a88e5ef0c3c0d6bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000533_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02303:0.0760832,(GCF_005280335_PROKKA_02421:0.0148732,(GCF_023573625_PROKKA_00531:0.00098132,(GCF_002008305_PROKKA_00531:0.00316664,GCF_003691675_PROKKA_00252:0.00739529)n3:0.00244025)n2:0.0277058)n1:0.0760832)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000535_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000535_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5df0b2d293c4677379e4c65e656a2142c88ea88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000535_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02301:0.220971,(GCF_005280335_PROKKA_02419:0.218117,(GCF_002008305_PROKKA_00533:0.0054236,(GCF_003691675_PROKKA_00254:0.0144215,GCF_023573625_PROKKA_00533:0.00659499)n3:0.0216699)n2:0.19673)n1:0.220971)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000537_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000537_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca38fde2a861a9d718e787f12867402e7e64d610
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000537_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02296:0.177354,(GCF_005280335_PROKKA_02414:0.0582554,(GCF_023573625_PROKKA_00538:0.00982058,(GCF_002008305_PROKKA_00535:5e-09,GCF_003691675_PROKKA_00259:0.00299878)n3:0.0107088)n2:0.127115)n1:0.177354)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000539_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000539_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c05502c6a657b552e0de1ffbe000298979b7a80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000539_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02293:0.0845495,(GCF_005280335_PROKKA_02411:0.07618,(GCF_002008305_PROKKA_00538:0.0018059,(GCF_003691675_PROKKA_00262:0.00339954,GCF_023573625_PROKKA_00541:5e-09)n3:0.00329524)n2:0.105548)n1:0.0845495)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000541_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000541_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62c413cc3f09d5a1f62922f9952d29f7b2ecce78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000541_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02291:0.0717797,(GCF_005280335_PROKKA_02409:0.033684,(GCF_003691675_PROKKA_00264:0.00293723,(GCF_002008305_PROKKA_00540:5e-09,GCF_023573625_PROKKA_00543:0.0040248)n3:0.00925963)n2:0.0692899)n1:0.0717797)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000543_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000543_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d605e703fd0a223901b54cc714d862c1efa5f1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000543_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02287:0.17921,(GCF_005280335_PROKKA_02404:0.146743,(GCF_002008305_PROKKA_00543:0.0148815,(GCF_003691675_PROKKA_00268:0.00434703,GCF_023573625_PROKKA_00546:0.0223338)n3:0.0163612)n2:0.217578)n1:0.17921)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000544_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000544_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc1aab57c9657a43cbddd85d8b0bba58b370e972
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000544_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02286:0.0557967,(GCF_005280335_PROKKA_02403:0.042047,(GCF_002008305_PROKKA_00544:0.00471023,(GCF_003691675_PROKKA_00269:0.00660382,GCF_023573625_PROKKA_00547:0.0081622)n3:0.00394707)n2:0.0364232)n1:0.0557967)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000546_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000546_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ce6628130d64d0726b6d59f283308f8ddbff1a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000546_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02284:0.0392128,(GCF_005280335_PROKKA_02401:0.00728324,((GCF_002008305_PROKKA_00546:0,GCF_023573625_PROKKA_00549:0)n3:5e-09,GCF_003691675_PROKKA_00271:0.0018609)n2:0.0179141)n1:0.0392128)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000547_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000547_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..588462ff0abf15847d8aca17d7431ce21eda2c96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000547_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02282:0.239262,(GCF_005280335_PROKKA_02398:0.0730089,(GCF_003691675_PROKKA_00273:0.00388077,(GCF_002008305_PROKKA_00548:0.0117731,GCF_023573625_PROKKA_00551:0.00563616)n3:0.0137864)n2:0.133122)n1:0.239262)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000548_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000548_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eca51bfc18857172e2d73d4239d65d74f65cd3a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000548_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02281:0.115185,(GCF_005280335_PROKKA_02397:0.0695351,(GCF_002008305_PROKKA_00549:0.00508667,(GCF_003691675_PROKKA_00274:5e-09,GCF_023573625_PROKKA_00552:0.00751927)n3:0.00495922)n2:0.0479088)n1:0.115185)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000549_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000549_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9cafb4995eefe4bbb15691db4836711068175999
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000549_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02280:0.0940854,((GCF_002008305_PROKKA_00550:0,GCF_003691675_PROKKA_00275:0,GCF_023573625_PROKKA_00553:0)n2:0.0745542,GCF_005280335_PROKKA_02396:0.060993)n1:0.0940854)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000552_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000552_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43562cc83cb8c4c596602c83b4237b8bfc73ba08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000552_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02273:0.0540662,(GCF_005280335_PROKKA_02390:0.138559,((GCF_002008305_PROKKA_00555:0,GCF_023573625_PROKKA_00558:0)n3:5e-09,GCF_003691675_PROKKA_00280:0.00983414)n2:0.0381939)n1:0.0540662)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000555_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000555_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4134d69d3531fec2d8a8bf84e2d9ef3b9503382
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000555_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02269:0.101869,(GCF_005280335_PROKKA_02385:0.17835,(GCF_023573625_PROKKA_00561:0.0040584,(GCF_002008305_PROKKA_00558:0.0318605,GCF_003691675_PROKKA_00283:0.00281049)n3:0.00445256)n2:0.117384)n1:0.101869)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000557_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000557_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16218f099c719377e2c72544f41c013acf371fce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000557_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02267:0.0414377,(GCF_005280335_PROKKA_02383:0.0551284,(GCF_002008305_PROKKA_00560:0.0068074,(GCF_003691675_PROKKA_00285:5e-09,GCF_023573625_PROKKA_00563:0.0288874)n3:0.00753224)n2:0.0598313)n1:0.0414377)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000558_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000558_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..590c89a1cc7ff1d9ce428df1aa2aad04676bc261
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000558_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02266:0.0870346,(GCF_005280335_PROKKA_02382:0.0283476,(GCF_023573625_PROKKA_00564:0.00216573,(GCF_002008305_PROKKA_00561:0.00433552,GCF_003691675_PROKKA_00286:0.00217358)n3:0.00219126)n2:0.0251538)n1:0.0870346)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000559_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000559_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80d51d2900034ab3f38e77b2442f9eb6f6b1e217
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000559_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02265:0.154363,(GCF_005280335_PROKKA_02381:0.0780985,(GCF_003691675_PROKKA_00287:0.00366196,(GCF_002008305_PROKKA_00562:0.00264586,GCF_023573625_PROKKA_00565:0.00264491)n3:0.00429927)n2:0.0603857)n1:0.154363)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000562_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000562_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98b925602aa0f413ee25f61870638a158ed244e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000562_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02262:0.0654399,(GCF_005280335_PROKKA_02378:0.115506,((GCF_002008305_PROKKA_00565:0,GCF_023573625_PROKKA_00568:0)n3:0.0250804,GCF_003691675_PROKKA_00290:5e-09)n2:0.0462702)n1:0.0654399)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000564_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000564_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aedc3c7f8b63403f3df877651435b7b345162374
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000564_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02260:0.0619843,(GCF_002008305_PROKKA_00567:0.161307,(GCF_005280335_PROKKA_02376:0.0401764,(GCF_003691675_PROKKA_00292:0.00624765,GCF_023573625_PROKKA_00570:0.0212232)n3:0.0686859)n2:0.286982)n1:0.0619843)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000567_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000567_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95e118484ba5291fcaddb10308ad88824f6b108a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000567_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02250:0.0326222,(GCF_005280335_PROKKA_02359:0.0589048,(GCF_023573625_PROKKA_00575:0.00400463,(GCF_002008305_PROKKA_00574:0.00484646,GCF_003691675_PROKKA_00306:0.00659511)n3:0.00994213)n2:0.027311)n1:0.0326222)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000571_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000571_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e975aedfa3d0fcae147d539b0d6afa6e0af7fba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000571_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02246:0.0626028,(GCF_005280335_PROKKA_02351:0.0301153,(GCF_023573625_PROKKA_00584:0.00485844,(GCF_002008305_PROKKA_00583:0.00643601,GCF_003691675_PROKKA_00316:0.00159958)n3:0.00490687)n2:0.0306983)n1:0.0626028)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000573_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000573_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d547580fc57d65be5c95b06fbae4ebb0cb4aced
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000573_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00729:0.152744,(GCF_005280335_PROKKA_00728:0.278222,GCF_005280335_PROKKA_02365:0.0864523)n2:0.0576136)n1:0.0432156,(GCF_002008305_PROKKA_00608:0.0427432,GCF_003691675_PROKKA_01768:0.0275979)n3:0.0432156)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000576_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000576_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5159cddc82ed3a47ec152a8dd63237d4be1d6256
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000576_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_PROKKA_00408:0.096765,GCF_023573625_PROKKA_00595:5e-09)n2:0.00333113,GCF_002008305_PROKKA_00636:0.00333991)n1:8.17685e-05,(GCF_020097155_PROKKA_02193:0.0232575,GCF_020097155_PROKKA_02192:0.0046953)n3:8.17685e-05)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000578_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000578_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d3f6672cdf11789349e3298d7ab8b83872e1067
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000578_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02184:0.00157063,(GCF_002008305_PROKKA_00641:5e-09,(GCF_003691675_PROKKA_00378:5e-09,(GCF_005280335_PROKKA_02321:0.0949064,GCF_023573625_PROKKA_00611:0.00318555)n3:0.00939523)n2:0.00945666)n1:0.00157063)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000580_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000580_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef4a6ce9a1a50a7258899ccfc8a17608aa212bcd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000580_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02182:0.0377387,(GCF_005280335_PROKKA_00385:0.20328,(GCF_023573625_PROKKA_00613:0.0193213,(GCF_002008305_PROKKA_00643:0.005533,GCF_003691675_PROKKA_00380:0.00831088)n3:5e-09)n2:0.0522775)n1:0.0377387)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000582_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000582_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da9a4eea77dc0a803fb4f5ae944ec336304f6c7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000582_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02175:0.121257,(GCF_005280335_PROKKA_02316:0.0358152,(GCF_023573625_PROKKA_00617:0.00956273,(GCF_002008305_PROKKA_00647:5e-09,GCF_003691675_PROKKA_00384:0.00479609)n3:0.00246553)n2:0.0456424)n1:0.121257)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000585_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000585_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcd192c718183ce3a59786e26aa8d02a1977f678
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000585_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02168:0.0382236,(GCF_005280335_PROKKA_02311:0.0630178,(GCF_023573625_PROKKA_00622:0.00137673,(GCF_002008305_PROKKA_00652:0.001915,GCF_003691675_PROKKA_00389:0.00348262)n3:1.7144e-05)n2:0.00985673)n1:0.0382236)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000587_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000587_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..716989473e8c84eeb5cfa21b9e8399192d746bc8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000587_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02166:0.070315,((GCF_002008305_PROKKA_00654:0,GCF_003691675_PROKKA_00391:0,GCF_023573625_PROKKA_00624:0)n2:0.0182473,GCF_005280335_PROKKA_02309:0.0244962)n1:0.070315)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000590_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000590_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..55e238dfe62cfee2b6f829daf1e66cdd847fc24c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000590_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02161:0.211371,(GCF_005280335_PROKKA_02305:0.0311968,(GCF_023573625_PROKKA_00628:5e-09,(GCF_002008305_PROKKA_00658:0.00257448,GCF_003691675_PROKKA_00395:0.00257168)n3:0.00256753)n2:0.0292409)n1:0.211371)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000591_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000591_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f26bbe8fc8b9b8a8f09007f45f80f3e2b1f6696d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000591_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02160:0.0904668,(GCF_005280335_PROKKA_02304:0.0097094,(GCF_003691675_PROKKA_00396:0.00279828,(GCF_002008305_PROKKA_00659:0.00280109,GCF_023573625_PROKKA_00629:5e-09)n3:5e-09)n2:0.0218777)n1:0.0904668)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000594_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000594_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1b18facc6530d0cc40f59e75866f5d1636a1bf4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000594_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02157:0.208826,(GCF_005280335_PROKKA_02301:0.091013,(GCF_023573625_PROKKA_00632:0.00251321,(GCF_002008305_PROKKA_00662:0.0089031,GCF_003691675_PROKKA_00399:5e-09)n3:0.00650348)n2:0.0966367)n1:0.208826)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000598_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000598_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f043a392cb47391e614cb9daebd8d3f0cce51dc7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000598_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02154:0.0659006,(GCF_005280335_PROKKA_02292:0.0433939,(GCF_002008305_PROKKA_00670:0.00233352,(GCF_003691675_PROKKA_00407:0.0116995,GCF_023573625_PROKKA_00640:5e-09)n3:0.00232084)n2:0.0859936)n1:0.0659006)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000600_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000600_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5b0fee6e5a41289baee20b9cc3b9359eeab1609
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000600_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02152:0.023483,(GCF_005280335_PROKKA_02290:0.0211007,(GCF_002008305_PROKKA_00672:0.00252299,(GCF_003691675_PROKKA_00409:0,GCF_023573625_PROKKA_00642:0)n3:5e-09)n2:0.0233795)n1:0.023483)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000602_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000602_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5ebc7c6f94f5e3cac1f33095018b6896575a02f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000602_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02150:0.0331509,(GCF_005280335_PROKKA_02288:0.158969,(GCF_023573625_PROKKA_00644:5e-09,(GCF_002008305_PROKKA_00674:0.00330098,GCF_003691675_PROKKA_00411:0.00331037)n3:0.00165156)n2:0.0610629)n1:0.0331509)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000603_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000603_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69c7f58c3e4b8ef5dc06e8c70e070a32bb367517
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000603_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02149:0.161065,(GCF_005280335_PROKKA_02287:0.0208804,((GCF_002008305_PROKKA_00675:0,GCF_023573625_PROKKA_00645:0)n3:0.00404487,GCF_003691675_PROKKA_00412:5e-09)n2:0.0656668)n1:0.161065)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000606_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000606_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47f63dc04c107740f5fd70c4cde2c6736a394c4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000606_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02145:0.0299911,(GCF_005280335_PROKKA_02284:0.027097,(GCF_002008305_PROKKA_00679:0.00212244,(GCF_003691675_PROKKA_00416:0.0031836,GCF_023573625_PROKKA_00649:6e-09)n3:5e-09)n2:0.0278771)n1:0.0299911)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000607_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000607_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b593eeee4d83f9d67d88f707f8c4d7e6a3d8730
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000607_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02144:0.035354,(GCF_005280335_PROKKA_02283:0.0373662,((GCF_002008305_PROKKA_00680:0,GCF_003691675_PROKKA_00417:0)n3:5e-09,GCF_023573625_PROKKA_00650:0.0064166)n2:0.0366625)n1:0.035354)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000608_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000608_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ec27cee8984ce078157f8c461e26ef2056038a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000608_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02143:0.088926,(GCF_005280335_PROKKA_02282:0.0502936,(GCF_023573625_PROKKA_00651:0.00321746,(GCF_002008305_PROKKA_00681:5e-09,GCF_003691675_PROKKA_00418:0.0032165)n3:5e-09)n2:0.0212502)n1:0.088926)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000610_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000610_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da92c9d8cc8fc543a57f48b49f932f1bb755d3e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000610_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02141:0.115374,((GCF_002008305_PROKKA_00683:0,GCF_003691675_PROKKA_00420:0,GCF_023573625_PROKKA_00653:0)n2:0.0864833,GCF_005280335_PROKKA_02280:0.118886)n1:0.115374)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000614_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000614_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..836d989c51a1b48afe325695730b7dbda0493eed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000614_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02137:0,(GCF_002008305_PROKKA_00687:0,GCF_003691675_PROKKA_00424:0,GCF_005280335_PROKKA_02270:0,GCF_023573625_PROKKA_00657:0)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000615_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000615_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f641cb1d689a434cf21b58f293dbaaba69110781
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000615_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02136:0.0273553,(GCF_005280335_PROKKA_02269:0.030883,((GCF_002008305_PROKKA_00688:0,GCF_023573625_PROKKA_00658:0)n3:5e-09,GCF_003691675_PROKKA_00425:0.00128559)n2:0.0141544)n1:0.0273553)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000619_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000619_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..131d32e6ec3dba144886f4fd9959df303491cd36
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000619_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02131:0.0916049,(GCF_005280335_PROKKA_02261:0.0331258,(GCF_023573625_PROKKA_00663:0.00782939,(GCF_002008305_PROKKA_00693:0.00313689,GCF_003691675_PROKKA_00430:0.00312995)n3:0.00157023)n2:0.0227381)n1:0.0916049)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000620_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000620_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ca14446c1ecdeaaeef0c1810725dbf31a558163
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000620_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00464:0.32222,(GCF_005280335_PROKKA_02260:0.00820002,(GCF_003691675_PROKKA_00431:5e-09,(GCF_023573625_PROKKA_00664:0.00523955,GCF_002008305_PROKKA_00694:5e-09)n3:0.00174344)n2:0.0129092)n1:0.32222)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000622_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000622_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9355a5c733400fa5fa6a0ff207491dc924751a4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000622_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02129:0.084108,(GCF_005280335_PROKKA_02258:0.0234497,(GCF_002008305_PROKKA_00696:0.00501032,(GCF_003691675_PROKKA_00433:5e-09,GCF_023573625_PROKKA_00666:0.0207708)n3:0.00526149)n2:0.0696474)n1:0.084108)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000623_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000623_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6798845aee600132e6dfaf2ede314e74f2fee174
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000623_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02128:0.193566,(GCF_005280335_PROKKA_02257:0.0849127,(GCF_023573625_PROKKA_00667:0.00965625,(GCF_002008305_PROKKA_00697:0.0414919,GCF_003691675_PROKKA_00434:0.00565153)n3:0.00779613)n2:0.175662)n1:0.193566)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000624_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000624_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd9987a9ef9c6e443ea9557da22832f1fff1516f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000624_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02127:0.10974,((GCF_002008305_PROKKA_00699:0,GCF_003691675_PROKKA_00436:0,GCF_023573625_PROKKA_00669:0)n2:0.0138689,GCF_005280335_PROKKA_02255:0.051324)n1:0.10974)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000627_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000627_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a669cc8ddf0a8bf802088a126a752c7a276900b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000627_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02124:0.111186,(GCF_005280335_PROKKA_02252:0.104551,(GCF_002008305_PROKKA_00705:0.0290785,(GCF_003691675_PROKKA_00439:0.010609,GCF_023573625_PROKKA_00672:0.00717105)n3:0.0307395)n2:0.214122)n1:0.111186)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000628_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000628_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..744eb6ae48c103942d81a85966c45bf99e541b9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000628_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02123:0.0224907,(GCF_005280335_PROKKA_02251:0.0537236,((GCF_002008305_PROKKA_00706:0,GCF_023573625_PROKKA_00673:0)n3:5e-09,GCF_003691675_PROKKA_00440:0.00378648)n2:0.0090729)n1:0.0224907)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000632_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000632_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7c3fbfadba20b677e9f58785363a9ac19e0e658
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000632_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02118:0.00540314,(GCF_005280335_PROKKA_02245:0.0158104,(GCF_002008305_PROKKA_00710:0.0221251,(GCF_003691675_PROKKA_00444:0,GCF_023573625_PROKKA_00677:0)n3:0.0134789)n2:0.385566)n1:0.00540314)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000634_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000634_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8fd5972956c671e05a65e0453be212b449cc0b33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000634_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02115:0.0499969,(GCF_005280335_PROKKA_02243:0.0350161,(GCF_002008305_PROKKA_00715:0.00811809,(GCF_003691675_PROKKA_00446:5e-09,GCF_023573625_PROKKA_00679:0.00281924)n3:0.00337349)n2:0.0344678)n1:0.0499969)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000637_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000637_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b01b4adcdcb58ed8707d26a846eab74b997520f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000637_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02112:0.0837607,(GCF_005280335_PROKKA_02240:0.0417151,((GCF_002008305_PROKKA_00718:0,GCF_023573625_PROKKA_00682:0)n3:0.00831769,GCF_003691675_PROKKA_00449:0.00770516)n2:0.0356281)n1:0.0837607)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000640_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000640_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed34772aed4f07c81c088e2b70d9ccb5c54771fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000640_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02109:0.0935358,((GCF_002008305_PROKKA_00721:0,GCF_003691675_PROKKA_00452:0,GCF_023573625_PROKKA_00685:0)n2:0.0148529,GCF_005280335_PROKKA_02237:0.0263008)n1:0.0935358)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000641_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000641_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..671d12cbdd0cda886374b9eccb0412638498e025
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000641_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02108:0.0596623,(GCF_005280335_PROKKA_02236:0.0130468,(GCF_002008305_PROKKA_00722:5e-09,(GCF_003691675_PROKKA_00453:0,GCF_023573625_PROKKA_00686:0)n3:0.00380803)n2:0.0220394)n1:0.0596623)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000642_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000642_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..739d55503b126215fb8cf79431683931713e405e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000642_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02107:0.0932517,(GCF_005280335_PROKKA_02235:0.043099,(GCF_003691675_PROKKA_00454:0.00614231,(GCF_002008305_PROKKA_00723:0.00292275,GCF_023573625_PROKKA_00687:0.00290939)n3:0.0114727)n2:0.0714206)n1:0.0932517)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000644_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000644_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a91edccf23d724064ef1c40aa7206fc5c36e9a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000644_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02105:0.126634,(GCF_005280335_PROKKA_02233:0.0869018,((GCF_002008305_PROKKA_00725:0,GCF_003691675_PROKKA_00456:0)n3:0.00607455,GCF_023573625_PROKKA_00689:0.0107233)n2:0.144328)n1:0.126634)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000645_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000645_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ccceca03eff496c0f25451db39624460cd84f1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000645_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02104:0.158814,((GCF_002008305_PROKKA_00726:0,GCF_003691675_PROKKA_00457:0,GCF_023573625_PROKKA_00690:0)n2:0.119693,GCF_005280335_PROKKA_02232:0.0621389)n1:0.158814)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000646_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000646_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81c3a3f386975ebda5cf9cae418bc5ebbde8119f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000646_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02103:0.0505368,((GCF_002008305_PROKKA_00727:0,GCF_003691675_PROKKA_00458:0,GCF_023573625_PROKKA_00691:0)n2:0.0515096,GCF_005280335_PROKKA_02231:0.050353)n1:0.0505368)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000647_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000647_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0cd0861e65a1e7aad7bce99149269eb7e99af2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000647_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02102:0.174513,(GCF_005280335_PROKKA_02229:0.0656024,((GCF_002008305_PROKKA_00728:0,GCF_023573625_PROKKA_00692:0)n3:0.0102412,GCF_003691675_PROKKA_00459:0.00505301)n2:0.114092)n1:0.174513)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000651_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000651_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..471d761fb986ffc01e497f53751e2e4e77879125
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000651_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02096:0.110518,(GCF_005280335_PROKKA_02220:0.028557,(GCF_002008305_PROKKA_00733:5e-09,(GCF_023573625_PROKKA_00697:0.0180416,GCF_003691675_PROKKA_00464:0.00720987)n3:0.00349021)n2:0.0784953)n1:0.110518)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000653_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000653_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a43970321908c8ad433cdf05a18173657616daba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000653_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02094:0.211001,(GCF_005280335_PROKKA_02195:0.143054,((GCF_002008305_PROKKA_00735:0,GCF_003691675_PROKKA_00466:0)n3:5e-09,GCF_023573625_PROKKA_00699:0.0145386)n2:0.0944869)n1:0.211001)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000657_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000657_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..174a648b617333d0ba63a43eedc454e565622f55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000657_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02087:0.0302525,(GCF_005280335_PROKKA_02189:0.0178592,((GCF_002008305_PROKKA_00740:0,GCF_023573625_PROKKA_00705:0)n3:0.00256091,GCF_003691675_PROKKA_00471:5e-09)n2:0.0116104)n1:0.0302525)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000658_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000658_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc3f5225bebd1951c38024f50580540fd06db173
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000658_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02086:0.00280699,(GCF_003691675_PROKKA_00472:0.00279737,((GCF_005280335_PROKKA_02188:0.0140975,GCF_023573625_PROKKA_00706:5e-09)n3:0.00279854,GCF_002008305_PROKKA_00741:0.00279866)n2:5e-09)n1:0.00280699)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000661_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000661_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..efda5a9c824470cdee01b2e0939129ed81af8fa5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000661_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02083:0.00442549,(GCF_002008305_PROKKA_00744:0.0134319,(GCF_023573625_PROKKA_00709:0.00441704,(GCF_003691675_PROKKA_00475:6e-09,GCF_005280335_PROKKA_02185:0.0463193)n3:0.00443383)n2:0.00446181)n1:0.00442549)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000662_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000662_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00ca6442fea12730337a0730623c57a74d78d404
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000662_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02082:0,(GCF_002008305_PROKKA_00745:0,GCF_023573625_PROKKA_00710:0,(GCF_003691675_PROKKA_00476:0.0117327,GCF_005280335_PROKKA_02184:0.0178432)n2:5e-09)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000665_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000665_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..85e39cb932f4fe3bdbc7737ed02a31d87704a72f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000665_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02073:0.195378,(GCF_005280335_PROKKA_02178:0.147732,(GCF_023573625_PROKKA_00716:0.0195178,(GCF_002008305_PROKKA_00752:0.0063725,GCF_003691675_PROKKA_00482:0.021318)n3:0.00610421)n2:0.122953)n1:0.195378)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000667_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000667_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60413cb3a0ada518d4791df5e650d0b6f3646e03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000667_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02071:0.135775,(GCF_005280335_PROKKA_02176:0.162494,(GCF_002008305_PROKKA_00754:0.0171816,(GCF_003691675_PROKKA_00484:0.0106326,GCF_023573625_PROKKA_00718:5e-09)n3:0.0370308)n2:0.0717428)n1:0.135775)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000668_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000668_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..847ece63cec4e24c27efb207744a240acfadb2b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000668_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02070:0.0802517,(GCF_005280335_PROKKA_02175:0.0216276,(GCF_002008305_PROKKA_00755:0.00495498,(GCF_003691675_PROKKA_00485:0,GCF_023573625_PROKKA_00719:0)n3:5e-09)n2:0.0473509)n1:0.0802517)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000671_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000671_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06a30ad3a76631677add7ec502817dfa73f23917
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000671_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02067:0.0782366,(GCF_005280335_PROKKA_02172:0.0393259,((GCF_002008305_PROKKA_00758:0,GCF_003691675_PROKKA_00488:0)n3:0.0054021,GCF_023573625_PROKKA_00722:0.00358697)n2:0.0588345)n1:0.0782366)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000672_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000672_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..800adb1936eec268b86a8d092691e2fed736f86a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000672_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02066:0.0759111,(GCF_005280335_PROKKA_02171:0.0346883,((GCF_002008305_PROKKA_00759:0,GCF_003691675_PROKKA_00489:0)n3:6e-09,GCF_023573625_PROKKA_00723:0.00839093)n2:0.0389905)n1:0.0759111)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000674_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000674_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9774b2453ce8f26b2a7cc026f463983669065e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000674_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02064:0.0809072,(GCF_005280335_PROKKA_02169:0.141661,(GCF_002008305_PROKKA_00761:0.00421372,(GCF_003691675_PROKKA_00491:0.00324963,GCF_023573625_PROKKA_00725:5e-09)n3:0.00555533)n2:0.150302)n1:0.0809072)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000675_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000675_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9e81e6f85668fc91b75f665fa0107886b669009
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000675_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02062:0.124114,(GCF_005280335_PROKKA_02167:0.131736,(GCF_023573625_PROKKA_00727:6e-09,(GCF_002008305_PROKKA_00763:0.0132895,GCF_003691675_PROKKA_00493:0.00638732)n3:0.0129118)n2:0.0697473)n1:0.124114)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000677_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000677_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5b15bf1d6ba82b7bf938a0b5feb677dadf961b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000677_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02060:0.115343,(GCF_005280335_PROKKA_02164:0.0783587,((GCF_002008305_PROKKA_00765:0,GCF_003691675_PROKKA_00495:0)n3:5e-09,GCF_023573625_PROKKA_00729:0.0137265)n2:0.0891822)n1:0.115343)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000680_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000680_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e9eb3b917f37e2b2c4d389b14c3543c7ef316df1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000680_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02056:0.0910652,(GCF_005280335_PROKKA_02160:0.141428,(GCF_003691675_PROKKA_00501:0.007312,(GCF_002008305_PROKKA_00770:0.00707892,GCF_023573625_PROKKA_00734:0.0176087)n3:0.022486)n2:0.0876421)n1:0.0910652)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000681_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000681_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca9b75c06d10e2fa9787fb475b892bd46e066028
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000681_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02054:0.0184214,(GCF_023573625_PROKKA_00738:0.00793347,(GCF_002008305_PROKKA_00771:5e-09,(GCF_005280335_PROKKA_02159:0.00996236,GCF_003691675_PROKKA_00502:0.0032729)n3:0.00162861)n2:0.00440918)n1:0.0184214)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000683_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000683_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d29279baa104876e0ac3103b1dca0f7fcaf5fdf4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000683_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02052:0.116883,(GCF_005280335_PROKKA_02157:0.0287507,(GCF_003691675_PROKKA_00504:5e-09,(GCF_002008305_PROKKA_00773:0.00336618,GCF_023573625_PROKKA_00740:5e-09)n3:0.00337443)n2:0.0238496)n1:0.116883)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000684_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000684_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6446b25c608a157cbe86c80d2ce3149673ef0d9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000684_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02050:0.029569,(GCF_023573625_PROKKA_00742:0.0171272,((GCF_002008305_PROKKA_00775:0,GCF_003691675_PROKKA_00506:0)n3:0.0175761,GCF_005280335_PROKKA_02155:0.0445348)n2:0.00796495)n1:0.029569)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000688_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000688_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a5a5be54477022e7130475f6ee00ee75b91c2bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000688_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02046:0.100937,(GCF_005280335_PROKKA_02151:0.0197485,(GCF_003691675_PROKKA_00510:0.0124211,(GCF_002008305_PROKKA_00779:0.00499212,GCF_023573625_PROKKA_00746:0.00506773)n3:0.00266556)n2:0.0159038)n1:0.100937)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000690_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000690_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50c1a1ff1d59acc6d54b0e9c41c704018f28719c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000690_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02043:0.105452,(GCF_005280335_PROKKA_02149:0.0227948,(GCF_023573625_PROKKA_00748:0.00622259,(GCF_002008305_PROKKA_00781:0.00199671,GCF_003691675_PROKKA_00512:0.00201529)n3:0.00992523)n2:0.0147166)n1:0.105452)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000691_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000691_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44ddb4657029ec2ca6d10480c7b6d59a5352cf5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000691_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02042:0.0801097,(GCF_005280335_PROKKA_02148:0.0327752,((GCF_002008305_PROKKA_00782:0,GCF_003691675_PROKKA_00513:0)n3:5e-09,GCF_023573625_PROKKA_00749:0.00218359)n2:0.0241414)n1:0.0801097)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000692_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000692_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb3bb434f5859af58c56ded3c2ce20404eb22ff7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000692_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02041:0.0472908,((GCF_002008305_PROKKA_00783:0,GCF_003691675_PROKKA_00514:0,GCF_023573625_PROKKA_00750:0)n2:0.0290363,GCF_005280335_PROKKA_02147:0.0133714)n1:0.0472908)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000695_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000695_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96ba220b953a8a5dfe4a69f032962c706538ca20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000695_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02038:0.0688439,(GCF_005280335_PROKKA_02144:0.0508174,((GCF_002008305_PROKKA_00786:0,GCF_003691675_PROKKA_00517:0)n3:0.0027169,GCF_023573625_PROKKA_00753:0.00256207)n2:0.0156241)n1:0.0688439)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000697_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000697_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb5ef948b14dcce4710f0e868d2744b084a7413b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000697_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02035:0.160508,(GCF_005280335_PROKKA_02142:0.0747084,((GCF_002008305_PROKKA_00789:0,GCF_003691675_PROKKA_00520:0)n3:0.00680903,GCF_023573625_PROKKA_00756:0.00677392)n2:0.0725989)n1:0.160508)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000699_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000699_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..103f751cb1bf65c145d89e56f5783d7d86a1da37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000699_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02033:0.0886524,(GCF_005280335_PROKKA_02140:0.0267454,((GCF_002008305_PROKKA_00791:0,GCF_003691675_PROKKA_00522:0)n3:5e-09,GCF_023573625_PROKKA_00758:0.00386904)n2:0.0128504)n1:0.0886524)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000700_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000700_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f914ea1629bcf4fc948dcff98def11736c8c8119
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000700_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_00792:0,GCF_003691675_PROKKA_00523:0,GCF_005280335_PROKKA_02139:0,GCF_023573625_PROKKA_00759:0)n1:0.0228128,GCF_020097155_PROKKA_02032:0.0228128)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000702_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000702_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96548cdfea823eb64d2074215993883fb725637a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000702_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02030:0.102958,(GCF_005280335_PROKKA_02137:0.0222483,(GCF_023573625_PROKKA_00761:5e-09,(GCF_002008305_PROKKA_00794:0.00363416,GCF_003691675_PROKKA_00525:5e-09)n3:0.0182623)n2:0.0258746)n1:0.102958)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000703_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000703_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41d4cebab0204e312e307786f17ba89176bcd891
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000703_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02029:0.0319928,(GCF_005280335_PROKKA_02136:0.0065124,(GCF_002008305_PROKKA_00795:0.00529032,(GCF_003691675_PROKKA_00526:0.00175964,GCF_023573625_PROKKA_00762:5e-09)n3:5e-09)n2:0.0171517)n1:0.0319928)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000705_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000705_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6463b6bb2ce990ce8476cf7a04577db6213b2e86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000705_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02027:0.0244512,(GCF_005280335_PROKKA_02134:0.0184848,(GCF_002008305_PROKKA_00797:0.00200195,(GCF_003691675_PROKKA_00528:0.00401433,GCF_023573625_PROKKA_00764:0.00200556)n3:6e-09)n2:0.00758977)n1:0.0244512)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000707_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000707_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cec4575b286b1ff1af4dfae13775fbabdc86d63b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000707_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02025:0.475005,(GCF_005280335_PROKKA_02132:0.176231,(GCF_002008305_PROKKA_00799:0.0141233,(GCF_003691675_PROKKA_00530:0.00693276,GCF_023573625_PROKKA_00766:0.010237)n3:0.0130613)n2:0.201528)n1:0.475005)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000710_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000710_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d96045f03debac1573ae70e628589fb74249cbef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000710_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02021:0.184933,(GCF_005280335_PROKKA_02128:0.0994484,(GCF_002008305_PROKKA_00802:0.0225344,(GCF_003691675_PROKKA_00533:0.0114607,GCF_023573625_PROKKA_00769:0.00567144)n3:0.0251303)n2:0.113954)n1:0.184933)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000711_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000711_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a724535ef8af39c18205c33ff30705123392266e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000711_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02020:0.131326,(GCF_005280335_PROKKA_02127:0.075681,(GCF_002008305_PROKKA_00803:0.0123051,(GCF_003691675_PROKKA_00534:0.00616163,GCF_023573625_PROKKA_00770:0.00294733)n3:0.00300109)n2:0.0476661)n1:0.131326)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000712_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000712_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64c3b1ba32fc8c14a4a0e5e50b8d92712132db05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000712_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02019:0.0396974,(GCF_005280335_PROKKA_02126:0.0498427,(GCF_002008305_PROKKA_00804:0.0180911,(GCF_003691675_PROKKA_00535:0.00721331,GCF_023573625_PROKKA_00771:0.0108384)n3:6e-09)n2:0.0621029)n1:0.0396974)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000713_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000713_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f0ad657e3d025f4bfe2f0ee4ec5e0e7d4449053
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000713_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02018:0.196328,(GCF_005280335_PROKKA_02125:0.222534,(GCF_002008305_PROKKA_00805:0.0296127,(GCF_003691675_PROKKA_00536:0.00918556,GCF_023573625_PROKKA_00772:0.0142728)n3:0.0100098)n2:0.121327)n1:0.196328)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000716_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000716_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe1d1f84ffeca47bcdaaef0ea49d92f860eb8b09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000716_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02012:0.188611,(GCF_005280335_PROKKA_02121:0.0273918,(GCF_002008305_PROKKA_00809:0.00421882,(GCF_003691675_PROKKA_00541:0,GCF_023573625_PROKKA_00778:0)n3:0.00429731)n2:5e-09)n1:0.188611)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000720_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000720_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9900e67b635b749bcd24c2f48f9173a2bea09d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000720_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02008:0.0660282,(GCF_005280335_PROKKA_02117:0.0486511,(GCF_002008305_PROKKA_00813:0.00513442,(GCF_003691675_PROKKA_00545:0,GCF_023573625_PROKKA_00782:0)n3:0.0106773)n2:0.12732)n1:0.0660282)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000721_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000721_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd1898017978b641dbdcf72d90c662b3c5656e73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000721_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02007:0.0897134,(GCF_005280335_PROKKA_02116:0.0554566,(GCF_002008305_PROKKA_00814:5e-09,(GCF_003691675_PROKKA_00546:6e-09,GCF_023573625_PROKKA_00783:0.00381138)n3:0.00762579)n2:0.101155)n1:0.0897134)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000722_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000722_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f953e434ad0b2d1e76f625e6b25a8727fc07831
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000722_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02006:0.0606834,(GCF_005280335_PROKKA_02115:0.0231954,((GCF_002008305_PROKKA_00815:0,GCF_023573625_PROKKA_00784:0)n3:5e-09,GCF_003691675_PROKKA_00547:0.00380545)n2:0.0376917)n1:0.0606834)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000724_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000724_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64e1325f56b7fbe9e6c944e8e4bd41c92d5f63e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000724_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02004:0.165586,(GCF_005280335_PROKKA_02113:0.110438,(GCF_003691675_PROKKA_00549:0.00360702,(GCF_002008305_PROKKA_00817:0.0111273,GCF_023573625_PROKKA_00786:0.00251041)n3:0.00426372)n2:0.0516542)n1:0.165586)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000725_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000725_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c417e1d3c896d4df38870b25f040d0b8a19141ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000725_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02003:0.142055,(GCF_005280335_PROKKA_02112:0.168728,(GCF_003691675_PROKKA_00550:5e-09,(GCF_023573625_PROKKA_00787:0.0157986,GCF_002008305_PROKKA_00818:5e-09)n3:0.00517328)n2:0.197159)n1:0.142055)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000726_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000726_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4007da0432ca0afd9802bc6ba8a48e953ab22d0b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000726_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02002:0.0537756,(GCF_005280335_PROKKA_02111:0.101474,(GCF_003691675_PROKKA_00551:0.00528864,(GCF_002008305_PROKKA_00819:0.00245333,GCF_023573625_PROKKA_00788:5e-09)n3:0.00208045)n2:0.236313)n1:0.0537756)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000728_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000728_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67ab8f93288f62d9c0a2f8dc8dd9a0ef78d5bc97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000728_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02000:0.110671,(GCF_005280335_PROKKA_02109:0.066744,(GCF_002008305_PROKKA_00821:0.00885085,(GCF_003691675_PROKKA_00553:5e-09,GCF_023573625_PROKKA_00790:0.00179671)n3:0.00293267)n2:0.0820055)n1:0.110671)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000731_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000731_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e3d6d77735f8969371545b4e02058913daa465f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000731_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01996:0.0478163,(GCF_005280335_PROKKA_02097:0.0274323,((GCF_002008305_PROKKA_00825:0,GCF_003691675_PROKKA_00557:0)n3:5e-09,GCF_023573625_PROKKA_00794:0.00611883)n2:0.0559516)n1:0.0478163)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000733_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000733_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7454e15503d2d4168f7585fc150fc55b5f59e12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000733_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01993:0.0149645,(GCF_005280335_PROKKA_02094:0.0773263,((GCF_002008305_PROKKA_00828:0,GCF_003691675_PROKKA_00560:0)n3:0.00251462,GCF_023573625_PROKKA_00797:0.00427882)n2:0.0295592)n1:0.0149645)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000737_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000737_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b46ab524234948090e7005dd91b5e371bd781908
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000737_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01990:0.0349736,(GCF_023573625_PROKKA_00803:0.0028883,(GCF_003691675_PROKKA_00565:5e-09,(GCF_002008305_PROKKA_00833:0.00289265,GCF_005280335_PROKKA_02091:0.00578597)n3:0.00289378)n2:5e-09)n1:0.0349736)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000738_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000738_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..faf536a8a8963b5b42d69ebbc51e1a3ea5393f56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000738_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01989:0.0949316,(GCF_005280335_PROKKA_02090:0.0330462,(GCF_002008305_PROKKA_00834:0.00719394,(GCF_003691675_PROKKA_00566:0,GCF_023573625_PROKKA_00804:0)n3:5e-09)n2:0.0300741)n1:0.0949316)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000739_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000739_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7b68127c0f4628cf02aa151b43974f7cbe0370d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000739_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01988:0.0815156,(GCF_005280335_PROKKA_02088:0.0378663,((GCF_002008305_PROKKA_00847:0,GCF_023573625_PROKKA_00806:0)n3:5e-09,GCF_003691675_PROKKA_00569:0.00185026)n2:0.0589218)n1:0.0815156)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000743_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000743_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cda9946615b6ad7d6880409b07588dce961b78cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000743_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01984:0.0561719,(GCF_005280335_PROKKA_02084:0.151807,(GCF_002008305_PROKKA_00851:0.0968257,(GCF_003691675_PROKKA_00573:0,GCF_023573625_PROKKA_00810:0)n3:0.0914709)n2:0.133003)n1:0.0561719)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000745_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000745_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd66aca739868e13ce3aaca11b318f6d7b0b7100
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000745_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01976:0.0498516,(GCF_005280335_PROKKA_02081:0.0395183,(GCF_002008305_PROKKA_00853:0.00411016,(GCF_003691675_PROKKA_00575:0,GCF_023573625_PROKKA_00812:0)n3:0.0113096)n2:0.0360499)n1:0.0498516)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000746_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000746_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99a252fa3aca71c1e585a54ca5e6575414517fac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000746_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01970:0.086002,(GCF_005280335_PROKKA_02076:0.0549648,(GCF_002008305_PROKKA_00859:0.00507998,(GCF_003691675_PROKKA_00581:0.00879425,GCF_023573625_PROKKA_00818:0.00682369)n3:0.0017565)n2:0.0471188)n1:0.086002)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000748_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000748_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c209ef16b06040b2d761ef4ed2ea2908db17d665
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000748_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01968:0.0610696,(GCF_005280335_PROKKA_02074:0.0855667,(GCF_023573625_PROKKA_00820:0.00270013,(GCF_002008305_PROKKA_00861:0.00200721,GCF_003691675_PROKKA_00583:5e-09)n3:0.00736741)n2:0.0394899)n1:0.0610696)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000749_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000749_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dcaebf53db98a69862c29299cb24988259cf8d03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000749_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01967:0.0520739,(GCF_005280335_PROKKA_02073:0.0254641,((GCF_002008305_PROKKA_00862:0,GCF_003691675_PROKKA_00584:0)n3:0.00375807,GCF_023573625_PROKKA_00821:5e-09)n2:0.0171777)n1:0.0520739)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000750_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000750_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c5524f4a93807620c1cdbccc6f91f659e4f9418
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000750_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01966:0.0334099,(GCF_005280335_PROKKA_02072:0.0162833,((GCF_002008305_PROKKA_00863:0,GCF_023573625_PROKKA_00822:0)n3:0.0075372,GCF_003691675_PROKKA_00585:0.00274695)n2:0.0266806)n1:0.0334099)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000752_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000752_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2372375228421c62df072d77dc3b8a86ab94673
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000752_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01964:0.0248968,(GCF_005280335_PROKKA_02070:0.0150563,(GCF_023573625_PROKKA_00824:0.00224152,(GCF_002008305_PROKKA_00865:5e-09,GCF_003691675_PROKKA_00587:0.00224519)n3:5e-09)n2:0.0213455)n1:0.0248968)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000755_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000755_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b7d9d802076f51fb1f772044419ef9bd51e9bf5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000755_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01961:0.0856614,(GCF_005280335_PROKKA_02067:0.050298,(GCF_023573625_PROKKA_00827:0.00626995,(GCF_002008305_PROKKA_00868:5e-09,GCF_003691675_PROKKA_00590:0.0053449)n3:0.00450078)n2:0.0506588)n1:0.0856614)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000756_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000756_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0562dce6da16df6584e0360fc1cdd304d73ea71a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000756_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01960:0.159874,(GCF_005280335_PROKKA_02066:0.081438,(GCF_023573625_PROKKA_00828:5e-09,(GCF_002008305_PROKKA_00869:0.00605052,GCF_003691675_PROKKA_00591:5e-09)n3:0.0120247)n2:0.0325075)n1:0.159874)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000757_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000757_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90270407084d0538ae563b4c3d659d4a88085c31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000757_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01959:0.232342,(GCF_003691675_PROKKA_00592:0.00258979,(GCF_005280335_PROKKA_02065:0.0115417,(GCF_002008305_PROKKA_00870:0.00257981,GCF_023573625_PROKKA_00829:0.00258821)n3:0.0051352)n2:0.0052596)n1:0.232342)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000759_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000759_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6982e9f88cd37923563ae5dd36b50c1fa4a5f636
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000759_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01957:0.0821337,(GCF_005280335_PROKKA_02063:0.0509945,(GCF_003691675_PROKKA_00594:0.00548712,(GCF_002008305_PROKKA_00872:0.00701758,GCF_023573625_PROKKA_00831:0.00652096)n3:0.00425893)n2:0.0253488)n1:0.0821337)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000760_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000760_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..274f8f4b97babb3dbb0b3a9550fff61b31e75717
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000760_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01956:0.117814,(GCF_005280335_PROKKA_02062:0.0338997,(GCF_003691675_PROKKA_00595:0.0105679,(GCF_002008305_PROKKA_00873:0.00533771,GCF_023573625_PROKKA_00832:0.0106869)n3:0.00558214)n2:0.0742855)n1:0.117814)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000761_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000761_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0507ed1105ec791bebe7424be880c424907499b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000761_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01955:0.153782,(GCF_005280335_PROKKA_02061:0.0370432,(GCF_003691675_PROKKA_00596:0.0116782,(GCF_002008305_PROKKA_00874:0.00915419,GCF_023573625_PROKKA_00833:0.00991886)n3:0.0126914)n2:0.0292887)n1:0.153782)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000762_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000762_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc0ee1962032dbc2db2012b53cc470b17d79e432
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000762_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01954:0.101135,(GCF_005280335_PROKKA_02060:0.0408415,(GCF_023573625_PROKKA_00834:0.00624381,(GCF_002008305_PROKKA_00875:5e-09,GCF_003691675_PROKKA_00597:0.00624025)n3:5e-09)n2:0.0654836)n1:0.101135)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000763_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000763_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd1b5e7e4e43bd3709f78b967de2f1e932e85d99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000763_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01953:0.0818785,(GCF_005280335_PROKKA_02059:0.0285173,(GCF_003691675_PROKKA_00598:0.00319004,(GCF_002008305_PROKKA_00876:0.00329563,GCF_023573625_PROKKA_00835:0.00330134)n3:0.00342339)n2:0.0597035)n1:0.0818785)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000765_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000765_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e9c7d153eb6075b1fd6d0a1de587ce396a9e07e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000765_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01951:0.0303888,((GCF_002008305_PROKKA_00878:0,GCF_003691675_PROKKA_00600:0,GCF_023573625_PROKKA_00837:0)n2:0.0133131,GCF_005280335_PROKKA_02057:0.000695741)n1:0.0303888)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000766_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000766_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..297cdf301e89fc685fcb55da151807d96773423b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000766_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01950:0.0689187,(GCF_005280335_PROKKA_02056:0.0422257,(GCF_002008305_PROKKA_00879:5e-09,(GCF_003691675_PROKKA_00601:0,GCF_023573625_PROKKA_00838:0)n3:0.00447745)n2:0.00339979)n1:0.0689187)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000769_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000769_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc044e3639f02071229aad88ae757fb0978d6eb4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000769_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01947:0.179464,((GCF_005280335_PROKKA_02053:0.0774675,GCF_023573625_PROKKA_00841:0.00184129)n2:0.105849,(GCF_002008305_PROKKA_00882:0.00872689,GCF_003691675_PROKKA_00604:0.00943392)n3:0.0304066)n1:0.179464)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000770_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000770_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31d432c79cdcd9206e8435985feca4488011a882
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000770_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01945:0.0494756,((GCF_002008305_PROKKA_00885:5e-09,GCF_003691675_PROKKA_00607:0.00232561)n2:0.116678,(GCF_005280335_PROKKA_02051:0.00368183,GCF_023573625_PROKKA_00843:0.00808331)n3:0.110736)n1:0.0494756)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000774_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000774_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7ae181e1f94012a3f50f85aa60064468cbef2c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000774_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01939:0.0392093,(GCF_002008305_PROKKA_00900:0.109689,(GCF_003691675_PROKKA_00620:0.0838495,(GCF_023573625_PROKKA_00849:0.0695006,GCF_005280335_PROKKA_02041:0.0389006)n3:0.0242949)n2:0.13148)n1:0.0392093)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000777_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000777_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a6e989b64e349b47786cd7f4f42ce5ea3fac828a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000777_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01936:0.0398962,(GCF_005280335_PROKKA_02038:0.0195761,(GCF_023573625_PROKKA_00852:5e-09,(GCF_002008305_PROKKA_00904:0.00556852,GCF_003691675_PROKKA_00623:0.00185569)n3:0.00184628)n2:0.0193547)n1:0.0398962)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000781_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000781_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a0abdee623ce876a9e02618fad8fb2a0c966b24
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000781_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01932:0.0915511,(GCF_005280335_PROKKA_02034:0.0462906,((GCF_002008305_PROKKA_00908:0,GCF_023573625_PROKKA_00856:0)n3:5e-09,GCF_003691675_PROKKA_00627:0.00414786)n2:0.0295157)n1:0.0915511)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000789_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000789_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a43c795be159bd6d96c7a92ea34107584b77c26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000789_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01924:0.149268,(GCF_005280335_PROKKA_02026:0.162715,(GCF_002008305_PROKKA_00916:0.00353306,(GCF_003691675_PROKKA_00635:0.0138137,GCF_023573625_PROKKA_00864:0.00560736)n3:0.0101574)n2:0.101176)n1:0.149268)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000791_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000791_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c157b2c0c2a755bb1e763708c7ada025b35605fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000791_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01922:0.131313,(GCF_005280335_PROKKA_02023:0.0493071,((GCF_002008305_PROKKA_00918:0,GCF_003691675_PROKKA_00637:0)n3:0.00583691,GCF_023573625_PROKKA_00866:5e-09)n2:0.045451)n1:0.131313)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000794_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000794_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..721330076ff7aef64ce3b643c91b9daa0a7199e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000794_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01919:0.0590743,(GCF_005280335_PROKKA_02020:0.0928257,(GCF_003691675_PROKKA_00640:5e-09,(GCF_002008305_PROKKA_00921:5e-09,GCF_023573625_PROKKA_00869:0.00272796)n3:0.00272469)n2:0.0195762)n1:0.0590743)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000799_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000799_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65132f9cec0f62362b34f97402abd8c83b82e4cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000799_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01914:0.285004,(GCF_005280335_PROKKA_02015:0.0982253,((GCF_002008305_PROKKA_00926:0,GCF_023573625_PROKKA_00874:0)n3:0.00577749,GCF_003691675_PROKKA_00645:0.0186164)n2:0.166308)n1:0.285004)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000801_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000801_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2a9c339ab4fe880f3ce3cf73e1bf0bc44496a53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000801_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01910:0.127557,(GCF_005280335_PROKKA_02011:0.0548941,(GCF_023573625_PROKKA_00877:5e-09,(GCF_002008305_PROKKA_00929:0.0174036,GCF_003691675_PROKKA_00648:5e-09)n3:0.0085981)n2:0.074233)n1:0.127557)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000803_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000803_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1012577bb08706ac5baa829d91a42c84b9082ca1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000803_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01907:0.172608,((GCF_002008305_PROKKA_00931:0,GCF_003691675_PROKKA_00650:0,GCF_023573625_PROKKA_00880:0)n2:0.0125591,GCF_005280335_PROKKA_02009:0.0424573)n1:0.172608)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000805_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000805_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c10a8045d57e8cf7d9ea7108369dd28a6b8d999c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000805_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01903:0.0594487,(GCF_005280335_PROKKA_02007:0.0152645,(GCF_023573625_PROKKA_00882:0.00924167,(GCF_002008305_PROKKA_00933:0.0018981,GCF_003691675_PROKKA_00652:0.00571045)n3:0.00219967)n2:0.0204395)n1:0.0594487)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000807_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000807_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40f7bc87f4a848b23d76127606bda237b0c531df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000807_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01901:0.0453124,(GCF_005280335_PROKKA_02004:0.0197975,(GCF_002008305_PROKKA_00935:0.00312607,(GCF_003691675_PROKKA_00654:0,GCF_023573625_PROKKA_00884:0)n3:0.00632632)n2:0.0256374)n1:0.0453124)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000811_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000811_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52e94f3d39f0a711d897bf57b3c0123bd765aa92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000811_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01897:0.162326,(GCF_003691675_PROKKA_00658:0.0121659,(GCF_023573625_PROKKA_00888:0.012026,(GCF_005280335_PROKKA_02000:0.16765,GCF_002008305_PROKKA_00939:5e-09)n3:0.00599058)n2:0.00914722)n1:0.162326)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000815_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000815_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a9bf256101ca56ce048bf0d5194ab3e931d3a62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000815_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01892:0.111808,(GCF_005280335_PROKKA_01995:0.142224,(GCF_003691675_PROKKA_00662:5e-09,(GCF_002008305_PROKKA_00943:0.00965859,GCF_023573625_PROKKA_00893:0.0159285)n3:0.00478481)n2:0.0505396)n1:0.111808)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000819_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000819_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad7909719e3ea4b19edf2eea55421ca2db65f7cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000819_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01880:0.109023,(GCF_005280335_PROKKA_01929:0.0582428,(GCF_003691675_PROKKA_00672:0.00273715,(GCF_002008305_PROKKA_00959:0.00210589,GCF_023573625_PROKKA_00905:0.0147174)n3:0.00359585)n2:0.0713538)n1:0.109023)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000820_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000820_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67b1a6c21d7d6ac4d39a3d65d7ccc80e646d9016
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000820_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01879:0.0980861,(GCF_005280335_PROKKA_01928:0.0706377,(GCF_003691675_PROKKA_00673:6e-09,(GCF_002008305_PROKKA_00960:0.00843964,GCF_023573625_PROKKA_00906:0.00210231)n3:0.00420176)n2:0.101765)n1:0.0980861)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000821_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000821_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bdc373cc4a12daa95e061378a98186010eb64f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000821_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01877:0.135599,(GCF_005280335_PROKKA_01926:0.167845,(GCF_003691675_PROKKA_00675:0.00719246,(GCF_002008305_PROKKA_00962:0.00455488,GCF_023573625_PROKKA_00908:0.00661736)n3:0.0305444)n2:0.183366)n1:0.135599)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000823_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000823_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f9de364ca44c0a904b5cba3016319f78e5b5b613
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000823_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01872:0.0648276,(GCF_005280335_PROKKA_01923:0.0959542,(GCF_023573625_PROKKA_00910:0.0188208,(GCF_002008305_PROKKA_00964:5e-09,GCF_003691675_PROKKA_00677:0.00625664)n3:0.00970852)n2:0.0138289)n1:0.0648276)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000824_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000824_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4369cb87c6e5c3aa70442737e6d1d48570bd8c84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000824_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01869:0.120709,(GCF_005280335_PROKKA_01921:0.0439533,(GCF_002008305_PROKKA_00966:0.00358958,(GCF_023573625_PROKKA_00912:0.00836175,GCF_003691675_PROKKA_00679:0.00840429)n3:0.00480392)n2:0.0810425)n1:0.120709)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000827_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000827_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c48588e0bcb42e524ed96dd2b1780c6b6bcdd7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000827_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01863:0.141474,(GCF_005280335_PROKKA_01916:0.0976707,(GCF_003691675_PROKKA_00688:0.0221605,(GCF_002008305_PROKKA_00974:5e-09,GCF_023573625_PROKKA_00917:0.00325591)n3:0.0077497)n2:0.0832834)n1:0.141474)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000829_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000829_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a47915bcc9bb291b9a10c1b41b38c407e379cf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000829_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01860:0.0495534,(GCF_005280335_PROKKA_01913:0.00542216,(GCF_002008305_PROKKA_00977:5e-09,(GCF_003691675_PROKKA_00691:0,GCF_023573625_PROKKA_00920:0)n3:0.00477261)n2:0.00415892)n1:0.0495534)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000831_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000831_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..127af97c38207b11c7676753a3911ab56bbc3e44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000831_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01858:0.0239601,((GCF_002008305_PROKKA_00979:0,GCF_003691675_PROKKA_00693:0,GCF_023573625_PROKKA_00922:0)n2:0.0338437,GCF_005280335_PROKKA_01911:0.0187031)n1:0.0239601)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000832_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000832_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ab9907283527e7736833bd0032c50cba3d067e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000832_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01857:0.0409297,((GCF_002008305_PROKKA_00980:0,GCF_003691675_PROKKA_00694:0,GCF_023573625_PROKKA_00923:0)n2:0.346879,GCF_005280335_PROKKA_01910:0.126627)n1:0.0409297)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000834_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000834_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9fe0cdda7285a8f4eeed08e36ff127c99b55401d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000834_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01854:0.00473335,((GCF_002008305_PROKKA_00982:0.00347173,GCF_003691675_PROKKA_00696:0.00209832)n2:0.00148073,(GCF_005280335_PROKKA_01907:0.163335,GCF_023573625_PROKKA_00925:5e-09)n3:0.00245283)n1:0.00473335)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000835_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000835_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa0d7537e049250f7300a759894439031522a5b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000835_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01853:0.00170241,(GCF_005280335_PROKKA_01906:0.173736,((GCF_002008305_PROKKA_00983:0,GCF_023573625_PROKKA_00926:0)n3:5e-09,GCF_003691675_PROKKA_00697:0.0036575)n2:0.00389754)n1:0.00170241)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000837_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000837_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a5b99df7b19cbb713d89ffe31ab2fd7452741460
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000837_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01851:0.000886586,((GCF_002008305_PROKKA_00985:0,GCF_023573625_PROKKA_00928:0)n2:0.00532978,(GCF_003691675_PROKKA_00699:0.000902845,GCF_005280335_PROKKA_01904:0.0172799)n3:0.000869994)n1:0.000886586)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000839_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000839_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5df64b1531a71a926fa85914c701394a3b06cd6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000839_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01849:0,(GCF_002008305_PROKKA_00987:0,GCF_023573625_PROKKA_00930:0,(GCF_003691675_PROKKA_00701:0.00639249,GCF_005280335_PROKKA_01902:0.00640844)n2:5e-09)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000840_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000840_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74b1dd262153da9b6d3ccbcdac96c03ceaa9ce0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000840_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01848:0.00109552,(GCF_005280335_PROKKA_01901:0.00662096,((GCF_002008305_PROKKA_00988:0,GCF_023573625_PROKKA_00931:0)n3:5e-09,GCF_003691675_PROKKA_00702:0.00438584)n2:0.00438898)n1:0.00109552)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000841_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000841_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1921f9882f11f2b115b1cb64907a912fb85a5bc9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000841_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01847:0.00416912,(GCF_005280335_PROKKA_01900:0.0168039,((GCF_002008305_PROKKA_00989:0,GCF_023573625_PROKKA_00932:0)n3:0.00413119,GCF_003691675_PROKKA_00703:0.00419079)n2:0.0169419)n1:0.00416912)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000842_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000842_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..180251b2739953e76fba0845d3de268c7621fd4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000842_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01846:0.00333269,(GCF_005280335_PROKKA_01899:0.0270986,(GCF_002008305_PROKKA_00990:0.00385659,(GCF_003691675_PROKKA_00704:0.00388371,GCF_023573625_PROKKA_00933:0.00278586)n3:0.0134747)n2:0.0199242)n1:0.00333269)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000846_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000846_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c48b7dfc3f07ac6341ec9d905aeff813ccd7cb4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000846_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01839:0.113353,((GCF_002008305_PROKKA_00997:0,GCF_003691675_PROKKA_00711:0,GCF_023573625_PROKKA_00940:0)n2:0.0277728,GCF_005280335_PROKKA_01893:0.0701203)n1:0.113353)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000847_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000847_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a322496ecefaeeb6860f2a541631d62a829939f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000847_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01838:0.103446,(GCF_005280335_PROKKA_01892:0.0976167,((GCF_002008305_PROKKA_00998:0,GCF_003691675_PROKKA_00712:0)n3:0.0276576,GCF_023573625_PROKKA_00941:5e-09)n2:0.135041)n1:0.103446)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000848_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000848_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cd5997db3c975d21ba6b01f53c3f9cdaebe6c15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000848_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01819:0.136971,(GCF_005280335_PROKKA_01891:0.208708,((GCF_002008305_PROKKA_00999:0,GCF_003691675_PROKKA_00713:0)n3:0.005254,GCF_023573625_PROKKA_00942:0.0110194)n2:0.120882)n1:0.136971)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000850_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000850_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64f1e19cec668f1e2889eb437cb482c475c519c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000850_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01001:0,GCF_003691675_PROKKA_00715:0,GCF_005280335_PROKKA_01889:0,GCF_023573625_PROKKA_00944:0)n1:0.0486071,GCF_020097155_PROKKA_01817:0.0486071)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000851_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000851_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e33bd5541e1082df02b4f66befff69a85dc94fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000851_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01816:0.0588375,((GCF_002008305_PROKKA_01002:0,GCF_003691675_PROKKA_00716:0,GCF_023573625_PROKKA_00945:0)n2:0.0521419,GCF_005280335_PROKKA_01888:0.0242395)n1:0.0588375)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000852_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000852_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48dda64d18ff50e30e2c203aa859e478983f3a46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000852_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01815:0.0985913,(GCF_005280335_PROKKA_01887:0.0554346,(GCF_002008305_PROKKA_01003:5e-09,(GCF_003691675_PROKKA_00717:0.00235703,GCF_023573625_PROKKA_00946:0.0119599)n3:0.00714831)n2:0.0749728)n1:0.0985913)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000858_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000858_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ab3c29e9423a03f82c4002334b19ba89e1fca370
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000858_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01230:0.834006,(GCF_005280335_PROKKA_01874:0.00190213,((GCF_002008305_PROKKA_01014:0,GCF_023573625_PROKKA_00957:0)n3:0.00194824,GCF_003691675_PROKKA_00728:0.00195406)n2:0.0159031)n1:0.834006)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000861_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000861_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6536c3c2549083dc651a0da656138af941db54e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000861_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01760:0.279741,(GCF_005280335_PROKKA_01868:0.115318,(GCF_023573625_PROKKA_00963:0.00270091,(GCF_002008305_PROKKA_01019:0.0175246,GCF_003691675_PROKKA_00733:0.0133495)n3:0.0183972)n2:0.1302)n1:0.279741)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000863_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000863_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7e1326e80c558f5cc67f3284bb4e314f47d24fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000863_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01762:0.427105,(GCF_005280335_PROKKA_01866:0.126426,(GCF_002008305_PROKKA_01021:5e-09,(GCF_023573625_PROKKA_00965:0.0215704,GCF_003691675_PROKKA_00735:0.0107408)n3:0.00264404)n2:0.188765)n1:0.427105)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000864_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000864_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9eb00b659febc242baf5a1ed675c66bf035c5c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000864_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00782:0.518983,(GCF_023573625_PROKKA_00966:5e-09,(GCF_002008305_PROKKA_01022:5e-09,(GCF_003691675_PROKKA_00736:0.0123144,GCF_003691675_PROKKA_00737:0.00482373)n3:0.00053597)n2:0.0174833)n1:0.0232446)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000865_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000865_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a386f31712c1ba4e69b7a19aef46e3f4c7696e3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000865_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01758:0.0904837,(GCF_005280335_PROKKA_01865:0.102349,(GCF_003691675_PROKKA_00738:5e-09,(GCF_002008305_PROKKA_01023:5e-09,GCF_023573625_PROKKA_00967:0.0104112)n3:0.0104698)n2:0.160972)n1:0.0904837)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000866_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000866_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96505b47fb4e1837e2dfce00ec345028984bbd79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000866_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01751:0.0437887,((GCF_002008305_PROKKA_01024:0,GCF_003691675_PROKKA_00739:0,GCF_023573625_PROKKA_00968:0)n2:5e-09,GCF_005280335_PROKKA_01861:0.0357025)n1:0.0437887)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000868_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000868_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e11df6a13dd7f63a048384894a6b5caeb8f2a0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000868_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01749:0.0394004,(GCF_005280335_PROKKA_01859:0.0168384,((GCF_002008305_PROKKA_01026:0,GCF_003691675_PROKKA_00741:0)n3:0.00082536,GCF_023573625_PROKKA_00970:0.00326623)n2:0.0104352)n1:0.0394004)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000869_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000869_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13c3a3c3a1ec76a37093b9b93a5dff7a419df485
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000869_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01745:0.0347281,(GCF_005280335_PROKKA_01858:0.0324493,(GCF_023573625_PROKKA_00971:5e-09,(GCF_002008305_PROKKA_01027:0.00302533,GCF_003691675_PROKKA_00742:0.00302561)n3:0.00303039)n2:0.0360114)n1:0.0347281)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000871_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000871_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d78f647ac45df382df265da8f8b7fbd8938147c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000871_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01740:0.00797024,(GCF_005280335_PROKKA_01850:0.0205349,(GCF_003691675_PROKKA_00747:0.0178173,(GCF_002008305_PROKKA_01032:0.00387302,GCF_023573625_PROKKA_00976:5e-09)n3:0.022393)n2:0.0109131)n1:0.00797024)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000872_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000872_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfb39eed76bae9b41ab38c015d93b485054b167d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000872_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01739:2.5e-09,(GCF_005280335_PROKKA_01849:0.00514701,(GCF_023573625_PROKKA_00977:5e-09,(GCF_002008305_PROKKA_01035:0.0196559,GCF_003691675_PROKKA_00748:0.00511003)n3:0.00485773)n2:0.00483827)n1:2.5e-09)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000875_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000875_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1fdaa9447e4db92d31e4a607375cd19e7c40bc7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000875_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01736:0.114434,(GCF_005280335_PROKKA_01846:0.0572663,(GCF_003691675_PROKKA_00752:0.00497148,(GCF_002008305_PROKKA_01039:0.00486782,GCF_023573625_PROKKA_00981:0.00726988)n3:0.00449386)n2:0.154597)n1:0.114434)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000877_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000877_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbca83aa4025911c82ddc73cf5d667232455feb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000877_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01732:0.124125,(GCF_005280335_PROKKA_01845:0.0262547,(GCF_003691675_PROKKA_00757:0.00956274,(GCF_002008305_PROKKA_01044:5e-09,GCF_023573625_PROKKA_00985:0.00950289)n3:5e-09)n2:0.0619645)n1:0.124125)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000881_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000881_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..11b1d2b8607bf724e2f4121d589a6a96415dd974
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000881_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01728:0.131277,(GCF_005280335_PROKKA_01840:0.0511484,(GCF_002008305_PROKKA_01048:0.0181652,(GCF_003691675_PROKKA_00761:0.00494352,GCF_023573625_PROKKA_00989:0.00992388)n3:0.00758737)n2:0.0886825)n1:0.131277)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000882_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000882_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e31e04b98f7a20a7d4611a2f8277c3dec133a3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000882_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01727:0.111451,(GCF_005280335_PROKKA_01837:0.101831,(GCF_002008305_PROKKA_01049:5e-09,(GCF_003691675_PROKKA_00762:5e-09,GCF_023573625_PROKKA_00990:0.0057329)n3:0.0115948)n2:0.12647)n1:0.111451)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000883_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000883_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43f600599a62e8aea88b7c7ce34d3aea74ff2ff8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000883_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01726:0.0680974,(GCF_005280335_PROKKA_01836:0.0560898,((GCF_002008305_PROKKA_01050:0,GCF_003691675_PROKKA_00763:0)n3:6e-09,GCF_023573625_PROKKA_00991:0.00673945)n2:0.0572932)n1:0.0680974)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000885_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000885_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ddbcbbaaa476030d1ec4ed603a88b4ee121cf04b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000885_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01724:0.0408995,(GCF_005280335_PROKKA_01834:0.0431652,(GCF_003691675_PROKKA_00765:0.00286781,(GCF_002008305_PROKKA_01052:0.00286898,GCF_023573625_PROKKA_00993:0.00286785)n3:5e-09)n2:0.0430768)n1:0.0408995)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000886_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000886_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5325483c45ed71b11fba34401be79b1840c39d86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000886_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01719:0.0721587,(GCF_005280335_PROKKA_01829:0.0330095,(GCF_023573625_PROKKA_01004:0.00629278,(GCF_002008305_PROKKA_01057:0.00314665,GCF_003691675_PROKKA_00776:5e-09)n3:5e-09)n2:0.0208683)n1:0.0721587)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000887_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000887_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..451e5fd0a34a8b4a90b0954eae90c82a4b1e4119
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000887_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01718:0.118134,(GCF_005280335_PROKKA_01828:0.109914,(GCF_002008305_PROKKA_01058:0.00510913,(GCF_003691675_PROKKA_00777:6e-09,GCF_023573625_PROKKA_01005:0.015077)n3:0.00492943)n2:0.0483282)n1:0.118134)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000888_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000888_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5233fa5f0a91b332b7ee8efa29c75521f18b958b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000888_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01717:0.166081,(GCF_005280335_PROKKA_01827:0.133008,(GCF_023573625_PROKKA_01006:0.00620912,(GCF_002008305_PROKKA_01059:0.0135909,GCF_003691675_PROKKA_00778:0.0213996)n3:0.01025)n2:0.0823387)n1:0.166081)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000893_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000893_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..160ac7b9ab76cdd7930ed1c5a3652fac3ea13000
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000893_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01710:0.0731808,(GCF_005280335_PROKKA_01821:0.0602642,(GCF_002008305_PROKKA_01066:6e-09,(GCF_003691675_PROKKA_00785:0,GCF_023573625_PROKKA_01013:0)n3:0.00601575)n2:0.0435485)n1:0.0731808)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000896_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000896_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96cbd3b663ed6724d7cfda39c9e61e3dca486faf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000896_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01705:0.0599815,(GCF_005280335_PROKKA_01818:0.0236237,(GCF_002008305_PROKKA_01080:0.00736747,(GCF_003691675_PROKKA_00799:0,GCF_023573625_PROKKA_01029:0)n3:0.0039287)n2:0.029153)n1:0.0599815)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000897_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000897_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5079c4a1d55c25165280deeb90a2f0032591ff5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000897_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01704:0.110456,(GCF_005280335_PROKKA_01816:0.0980443,(GCF_002008305_PROKKA_01081:0.00783603,(GCF_003691675_PROKKA_00800:0,GCF_023573625_PROKKA_01030:0)n3:5e-09)n2:0.0873013)n1:0.110456)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000898_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000898_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..edb22753cf4d122b396848a735b0cc9316d77300
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000898_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01703:0.0823206,(GCF_005280335_PROKKA_01815:0.0442047,(GCF_002008305_PROKKA_01082:0.014812,(GCF_003691675_PROKKA_00801:0,GCF_023573625_PROKKA_01031:0)n3:0.00250721)n2:0.032657)n1:0.0823206)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000901_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000901_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07f6a4edb048f2bb3070bb164086ab9e425c898c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000901_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01700:0.10423,(GCF_005280335_PROKKA_01812:0.0245864,(GCF_002008305_PROKKA_01085:0.00723258,(GCF_003691675_PROKKA_00804:0,GCF_023573625_PROKKA_01034:0)n3:5e-09)n2:0.0198945)n1:0.10423)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000903_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000903_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12dcd4633ec6b08a8ac9b6040678109114804c2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000903_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01698:0.138348,(GCF_005280335_PROKKA_01810:0.0217329,(GCF_002008305_PROKKA_01087:0.0104197,(GCF_003691675_PROKKA_00806:0,GCF_023573625_PROKKA_01036:0)n3:0.0147879)n2:0.0395624)n1:0.138348)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000905_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000905_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8dbd218f84430dfcc32b390860928358c8f0470d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000905_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01696:0.0227856,((GCF_002008305_PROKKA_01089:0,GCF_003691675_PROKKA_00808:0,GCF_023573625_PROKKA_01038:0)n2:0.060726,GCF_005280335_PROKKA_01807:0.269084)n1:0.0227856)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000908_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000908_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..87881053e3d356d3871b08b7cd22e947205f2165
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000908_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01693:0.0874587,((GCF_002008305_PROKKA_01092:0,GCF_003691675_PROKKA_00811:0,GCF_023573625_PROKKA_01041:0)n2:0.0703238,GCF_005280335_PROKKA_01804:0.0693126)n1:0.0874587)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000909_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000909_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f4e951c0df42fb846d868bc72cfa7f45b52827b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000909_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01691:0.0918353,(GCF_005280335_PROKKA_01801:0.126204,(GCF_002008305_PROKKA_01094:0.00153476,(GCF_003691675_PROKKA_00813:6e-09,GCF_023573625_PROKKA_01043:0.00102237)n3:0.000510911)n2:0.110319)n1:0.0918353)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000911_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000911_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee7f2e7f313d86ad3659da2e2895867c9898a69f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000911_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01689:0.105258,(GCF_005280335_PROKKA_01799:0.1728,(GCF_002008305_PROKKA_01096:0.00180819,(GCF_003691675_PROKKA_00815:0,GCF_023573625_PROKKA_01045:0)n3:5e-09)n2:0.110354)n1:0.105258)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000913_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000913_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f60feff688eb9e601830489b7c7954731169bf5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000913_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01687:0.0670069,((GCF_002008305_PROKKA_01098:0,GCF_003691675_PROKKA_00817:0,GCF_023573625_PROKKA_01047:0)n2:0.0885988,GCF_005280335_PROKKA_01797:0.0852872)n1:0.0670069)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000916_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000916_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f024fd886037c709c47b0846ce163b279282b7a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000916_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01684:0.0843598,(GCF_005280335_PROKKA_01794:0.040861,(GCF_003691675_PROKKA_00820:0.00212963,(GCF_002008305_PROKKA_01101:0.00745537,GCF_023573625_PROKKA_01050:0.00640199)n3:0.00110648)n2:0.0499427)n1:0.0843598)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000919_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000919_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20b683efc3ab4548ce6901c36812513143824659
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000919_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01680:0.276325,(GCF_005280335_PROKKA_01789:0.128887,(GCF_002008305_PROKKA_01105:0.00434404,(GCF_003691675_PROKKA_00824:0,GCF_023573625_PROKKA_01054:0)n3:0.00418533)n2:0.14708)n1:0.276325)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000920_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000920_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a067678e5bc6babe5c59136761f2f347cfa05214
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000920_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01678:0.127474,((GCF_002008305_PROKKA_01107:0,GCF_003691675_PROKKA_00826:0,GCF_023573625_PROKKA_01056:0)n2:0.0410778,GCF_005280335_PROKKA_01786:0.0601443)n1:0.127474)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000923_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000923_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cabd367fda103942492c7b4a42cde0e684bb7415
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000923_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01675:0.3263,(GCF_005280335_PROKKA_01782:0.436008,(GCF_002008305_PROKKA_01110:0.0288459,(GCF_003691675_PROKKA_00829:0,GCF_023573625_PROKKA_01059:0)n3:0.00711023)n2:0.173284)n1:0.3263)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000925_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000925_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26e058509e1dee5cf4b9e801288901ad01e25797
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000925_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01672:0.0518545,(GCF_005280335_PROKKA_01779:0.0238208,(GCF_002008305_PROKKA_01114:0.00269441,(GCF_003691675_PROKKA_00833:5e-09,GCF_023573625_PROKKA_01064:0.00225938)n3:0.00295978)n2:0.0151536)n1:0.0518545)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000926_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000926_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5eafe64f26054513c00d94f19b51d7df1d88d35c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000926_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01671:0.107961,(GCF_002008305_PROKKA_01115:0.00620453,((GCF_003691675_PROKKA_00834:0,GCF_023573625_PROKKA_01065:0)n3:0.00321585,GCF_005280335_PROKKA_01778:0.0132862)n2:0.00377461)n1:0.107961)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000927_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000927_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c81a9dc4e967dc785d15ac6e68e001f08e4b7827
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000927_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01670:0.110368,(GCF_002008305_PROKKA_01116:0.00549204,(GCF_005280335_PROKKA_01777:0.026639,(GCF_003691675_PROKKA_00835:0,GCF_023573625_PROKKA_01066:0)n3:0.0175048)n2:0.0075779)n1:0.110368)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000929_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000929_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70ede0de84de87be3014077344dcdbd0a3f8df7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000929_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01666:0.115488,((GCF_002008305_PROKKA_01120:0,GCF_003691675_PROKKA_00839:0,GCF_023573625_PROKKA_01070:0)n2:0.0776543,GCF_005280335_PROKKA_01773:0.0548276)n1:0.115488)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000930_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000930_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2561a901aa51b11a8cdcc3f9f457a2649a587859
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000930_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01665:0.114917,(GCF_005280335_PROKKA_01772:0.0381926,(GCF_003691675_PROKKA_00840:0.00730348,(GCF_002008305_PROKKA_01121:0.0112675,GCF_023573625_PROKKA_01071:5e-09)n3:0.00679961)n2:0.0418005)n1:0.114917)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000933_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000933_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f2ecfdfbc5bb646c9241b019d3396bdadba783cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000933_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01662:0.0636041,(GCF_005280335_PROKKA_01769:0.0315996,(GCF_003691675_PROKKA_00843:0.00585209,(GCF_002008305_PROKKA_01124:0.00290415,GCF_023573625_PROKKA_01074:5e-09)n3:6e-09)n2:0.0368873)n1:0.0636041)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000935_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000935_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..017df503126c283e0cbc47f097d2076cef4b2688
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000935_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01660:0.0866629,(GCF_005280335_PROKKA_01766:0.0463365,(GCF_023573625_PROKKA_01076:5e-09,(GCF_002008305_PROKKA_01126:0.00375553,GCF_003691675_PROKKA_00845:5e-09)n3:0.00753169)n2:0.0801066)n1:0.0866629)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000937_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000937_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91ef115dd7e2506a832499644162bb88239796dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000937_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01658:0.101975,((GCF_002008305_PROKKA_01128:0,GCF_003691675_PROKKA_00847:0,GCF_023573625_PROKKA_01078:0)n2:0.0337895,GCF_005280335_PROKKA_01764:0.025213)n1:0.101975)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000939_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000939_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0e153a52298ae5f8db2af18cfcd99c8a42eeb0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000939_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01656:0.150611,(GCF_005280335_PROKKA_01762:0.0807398,((GCF_002008305_PROKKA_01130:0,GCF_003691675_PROKKA_00849:0)n3:0.00188596,GCF_023573625_PROKKA_01080:5e-09)n2:0.0542635)n1:0.150611)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000940_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000940_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f3056c10b5d922487be50667e4a656f9e64d00c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000940_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01655:0.101552,(GCF_005280335_PROKKA_01761:0.0580831,((GCF_002008305_PROKKA_01131:0,GCF_003691675_PROKKA_00850:0)n3:0.00257035,GCF_023573625_PROKKA_01081:5e-09)n2:0.0473029)n1:0.101552)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000942_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000942_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..182f02b6ab45b59416e347ea955aefca5af52a04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000942_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01653:0.069524,(GCF_005280335_PROKKA_01759:0.0424577,((GCF_002008305_PROKKA_01133:0,GCF_003691675_PROKKA_00852:0)n3:5e-09,GCF_023573625_PROKKA_01083:0.00307919)n2:0.0351534)n1:0.069524)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000943_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000943_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8375515e73905ac870294cd4e9f04cfe79872706
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000943_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01652:0.318585,(GCF_005280335_PROKKA_01758:0.0658361,((GCF_002008305_PROKKA_01134:0,GCF_003691675_PROKKA_00853:0)n3:0.00798869,GCF_023573625_PROKKA_01084:0.00761949)n2:0.122542)n1:0.318585)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000947_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000947_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ba3c90480e59028822e5ef2d59b62dce3a561b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000947_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01648:0.0221992,(GCF_005280335_PROKKA_01754:0.0146857,(GCF_002008305_PROKKA_01138:0.00198699,(GCF_003691675_PROKKA_00857:0.00198688,GCF_023573625_PROKKA_01088:5e-09)n3:5e-09)n2:0.0158752)n1:0.0221992)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000951_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000951_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8c8c701148aef9df07384aca15ba08aca88e412
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000951_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01644:0.113678,(GCF_005280335_PROKKA_01749:0.0713674,(GCF_002008305_PROKKA_01142:0.0104309,(GCF_003691675_PROKKA_00861:0,GCF_023573625_PROKKA_01092:0)n3:0.00542578)n2:0.094928)n1:0.113678)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000953_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000953_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62a674ffb263bce84c7dc5f99089a22382d3ce03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000953_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01642:0.114969,(GCF_005280335_PROKKA_01747:0.122224,(GCF_002008305_PROKKA_01144:0.0267305,(GCF_003691675_PROKKA_00863:0,GCF_023573625_PROKKA_01094:0)n3:5e-09)n2:0.0985408)n1:0.114969)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000954_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000954_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea70487c3f08ac32e8b1bf83a4137efe11342bdd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000954_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01640:0.21874,(GCF_005280335_PROKKA_01746:0.189068,(GCF_002008305_PROKKA_01146:0.0116017,(GCF_003691675_PROKKA_00865:5e-09,GCF_023573625_PROKKA_01096:0.00650365)n3:0.0213947)n2:0.0978146)n1:0.21874)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000956_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000956_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..329ef6f8b7587cfc878d31104efa147be9eb7295
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000956_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01637:0.112327,(GCF_005280335_PROKKA_01743:0.0668176,(GCF_002008305_PROKKA_01149:0.00288514,(GCF_003691675_PROKKA_00868:0,GCF_023573625_PROKKA_01099:0)n3:0.00426835)n2:0.0317081)n1:0.112327)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000958_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000958_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94ea8dfd11202d446c966d4b849fccb6c40dea0b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000958_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01635:0.0547733,(GCF_005280335_PROKKA_01741:0.260895,(GCF_002008305_PROKKA_01151:5e-09,(GCF_003691675_PROKKA_00870:0,GCF_023573625_PROKKA_01101:0)n3:0.0035682)n2:0.0739978)n1:0.0547733)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000960_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000960_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a37fd7b89dc6828ac3f091b97e136242c542c86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000960_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01632:0.124496,((GCF_002008305_PROKKA_01154:0,GCF_003691675_PROKKA_00873:0,GCF_023573625_PROKKA_01104:0)n2:0.0726477,GCF_005280335_PROKKA_01736:0.0372678)n1:0.124496)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000962_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000962_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1330e36a8bc00a5a041ef701e51b72b29aab85dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000962_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01630:0.0553498,((GCF_002008305_PROKKA_01157:0,GCF_003691675_PROKKA_00876:0,GCF_023573625_PROKKA_01107:0)n2:0.0108689,GCF_005280335_PROKKA_01732:0.0108989)n1:0.0553498)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000964_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000964_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05945b6ba4f25ebe8f96f7e354ea2f15a9bcd998
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000964_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01628:0.0991183,(GCF_005280335_PROKKA_01730:0.0733402,(GCF_002008305_PROKKA_01159:0.00140055,(GCF_003691675_PROKKA_00878:0,GCF_023573625_PROKKA_01109:0)n3:5e-09)n2:0.0773688)n1:0.0991183)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000965_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000965_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2e2434558e4e2782941bfda5741c81d9dc351a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000965_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01626:0.0653352,(GCF_005280335_PROKKA_01729:0.039658,(GCF_003691675_PROKKA_00880:0.00507256,(GCF_002008305_PROKKA_01161:0.00221338,GCF_023573625_PROKKA_01111:0.00444176)n3:0.00398276)n2:0.0624154)n1:0.0653352)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000971_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000971_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80173ff59198a753f808b8208ce11c6f96680ccc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000971_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01619:0.0579798,((GCF_002008305_PROKKA_01168:0,GCF_003691675_PROKKA_00887:0,GCF_023573625_PROKKA_01118:0)n2:0.00965747,GCF_005280335_PROKKA_01721:0.0487676)n1:0.0579798)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000972_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000972_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7b427e5ad6f86e624a1d3b54dd1a894b2399b65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000972_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01618:0.0503223,((GCF_002008305_PROKKA_01169:0,GCF_003691675_PROKKA_00888:0,GCF_023573625_PROKKA_01119:0)n2:0.091067,GCF_005280335_PROKKA_01720:0.0445986)n1:0.0503223)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000974_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000974_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40a71b0f27c6d7b3645744ae4df3431fd04f6a11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000974_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01616:0.134893,(GCF_005280335_PROKKA_01718:0.0369282,(GCF_002008305_PROKKA_01171:0.00635202,(GCF_003691675_PROKKA_00890:0,GCF_023573625_PROKKA_01121:0)n3:0.00320837)n2:0.0685294)n1:0.134893)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000975_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000975_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09182b07a083df1e12d6a66ff2b89b8ff0404e73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000975_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01615:0.0961855,(GCF_005280335_PROKKA_01717:0.117687,(GCF_023573625_PROKKA_01122:0.0112386,(GCF_002008305_PROKKA_01172:0.0241205,GCF_003691675_PROKKA_00891:0.0103255)n3:0.0169901)n2:0.13999)n1:0.0961855)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000976_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000976_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..267708ae37e1d6e4c691785bcf6e4f12170fd69c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000976_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01614:0.22398,(GCF_005280335_PROKKA_01716:0.124208,(GCF_002008305_PROKKA_01173:0.0129332,(GCF_003691675_PROKKA_00892:0.00796163,GCF_023573625_PROKKA_01123:0.00526756)n3:0.0165624)n2:0.174246)n1:0.22398)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000977_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000977_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21e9f1110a311564ec854cc21a0e7a2c49661a5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000977_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01613:0.0757288,(GCF_005280335_PROKKA_01715:0.0253319,(GCF_002008305_PROKKA_01174:0.00560831,(GCF_003691675_PROKKA_00893:0.00280389,GCF_023573625_PROKKA_01124:5e-09)n3:6e-09)n2:0.0132821)n1:0.0757288)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000978_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000978_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ec51d99f0590a4a5b4416e35440bdf34c8cc594
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000978_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01612:0.122815,(GCF_005280335_PROKKA_01714:0.0281072,(GCF_003691675_PROKKA_00894:0.00667488,(GCF_002008305_PROKKA_01175:5e-09,GCF_023573625_PROKKA_01125:0.00499934)n3:5e-09)n2:0.00826512)n1:0.122815)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000979_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000979_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f6ca8770e592506ff093c5f1a18b63f0d27fbf8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000979_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01611:0.129242,(GCF_005280335_PROKKA_01713:0.00717538,(GCF_003691675_PROKKA_00895:0.00173742,(GCF_002008305_PROKKA_01176:5e-09,GCF_023573625_PROKKA_01126:0.00871744)n3:0.00172853)n2:0.00680007)n1:0.129242)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000980_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000980_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8be2b73727cb78236e7d6732ed92e753763d15c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000980_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01610:0.251231,(GCF_005280335_PROKKA_01712:0.034982,(GCF_023573625_PROKKA_01127:5e-09,(GCF_002008305_PROKKA_01177:0.0152658,GCF_003691675_PROKKA_00896:0.00499829)n3:0.0153537)n2:0.016872)n1:0.251231)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000981_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000981_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..624d2f8051c113dcdff51aa26cd1ddaeb4468ebb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000981_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01609:0.193023,(GCF_005280335_PROKKA_01711:0.00887086,((GCF_002008305_PROKKA_01178:0,GCF_003691675_PROKKA_00897:0)n3:0.00651483,GCF_023573625_PROKKA_01128:0.00706746)n2:0.0119072)n1:0.193023)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000983_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000983_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..712e394cb161311b0c5b0fd3ea4408c0f81843fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000983_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01607:0.089623,(GCF_005280335_PROKKA_01709:0.067093,(GCF_003691675_PROKKA_00899:0.00214288,(GCF_002008305_PROKKA_01180:0.0107138,GCF_023573625_PROKKA_01130:0.00213792)n3:0.00212145)n2:0.0320612)n1:0.089623)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000985_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000985_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8304ab5f29c225c88ec2a6fcb2a29b1d239ebda5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000985_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01604:0.227791,(GCF_005280335_PROKKA_01705:0.111028,(GCF_003691675_PROKKA_00902:0.0100559,(GCF_002008305_PROKKA_01183:0.00774789,GCF_023573625_PROKKA_01133:0.00388063)n3:0.00474472)n2:0.0713916)n1:0.227791)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000986_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000986_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..38dcba6817fdc55b2617f0857824bd5ea4fd5858
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000986_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01603:0.210103,((GCF_002008305_PROKKA_01184:0,GCF_003691675_PROKKA_00903:0,GCF_023573625_PROKKA_01134:0)n2:0.0461896,GCF_005280335_PROKKA_01704:0.0303743)n1:0.210103)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000992_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000992_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39858c945ba5ac4d412ed557eba81dba71573106
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000992_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01597:0.0820613,(GCF_005280335_PROKKA_01698:0.044688,((GCF_002008305_PROKKA_01190:0,GCF_023573625_PROKKA_01140:0)n3:5e-09,GCF_003691675_PROKKA_00909:0.00726748)n2:0.0543401)n1:0.0820613)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000993_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000993_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ecac310fc8a15cf3753ee0d85cad11ece64083b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000993_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01596:0.259417,(GCF_005280335_PROKKA_01697:0.0520508,((GCF_002008305_PROKKA_01191:0,GCF_023573625_PROKKA_01141:0)n3:0.00605528,GCF_003691675_PROKKA_00910:0.00682789)n2:0.0624215)n1:0.259417)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000994_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000994_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41f1f9334db33fe3659c8db556539002966d7074
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000994_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01595:0.158841,(GCF_005280335_PROKKA_01696:0.0991509,(GCF_002008305_PROKKA_01192:6e-09,(GCF_003691675_PROKKA_00911:0.00978972,GCF_023573625_PROKKA_01142:0.00278654)n3:0.00417018)n2:0.0975429)n1:0.158841)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001003_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001003_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e65ca3062382b0386181accd6127dae4e2d7af2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001003_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01583:0.078874,(GCF_002008305_PROKKA_01201:0.0123424,((GCF_005280335_PROKKA_01686:0.0576767,GCF_023573625_PROKKA_01155:5e-09)n3:0.0237905,GCF_003691675_PROKKA_00921:0.00555709)n2:0.0121674)n1:0.078874)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001004_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001004_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..514881668516ef165e98aac31b912fad244a3e60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001004_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01582:0.107515,(GCF_005280335_PROKKA_01684:0.0500151,(GCF_003691675_PROKKA_00922:0.0219585,(GCF_002008305_PROKKA_01203:0.0237404,GCF_023573625_PROKKA_01160:0.0175377)n3:0.0825781)n2:0.065314)n1:0.107515)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001006_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001006_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e81d22f2615e71cf5c802e40f130f654fe7dd706
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001006_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01580:0.100304,(GCF_005280335_PROKKA_01682:0.0224237,(GCF_003691675_PROKKA_00924:0.00783915,(GCF_023573625_PROKKA_01162:0.0071006,GCF_002008305_PROKKA_01205:0.0213655)n3:0.00270227)n2:0.0205855)n1:0.100304)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001008_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001008_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f22a00922ea30f9284a76d38c4f091ad6f35ab7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001008_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01578:0.108351,(GCF_005280335_PROKKA_01680:0.0609061,(GCF_003691675_PROKKA_00926:0.0103929,(GCF_002008305_PROKKA_01207:0.0130804,GCF_023573625_PROKKA_01164:0.00795934)n3:0.00233376)n2:0.055475)n1:0.108351)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001009_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001009_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b6b7eb74b0fdd7827a17d155ea5caa61013c0d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001009_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01577:0.15832,(GCF_005280335_PROKKA_01679:0.138367,((GCF_002008305_PROKKA_01208:0,GCF_023573625_PROKKA_01165:0)n3:0.00627739,GCF_003691675_PROKKA_00927:0.0237286)n2:0.0340967)n1:0.15832)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001015_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001015_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34da031de87eb36564ce51c5ffc98eaf2a3b65c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001015_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01570:0.135824,(GCF_005280335_PROKKA_01673:0.0598757,((GCF_002008305_PROKKA_01215:0,GCF_023573625_PROKKA_01172:0)n3:0.000820604,GCF_003691675_PROKKA_00934:0.00804433)n2:0.0575432)n1:0.135824)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001016_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001016_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8dd61669a78d3c6ea50f3eeeead1d1d905efd044
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001016_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01569:0.0545412,((GCF_002008305_PROKKA_01216:0,GCF_003691675_PROKKA_00935:0,GCF_023573625_PROKKA_01173:0)n2:0.033319,GCF_005280335_PROKKA_01672:0.0644614)n1:0.0545412)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001018_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001018_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a8d13c29062dcf5d6ad2e8036080c845c393fd06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001018_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01567:0.118859,(GCF_005280335_PROKKA_01670:0.0592686,(GCF_002008305_PROKKA_01218:5e-09,(GCF_003691675_PROKKA_00937:0.00386063,GCF_023573625_PROKKA_01176:5e-09)n3:0.00384596)n2:0.0823526)n1:0.118859)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001020_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001020_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e37f80f3c080562685492f8c28cb66cb61214824
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001020_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01565:0.0819215,(GCF_005280335_PROKKA_01668:0.0388258,(GCF_003691675_PROKKA_00939:5e-09,(GCF_002008305_PROKKA_01220:0.00571701,GCF_023573625_PROKKA_01178:5e-09)n3:0.00857443)n2:0.0634361)n1:0.0819215)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001023_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001023_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6351bccaf509842f8afca0f3e53b5fc7c1dc324
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001023_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01561:0.0298749,(GCF_005280335_PROKKA_01664:0.0164595,(GCF_002008305_PROKKA_01224:0.00902098,(GCF_003691675_PROKKA_00943:0.0031836,GCF_023573625_PROKKA_01182:5e-09)n3:0.00415048)n2:0.0237042)n1:0.0298749)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001024_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001024_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be655b4a393b8f09ef38aaee6d49281c9ef1863e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001024_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01560:0.197191,(GCF_005280335_PROKKA_01663:0.112993,(GCF_023573625_PROKKA_01183:5e-09,(GCF_003691675_PROKKA_00944:0.0288344,GCF_002008305_PROKKA_01225:0.00447833)n3:0.0143597)n2:0.212818)n1:0.197191)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001028_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001028_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..628e0069286981a8cbc0dcd77340e909072968e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001028_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01556:0.26139,(GCF_005280335_PROKKA_01659:0.298819,(GCF_002008305_PROKKA_01229:0.0133629,(GCF_003691675_PROKKA_00948:5e-09,GCF_023573625_PROKKA_01187:5e-09)n3:0.0632619)n2:0.154928)n1:0.26139)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001030_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001030_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..532ba80eb28edef07c1283b4ad2167dd6cc6aeff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001030_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01554:0.0453156,(GCF_005280335_PROKKA_01657:0.0332945,(GCF_002008305_PROKKA_01231:0.00538494,(GCF_003691675_PROKKA_00950:0,GCF_023573625_PROKKA_01189:0)n3:0.004235)n2:0.0285051)n1:0.0453156)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001032_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001032_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65fc71b3608f652199bfe5b79bda018a0c52b90b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001032_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01552:0.117377,(GCF_005280335_PROKKA_01655:0.128229,(GCF_023573625_PROKKA_01191:0.0128002,(GCF_002008305_PROKKA_01233:0.0347476,GCF_003691675_PROKKA_00952:0.0272318)n3:0.0145722)n2:0.0987666)n1:0.117377)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001036_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001036_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93f90e4f4671c9edc86cb01324a211b1703784a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001036_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01548:0.195834,(GCF_002008305_PROKKA_01237:0.0138343,(GCF_005280335_PROKKA_01651:0.0477392,(GCF_003691675_PROKKA_00956:0,GCF_023573625_PROKKA_01195:0)n3:0.00820253)n2:0.0113429)n1:0.195834)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001038_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001038_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4bfc2c84e224303dc20dc7485547e2b2160f013c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001038_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01546:0.121442,(GCF_005280335_PROKKA_01649:0.0314098,((GCF_002008305_PROKKA_01239:0,GCF_023573625_PROKKA_01197:0)n3:0.0160565,GCF_003691675_PROKKA_00958:0.0329465)n2:0.124275)n1:0.121442)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001039_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001039_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aecaa1b9a88e41eb81c004fde85b3449db9ea246
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001039_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01545:0.135584,(GCF_005280335_PROKKA_01648:0.0663455,(GCF_003691675_PROKKA_00959:5e-09,(GCF_002008305_PROKKA_01240:0.00333605,GCF_023573625_PROKKA_01198:5e-09)n3:0.00333664)n2:0.112055)n1:0.135584)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001040_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001040_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fffe2c6f0215983623d145d9ce6ad5354bb6e84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001040_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01544:0.037129,(GCF_005280335_PROKKA_01647:0.0223863,((GCF_002008305_PROKKA_01241:0,GCF_023573625_PROKKA_01199:0)n3:5e-09,GCF_003691675_PROKKA_00960:0.000884569)n2:0.0169484)n1:0.037129)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001043_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001043_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..780b0e044361d36ee567bf60d9cf514c0042ca1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001043_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01540:0.0800257,(GCF_005280335_PROKKA_01643:0.0394278,((GCF_002008305_PROKKA_01245:0,GCF_003691675_PROKKA_00964:0)n3:5e-09,GCF_023573625_PROKKA_01203:0.0059041)n2:0.00922539)n1:0.0800257)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001044_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001044_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..83f37d7593f78dd6de86c35881032be47db17a4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001044_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01539:0.07353,((GCF_002008305_PROKKA_01246:0,GCF_003691675_PROKKA_00965:0,GCF_023573625_PROKKA_01204:0)n2:0.0341091,GCF_005280335_PROKKA_01642:0.0668553)n1:0.07353)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001045_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001045_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c928e98c3a004c7870bd53586109f435932fc220
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001045_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01538:0.0474208,((GCF_002008305_PROKKA_01247:0,GCF_003691675_PROKKA_00966:0,GCF_023573625_PROKKA_01205:0)n2:0.0357284,GCF_005280335_PROKKA_01641:0.0195437)n1:0.0474208)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001046_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001046_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f04659ad36a78ae7a644cf50886af4688ebe2e7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001046_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01537:0.0350675,((GCF_002008305_PROKKA_01248:0,GCF_003691675_PROKKA_00967:0,GCF_023573625_PROKKA_01206:0)n2:0.0201336,GCF_005280335_PROKKA_01640:0.0178894)n1:0.0350675)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001051_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001051_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ae7121284c09b3fd57456bd616cdc85ae341d2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001051_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01531:0.166503,(GCF_005280335_PROKKA_01634:0.0874721,(GCF_002008305_PROKKA_01254:0.0115542,(GCF_003691675_PROKKA_00973:0.00572609,GCF_023573625_PROKKA_01212:5e-09)n3:0.0121592)n2:0.0212354)n1:0.166503)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001053_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001053_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1dc51f0b6bcb57f8ddc1af73de6f8cb2f69a8a94
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001053_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01529:0.377717,((GCF_002008305_PROKKA_01256:0,GCF_003691675_PROKKA_00975:0,GCF_023573625_PROKKA_01214:0)n2:0.194614,GCF_005280335_PROKKA_01632:0.079898)n1:0.377717)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001054_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001054_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..687452402e086b1ffa68e7feae5c7f664d54ab4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001054_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01528:0.0023814,(GCF_005280335_PROKKA_01630:5e-09,(GCF_002008305_PROKKA_01257:5e-09,(GCF_003691675_PROKKA_00976:0,GCF_023573625_PROKKA_01215:0)n3:0.00477853)n2:0.00958802)n1:0.0023814)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001056_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001056_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a4dd1d689f9e872b4535b6e50ebef77f3659808
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001056_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01526:0.0612126,(GCF_005280335_PROKKA_01628:0.0497037,(GCF_002008305_PROKKA_01259:0.00321673,(GCF_003691675_PROKKA_00978:0,GCF_023573625_PROKKA_01217:0)n3:0.00523236)n2:0.0459355)n1:0.0612126)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001059_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001059_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9f3da3151ee2507cc4451e92f3d2d64865b9477
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001059_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01522:0.0517783,((GCF_002008305_PROKKA_01262:0,GCF_003691675_PROKKA_00981:0,GCF_023573625_PROKKA_01220:0)n2:0.123477,GCF_005280335_PROKKA_01626:0.147296)n1:0.0517783)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001060_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001060_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d605af67fa6df4d2f559b8c70267052b9bf4d0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001060_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01521:0.0327829,(GCF_005280335_PROKKA_01624:0.0236304,(GCF_023573625_PROKKA_01221:0.00153647,(GCF_002008305_PROKKA_01263:5e-09,GCF_003691675_PROKKA_00982:0.00335644)n3:0.00184542)n2:0.0219403)n1:0.0327829)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001061_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001061_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c6106b2d1926c9b1a5fccaf9fad29034c2a8688
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001061_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01520:0.13861,(GCF_005280335_PROKKA_01623:0.117296,(GCF_002008305_PROKKA_01264:0.019443,(GCF_003691675_PROKKA_00983:0.00460241,GCF_023573625_PROKKA_01222:5e-09)n3:0.00376014)n2:0.0748924)n1:0.13861)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001064_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001064_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f827657161a92357bb4e05e6d9220f1cf582f183
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001064_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01515:0.247365,(GCF_005280335_PROKKA_01620:0.189451,(GCF_002008305_PROKKA_01267:0.00641303,(GCF_003691675_PROKKA_00986:0,GCF_023573625_PROKKA_01225:0)n3:0.0189168)n2:0.145132)n1:0.247365)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001068_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001068_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed73d07bcdfda899ce279d8e37959d6977951b69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001068_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01511:0.247831,(GCF_005280335_PROKKA_01616:0.0693543,(GCF_002008305_PROKKA_01271:0.00683969,(GCF_003691675_PROKKA_00990:0,GCF_023573625_PROKKA_01229:0)n3:5e-09)n2:0.095283)n1:0.247831)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001075_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001075_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2214f49fda5b75fe858c475041a879650cc3788
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001075_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01502:0.173909,(GCF_005280335_PROKKA_01607:0.0729545,(GCF_002008305_PROKKA_01279:0.00486801,(GCF_003691675_PROKKA_00998:0,GCF_023573625_PROKKA_01237:0)n3:5e-09)n2:0.117127)n1:0.173909)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001076_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001076_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d1d970b2baa45f7d8af9819e60500c6a5a3723b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001076_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01501:0.1179,(GCF_005280335_PROKKA_01606:0.254276,(GCF_002008305_PROKKA_01280:5e-09,(GCF_003691675_PROKKA_00999:0.00471623,GCF_023573625_PROKKA_01238:5e-09)n3:0.00235803)n2:0.0798706)n1:0.1179)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001078_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001078_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3253a19e85d94d19a4019033e9e414f7bd69e00f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001078_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01499:0.298118,(GCF_005280335_PROKKA_01603:0.100986,(GCF_002008305_PROKKA_01282:0.0131051,(GCF_003691675_PROKKA_01001:0,GCF_023573625_PROKKA_01240:0)n3:0.00533023)n2:0.144523)n1:0.298118)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001081_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001081_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fda8a9def80ab9adae156530f8562eb11b296602
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001081_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01495:0.200244,(GCF_005280335_PROKKA_01599:0.0836434,(GCF_002008305_PROKKA_01286:0.0239149,(GCF_003691675_PROKKA_01005:0,GCF_023573625_PROKKA_01244:0)n3:0.0107792)n2:0.0936544)n1:0.200244)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001082_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001082_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..709c9b3f37c1cf491eab365045f41b6137f13f7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001082_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01494:0.0624822,(GCF_005280335_PROKKA_01598:0.0381298,(GCF_023573625_PROKKA_01245:0.00291908,(GCF_002008305_PROKKA_01287:0.00145488,GCF_003691675_PROKKA_01006:5e-09)n3:6e-09)n2:0.0322865)n1:0.0624822)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001084_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001084_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9fa7e3ecf8b6602eb929a7b5cfbebf5a198c8f1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001084_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01492:0.10366,((GCF_002008305_PROKKA_01296:0,GCF_003691675_PROKKA_01019:0,GCF_023573625_PROKKA_01254:0)n2:0.0290442,GCF_005280335_PROKKA_01596:0.0395873)n1:0.10366)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001085_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001085_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4765c9735974b4447c2cbadac01143d349cbf32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001085_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01491:0.149294,((GCF_002008305_PROKKA_01297:0,GCF_003691675_PROKKA_01020:0,GCF_023573625_PROKKA_01255:0)n2:0.0953927,GCF_005280335_PROKKA_01595:0.0708716)n1:0.149294)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001087_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001087_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca1429a973fbd819987928030f6b4842f94b2b5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001087_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01489:0.0912149,((GCF_002008305_PROKKA_01299:0,GCF_003691675_PROKKA_01022:0,GCF_023573625_PROKKA_01257:0)n2:0.0705719,GCF_005280335_PROKKA_01593:0.0867384)n1:0.0912149)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001088_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001088_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2199e594a2641e6881e63cf27150f8382608c3aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001088_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01488:0.222785,((GCF_002008305_PROKKA_01300:0,GCF_003691675_PROKKA_01023:0,GCF_023573625_PROKKA_01258:0)n2:0.126816,GCF_005280335_PROKKA_01592:0.0355788)n1:0.222785)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001091_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001091_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c45bae109ebe0a58de8e7e2f7868da7492e194f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001091_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01485:0.0876686,((GCF_002008305_PROKKA_01303:0,GCF_003691675_PROKKA_01026:0,GCF_023573625_PROKKA_01261:0)n2:0.0499,GCF_005280335_PROKKA_01589:0.0511898)n1:0.0876686)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001092_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001092_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa6eba7f102b5db010b856c16c9cc7f90af0cb0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001092_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01484:0.17434,((GCF_002008305_PROKKA_01304:0,GCF_003691675_PROKKA_01027:0,GCF_023573625_PROKKA_01262:0)n2:0.120813,GCF_005280335_PROKKA_01588:0.154078)n1:0.17434)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001093_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001093_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..59dd3785306c1bcee76954d8d6f6ba0e89cd5258
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001093_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01483:0.0145911,((GCF_002008305_PROKKA_01305:0,GCF_003691675_PROKKA_01028:0,GCF_023573625_PROKKA_01263:0)n2:0.0120182,GCF_005280335_PROKKA_01587:0.0195098)n1:0.0145911)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001095_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001095_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fab348e6aba036b3d6cbce9d0dc7759d58ceca79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001095_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01480:0.162209,(GCF_005280335_PROKKA_01584:0.0740484,(GCF_002008305_PROKKA_01308:0.008787,(GCF_003691675_PROKKA_01031:0,GCF_023573625_PROKKA_01266:0)n3:0.00448112)n2:0.0573976)n1:0.162209)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001096_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001096_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6cb5347d707cb4e5b6659ceff48297874854d3cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001096_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01479:0.09647,(GCF_005280335_PROKKA_01583:0.0453395,(GCF_002008305_PROKKA_01309:0.0150269,(GCF_003691675_PROKKA_01032:0,GCF_023573625_PROKKA_01267:0)n3:0.00117694)n2:0.0628016)n1:0.09647)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001102_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001102_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d809f810f6810e049239606d4caf91ad1f8e1020
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001102_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01471:0.117606,(GCF_005280335_PROKKA_01575:0.0372644,(GCF_002008305_PROKKA_01317:0.00404461,(GCF_003691675_PROKKA_01038:0.0106633,GCF_023573625_PROKKA_01273:0.00282957)n3:0.0293644)n2:0.0476177)n1:0.117606)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001106_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001106_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60ada2f319b9a9369037e28d26ced1dea4046693
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001106_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01466:0.0956163,(GCF_005280335_PROKKA_01570:0.0710192,(GCF_023573625_PROKKA_01277:0.00275302,(GCF_002008305_PROKKA_01321:5e-09,GCF_003691675_PROKKA_01042:0.0162939)n3:0.010332)n2:0.054615)n1:0.0956163)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001107_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001107_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00853f6edd06b42b0756711925ebaba5297bc892
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001107_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01465:0.44011,(GCF_005280335_PROKKA_01569:0.141254,(GCF_002008305_PROKKA_01322:5e-09,(GCF_003691675_PROKKA_01043:0.049444,GCF_023573625_PROKKA_01278:0.0171915)n3:0.00275622)n2:0.310473)n1:0.44011)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001108_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001108_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c604090d131a1bd8140fe0f9e09fbc6f706a2e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001108_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01464:0.148268,(GCF_005280335_PROKKA_01568:0.0848788,((GCF_002008305_PROKKA_01323:0,GCF_023573625_PROKKA_01279:0)n3:0.00631855,GCF_003691675_PROKKA_01044:5e-09)n2:0.0572524)n1:0.148268)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001109_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001109_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..619ca1989ad06c6e783ba39493c823e76e875e1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001109_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01463:0.102715,(GCF_005280335_PROKKA_01567:0.100875,(GCF_003691675_PROKKA_01045:6e-09,(GCF_002008305_PROKKA_01324:0.00950796,GCF_023573625_PROKKA_01280:0.00380434)n3:0.00952077)n2:0.0430542)n1:0.102715)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001110_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001110_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c20baba104cba2e4900b8f1fb064ca153228d44e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001110_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01462:0.00551603,(GCF_005280335_PROKKA_01566:0.0332873,(GCF_003691675_PROKKA_01046:0.00433461,(GCF_002008305_PROKKA_01325:0.00216683,GCF_023573625_PROKKA_01281:5e-09)n3:6e-09)n2:0.00423275)n1:0.00551603)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001111_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001111_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65211db94b4810d6d06354d746300c4e93832ecf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001111_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01461:0.0615618,(GCF_005280335_PROKKA_01565:0.0865239,(GCF_023573625_PROKKA_01282:0.0105175,(GCF_002008305_PROKKA_01326:0.00152108,GCF_003691675_PROKKA_01047:5e-09)n3:0.00473463)n2:0.0345546)n1:0.0615618)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001112_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001112_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d7c234938c67e2aa1a985ad9b2af257b005bc17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001112_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01460:0.0914322,(GCF_003691675_PROKKA_01048:0.00859493,((GCF_002008305_PROKKA_01327:0,GCF_005280335_PROKKA_01564:0)n3:5e-09,GCF_023573625_PROKKA_01283:0.00855209)n2:5e-09)n1:0.0914322)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001114_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001114_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea5cfc4925ff1e5de4063b9c7fd134267ca85ff8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001114_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01458:0.0962569,(GCF_002008305_PROKKA_01329:0.0042932,((GCF_005280335_PROKKA_01562:0,GCF_023573625_PROKKA_01285:0)n3:5e-09,GCF_003691675_PROKKA_01050:0.0042788)n2:5e-09)n1:0.0962569)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001116_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001116_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..899306686055822b13fb72738b86786b77989ff9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001116_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01456:0.186925,(GCF_005280335_PROKKA_01560:0.0483998,(GCF_023573625_PROKKA_01287:0.00366708,(GCF_003691675_PROKKA_01052:0.00368068,GCF_002008305_PROKKA_01331:5e-09)n3:5e-09)n2:0.0739005)n1:0.186925)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001117_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001117_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d789405eecef51780fd1ccf3b42d5e8885260528
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001117_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01455:0.0835999,((GCF_002008305_PROKKA_01332:0,GCF_003691675_PROKKA_01053:0,GCF_005280335_PROKKA_01559:0)n2:0.120401,GCF_023573625_PROKKA_01288:0.140901)n1:0.0835999)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001118_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001118_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99b976f9c4a84887e287351074a077b46eb07c15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001118_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01454:0.0598344,(GCF_005280335_PROKKA_01558:0.00565098,((GCF_002008305_PROKKA_01333:0,GCF_003691675_PROKKA_01054:0)n3:0.000942863,GCF_023573625_PROKKA_01289:0.0204587)n2:0.00399157)n1:0.0598344)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001120_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001120_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..951dd6b8007275edaea5d5be51e3f25f1871ff8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001120_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01451:0.0573902,(GCF_005280335_PROKKA_01555:0.0132295,(GCF_003691675_PROKKA_01057:6e-09,(GCF_002008305_PROKKA_01336:0.00898179,GCF_023573625_PROKKA_01292:0.00450856)n3:0.0137388)n2:0.0241943)n1:0.0573902)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001121_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001121_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..11a6a758bff2ee17d000893fd56f4c81e8e96710
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001121_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01450:0.107043,(GCF_005280335_PROKKA_01554:0.0381444,(GCF_002008305_PROKKA_01338:0.00414076,(GCF_003691675_PROKKA_01058:5e-09,GCF_023573625_PROKKA_01293:0.00339153)n3:0.0060513)n2:0.034942)n1:0.107043)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001122_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001122_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54fc16d1345a684c864c27a2b22cca8fe3a73ef6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001122_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01449:0.185321,(GCF_005280335_PROKKA_01553:0.144503,(GCF_002008305_PROKKA_01339:0.0372122,(GCF_003691675_PROKKA_01059:0,GCF_023573625_PROKKA_01294:0)n3:0.00488192)n2:0.146191)n1:0.185321)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001123_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001123_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5a2a78a6cad343a7a6d2e245fad9d4b76212f8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001123_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01448:0.0630306,(GCF_005280335_PROKKA_01552:0.032053,(GCF_003691675_PROKKA_01060:5e-09,(GCF_002008305_PROKKA_01340:0.012677,GCF_023573625_PROKKA_01295:5e-09)n3:0.00315697)n2:0.0302863)n1:0.0630306)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001125_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001125_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0e59b58a70633f73cea271e56b54c4e8b660c88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001125_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01445:0.0439035,(GCF_005280335_PROKKA_01549:0.0200571,(GCF_003691675_PROKKA_01063:0.00311725,(GCF_002008305_PROKKA_01343:0.000838914,GCF_023573625_PROKKA_01298:0.000838733)n3:0.00112378)n2:0.0168076)n1:0.0439035)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001126_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001126_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ea1ff85b2751b9d7265ba79ad62d9620b104e7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001126_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01444:0.0650156,(GCF_005280335_PROKKA_01548:0.111728,(GCF_023573625_PROKKA_01299:0.00578641,(GCF_002008305_PROKKA_01344:0.00303014,GCF_003691675_PROKKA_01064:0.00937232)n3:0.00699056)n2:0.0239327)n1:0.0650156)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001127_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001127_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..128bc138afdc6a201978d442fe5c37e0e3344136
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001127_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01443:0.167229,(GCF_005280335_PROKKA_01547:0.0573304,(GCF_023573625_PROKKA_01300:0.00726102,(GCF_002008305_PROKKA_01345:0.00630605,GCF_003691675_PROKKA_01065:0.00619679)n3:0.00546703)n2:0.115466)n1:0.167229)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001130_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001130_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d6f2951f434062822e6722882cef6c2d2b9948a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001130_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01440:0.130378,(GCF_005280335_PROKKA_01544:0.111443,(GCF_003691675_PROKKA_01068:0.0138518,(GCF_002008305_PROKKA_01348:0.00460778,GCF_023573625_PROKKA_01303:0.00460514)n3:5e-09)n2:0.0921969)n1:0.130378)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001131_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001131_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b9f3ba7293f619db0eb6244630f1b5768ff7ab15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001131_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01439:0.127076,(GCF_005280335_PROKKA_01543:0.0718907,(GCF_003691675_PROKKA_01069:0.0118956,(GCF_002008305_PROKKA_01349:0.0113188,GCF_023573625_PROKKA_01304:0.0112459)n3:0.00718847)n2:0.128494)n1:0.127076)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001134_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001134_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..82ff81b0c9925b6c95ccbf669d044efc6c1d0a10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001134_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01436:0.333734,(GCF_005280335_PROKKA_01540:0.247477,(GCF_002008305_PROKKA_01352:0.00970588,(GCF_003691675_PROKKA_01072:0.0232392,GCF_023573625_PROKKA_01307:0.0113)n3:0.0138812)n2:0.203854)n1:0.333734)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001135_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001135_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..638cc3eab64a96e06133f1ce4fd6744bdb3bc5b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001135_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01435:0.0747174,(GCF_005280335_PROKKA_01539:0.0501101,(GCF_023573625_PROKKA_01308:0.0027115,(GCF_002008305_PROKKA_01353:0.00390237,GCF_003691675_PROKKA_01073:5e-09)n3:0.00316679)n2:0.0761343)n1:0.0747174)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001137_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001137_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..854d20780fa2e417d907ca3da79b64dfdb8d5644
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001137_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01433:0.244614,(GCF_005280335_PROKKA_01537:0.0782414,(GCF_003691675_PROKKA_01075:5e-09,(GCF_002008305_PROKKA_01355:0.00944345,GCF_023573625_PROKKA_01310:0.00653836)n3:0.00569742)n2:0.106271)n1:0.244614)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001140_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001140_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0cf303dcc08584b7dbbdf71d274fb0a37a6f70c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001140_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01429:0.124131,(GCF_005280335_PROKKA_01534:0.101114,(GCF_003691675_PROKKA_01079:0.0179843,(GCF_002008305_PROKKA_01359:0.00670271,GCF_023573625_PROKKA_01314:0.00326799)n3:0.0111797)n2:0.0914694)n1:0.124131)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001141_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001141_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4109c786961e4c6ce23f161487b9febc64483c8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001141_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01428:0.181115,(GCF_005280335_PROKKA_01533:0.0783275,(GCF_003691675_PROKKA_01080:0.00413481,(GCF_002008305_PROKKA_01360:5e-09,GCF_023573625_PROKKA_01315:0.00166546)n3:0.00758962)n2:0.058926)n1:0.181115)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001143_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001143_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d38a8b7c1e7a1ba3d468a422758e852e0984e276
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001143_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01426:0.0835817,(GCF_005280335_PROKKA_01531:0.0398389,((GCF_002008305_PROKKA_01362:0,GCF_023573625_PROKKA_01317:0)n3:0.00883693,GCF_003691675_PROKKA_01082:0.00283647)n2:0.0225972)n1:0.0835817)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001144_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001144_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec34115cd4cbd75a339ae9c4b4548d0dda07a2aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001144_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01425:0.0583451,(GCF_005280335_PROKKA_01530:5e-09,((GCF_002008305_PROKKA_01363:0,GCF_023573625_PROKKA_01318:0)n3:0.00698559,GCF_003691675_PROKKA_01083:5e-09)n2:0.00699841)n1:0.0583451)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001146_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001146_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92f064251c0fc9c969789f2461627bcc5a4f4158
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001146_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01423:0.168774,(GCF_005280335_PROKKA_01528:0.105894,(GCF_023573625_PROKKA_01320:0.00488588,(GCF_002008305_PROKKA_01365:0.00452764,GCF_003691675_PROKKA_01085:0.00464275)n3:0.00445851)n2:0.119121)n1:0.168774)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001147_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001147_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fbe63117a2cc5b874d3b84a0f81145200b235120
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001147_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01422:0.148927,(GCF_005280335_PROKKA_01527:0.0956106,(GCF_023573625_PROKKA_01321:0.00521171,(GCF_002008305_PROKKA_01366:0.00802747,GCF_003691675_PROKKA_01086:0.00802496)n3:0.00552451)n2:0.147052)n1:0.148927)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001149_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001149_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..685729e957de37ba6b59aad1c165d14c0e3d536b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001149_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01420:0.274166,(GCF_005280335_PROKKA_01525:0.161234,(GCF_003691675_PROKKA_01088:0.0188392,(GCF_002008305_PROKKA_01368:0.00741432,GCF_023573625_PROKKA_01323:0.00246601)n3:0.0110127)n2:0.0458706)n1:0.274166)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001157_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001157_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..269531817d0020457bc8b00584dd381adeb766b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001157_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01410:0.209589,(GCF_005280335_PROKKA_01515:0.0768983,(GCF_023573625_PROKKA_01332:0.0120666,(GCF_002008305_PROKKA_01377:0.00567093,GCF_003691675_PROKKA_01097:0.0116059)n3:0.00521819)n2:0.0554767)n1:0.209589)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001158_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001158_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28fb6ffcd820661a8b9c5c0838699dddef0d1d46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001158_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01409:0.21682,(GCF_005280335_PROKKA_01514:0.106846,(GCF_002008305_PROKKA_01378:0.00977426,(GCF_003691675_PROKKA_01098:5e-09,GCF_023573625_PROKKA_01333:0.00812875)n3:0.0192271)n2:0.0803253)n1:0.21682)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001163_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001163_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7364bebab06b7b1591ab15397d994a76cd734a16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001163_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01403:0.0508645,(GCF_005280335_PROKKA_01491:0.0120867,(GCF_002008305_PROKKA_01404:0.00191289,(GCF_003691675_PROKKA_01134:0.00190843,GCF_023573625_PROKKA_01354:5e-09)n3:0.00190463)n2:0.0131791)n1:0.0508645)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001164_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001164_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de2a5801b4bdd73af96e717f63f9e82da494f70d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001164_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01401:0.122189,(GCF_005280335_PROKKA_01490:0.0934161,((GCF_002008305_PROKKA_01406:0,GCF_023573625_PROKKA_01356:0)n3:5e-09,GCF_003691675_PROKKA_01136:0.0025075)n2:0.0435086)n1:0.122189)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001166_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001166_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dae94a60851b7191bf9bcc0648b31d55d012adb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001166_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01394:0.0784116,(GCF_005280335_PROKKA_01487:0.0312418,(GCF_003691675_PROKKA_01143:0.00368271,(GCF_002008305_PROKKA_01412:0.00739766,GCF_023573625_PROKKA_01362:0.00807673)n3:0.00309779)n2:0.0271802)n1:0.0784116)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001167_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001167_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20445cdafaaedc16624d43768a6ef0274692578d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001167_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01393:0.141373,(GCF_005280335_PROKKA_01486:0.0197905,((GCF_002008305_PROKKA_01413:0,GCF_003691675_PROKKA_01144:0)n3:5e-09,GCF_023573625_PROKKA_01363:0.00426578)n2:0.0483324)n1:0.141373)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001168_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001168_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..054138b7ead0252c0c3878c9d74415f451544e61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001168_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01392:0.0273411,(GCF_005280335_PROKKA_01485:0.0216963,(GCF_003691675_PROKKA_01145:0.00382349,(GCF_002008305_PROKKA_01414:0.0019167,GCF_023573625_PROKKA_01364:0.0038536)n3:0.00195242)n2:0.0403396)n1:0.0273411)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001175_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001175_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56492742400e7e7a16945e850a7d6bec507ef89e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001175_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01385:0.0907118,(GCF_005280335_PROKKA_01477:0.118363,(GCF_002008305_PROKKA_01422:0.0326903,(GCF_003691675_PROKKA_01153:0.00350936,GCF_023573625_PROKKA_01372:0.00708031)n3:0.0219793)n2:0.168735)n1:0.0907118)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001176_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001176_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ccea5cf6a9ab8ebbc11cd3ebde700c76cb5772fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001176_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01384:0.157731,(GCF_005280335_PROKKA_01476:0.0959353,(GCF_002008305_PROKKA_01423:0.0210542,(GCF_003691675_PROKKA_01154:0,GCF_023573625_PROKKA_01373:0)n3:0.00443265)n2:0.127137)n1:0.157731)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001177_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001177_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..73cefdd6a9cccfaaa7d246005844b433d2ea6c9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001177_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01383:0.142753,(GCF_005280335_PROKKA_01475:0.144255,(GCF_002008305_PROKKA_01424:0.0364005,(GCF_003691675_PROKKA_01155:0,GCF_023573625_PROKKA_01374:0)n3:5e-09)n2:0.100235)n1:0.142753)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001180_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001180_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..08628beb6c6b8baa28fdade137704083653feffe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001180_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01376:0.0581643,(GCF_005280335_PROKKA_01469:0.0413807,(GCF_003691675_PROKKA_01162:0.00205241,(GCF_002008305_PROKKA_01430:0.00404957,GCF_023573625_PROKKA_01380:5e-09)n3:0.00405457)n2:0.0254736)n1:0.0581643)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001181_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001181_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed89818f97f95415aa19efaf8f7d8a11616ca48e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001181_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01375:0.0183631,(GCF_005280335_PROKKA_01468:0.0209682,(GCF_003691675_PROKKA_01163:0.00243612,(GCF_002008305_PROKKA_01431:0.00479112,GCF_023573625_PROKKA_01381:5e-09)n3:0.00236465)n2:0.00610442)n1:0.0183631)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001187_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001187_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d938c395b4a1f7da971ae9315e9456e347d21c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001187_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01369:0.0856638,(GCF_005280335_PROKKA_01461:0.0558178,(GCF_003691675_PROKKA_01169:0.00248591,(GCF_002008305_PROKKA_01437:0.00487034,GCF_023573625_PROKKA_01387:0.00985682)n3:0.00480542)n2:0.0956826)n1:0.0856638)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001188_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001188_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0ed1294d4cbf797d75416fd1e66d7830735eff7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001188_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01368:0.0570774,(GCF_005280335_PROKKA_01460:0.0524949,(GCF_003691675_PROKKA_01170:0.00295225,(GCF_023573625_PROKKA_01388:0.00581744,GCF_002008305_PROKKA_01438:0.0057311)n3:0.00279893)n2:0.038752)n1:0.0570774)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001190_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001190_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2fcea4cc6767797cad7b8efeaf1a155323c8ebeb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001190_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01365:0.187432,(GCF_005280335_PROKKA_01457:0.0422155,(GCF_002008305_PROKKA_01441:0.00447931,(GCF_003691675_PROKKA_01173:0,GCF_023573625_PROKKA_01391:0)n3:5e-09)n2:0.116209)n1:0.187432)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001192_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001192_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3722f882d7d908f0c0d161b18884d5cee45fa83d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001192_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01363:0.152924,(GCF_005280335_PROKKA_01455:0.0484765,(GCF_023573625_PROKKA_01393:0.0084574,(GCF_002008305_PROKKA_01443:0.00113937,GCF_003691675_PROKKA_01175:0.00114126)n3:0.00878496)n2:0.0533156)n1:0.152924)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001193_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001193_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6820d34e16aee86a331f89159ce8d3121c3e70a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001193_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01362:0.0785834,(GCF_005280335_PROKKA_01454:0.022704,(GCF_002008305_PROKKA_01444:5e-09,(GCF_003691675_PROKKA_01176:5e-09,GCF_023573625_PROKKA_01394:0.00278743)n3:0.00279439)n2:0.0257815)n1:0.0785834)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001195_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001195_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62d919330348d5da12ad40620ff081d0b8f94594
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001195_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01356:0.0905064,(GCF_005280335_PROKKA_01452:0.0854043,(GCF_003691675_PROKKA_01179:0.0173934,(GCF_002008305_PROKKA_01447:0.00869243,GCF_023573625_PROKKA_01397:5e-09)n3:0.0136454)n2:0.0959599)n1:0.0905064)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001196_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001196_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1279b2744ddcfb5ca73414252bf69a803574d549
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001196_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01355:0.157233,((GCF_002008305_PROKKA_01448:0,GCF_003691675_PROKKA_01180:0,GCF_023573625_PROKKA_01398:0)n2:0.0353675,GCF_005280335_PROKKA_01451:0.0518591)n1:0.157233)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001197_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001197_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8c59ce02ac6cba313809e41c43eacb36a7640d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001197_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01354:0.188582,(GCF_005280335_PROKKA_01450:0.165299,((GCF_002008305_PROKKA_01449:0,GCF_003691675_PROKKA_01181:0)n3:0.0151625,GCF_023573625_PROKKA_01399:6e-09)n2:0.107452)n1:0.188582)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001204_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001204_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd11d43c1eb965a35f77ede3d53d7332d9ba5af5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001204_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01458:0,GCF_003691675_PROKKA_01190:0,GCF_005280335_PROKKA_01442:0,GCF_023573625_PROKKA_01408:0)n1:0.0124044,GCF_020097155_PROKKA_01345:0.0124044)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001206_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001206_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b94f010d53ed2facdc3502823ad00808fac2fe2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001206_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01343:0.274978,(GCF_005280335_PROKKA_01440:0.183003,(GCF_002008305_PROKKA_01460:0.00753076,(GCF_003691675_PROKKA_01192:0,GCF_023573625_PROKKA_01410:0)n3:0.0152219)n2:0.206546)n1:0.274978)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001207_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001207_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aaa5f558dfdc28f3806cd8976cb1b52c976623a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001207_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01342:0.259714,(GCF_005280335_PROKKA_01439:0.143931,(GCF_003691675_PROKKA_01193:0.00584162,(GCF_002008305_PROKKA_01461:0.0094406,GCF_023573625_PROKKA_01411:5e-09)n3:0.0131523)n2:0.0530581)n1:0.259714)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001208_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001208_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ae99e1e48bdac87ea88200928d326eb1e773920
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001208_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01341:0.202495,(GCF_005280335_PROKKA_01438:0.113692,(GCF_002008305_PROKKA_01462:5e-09,(GCF_003691675_PROKKA_01194:0.0131269,GCF_023573625_PROKKA_01412:5e-09)n3:0.0131343)n2:0.0272805)n1:0.202495)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001213_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001213_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..274fe79dc32cf495b0b33104c3fa972b004f78a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001213_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01335:0.162317,(GCF_005280335_PROKKA_01433:0.0596435,(GCF_023573625_PROKKA_01417:0.00776645,(GCF_002008305_PROKKA_01467:0.00430546,GCF_003691675_PROKKA_01199:5e-09)n3:0.0051407)n2:0.0392184)n1:0.162317)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001214_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001214_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d7987219240fecbc0d95102f67c8d6d03b701bc9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001214_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01334:0.201991,(GCF_005280335_PROKKA_01432:0.1461,(GCF_003691675_PROKKA_01200:5e-09,(GCF_023573625_PROKKA_01418:0.015661,GCF_002008305_PROKKA_01468:5e-09)n3:0.00806196)n2:0.172401)n1:0.201991)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001215_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001215_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8364cd08ec6eb1504faa7aea353a07f043d25e6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001215_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01333:0.304437,(GCF_005280335_PROKKA_01431:0.101723,(GCF_023573625_PROKKA_01419:0.0140029,(GCF_002008305_PROKKA_01469:0.00667108,GCF_003691675_PROKKA_01201:0.015481)n3:0.0139899)n2:0.129444)n1:0.304437)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001216_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001216_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05d9eeae982ff977dbfcd4db7d2a92ab06fe0798
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001216_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01331:0.0508576,(GCF_005280335_PROKKA_01429:0.0350028,((GCF_002008305_PROKKA_01471:0,GCF_023573625_PROKKA_01421:0)n3:0.0140191,GCF_003691675_PROKKA_01203:0.00857113)n2:0.0247197)n1:0.0508576)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001218_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001218_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f7407c427eb9c8404497441469060a3ce61b597
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001218_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01329:0.131008,(GCF_005280335_PROKKA_01427:0.132086,((GCF_002008305_PROKKA_01473:0,GCF_003691675_PROKKA_01205:0)n3:0.0149243,GCF_023573625_PROKKA_01423:0.00852398)n2:0.0718112)n1:0.131008)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001220_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001220_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..414597c9a6971f0261b00dd0f46d3c5bf7fe78c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001220_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01327:0.00440254,(GCF_005280335_PROKKA_01425:0.154316,(GCF_002008305_PROKKA_01475:0.0146936,(GCF_003691675_PROKKA_01207:0.00241817,GCF_023573625_PROKKA_01425:6e-09)n3:0.0120043)n2:0.00443107)n1:0.00440254)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001221_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001221_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34e0a4c82e79b917b5dff030834a2b71543a5e99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001221_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01324:0.0855,((GCF_002008305_PROKKA_01478:0,GCF_003691675_PROKKA_01210:0,GCF_023573625_PROKKA_01428:0)n2:0.0812952,GCF_005280335_PROKKA_01424:0.16192)n1:0.0855)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001223_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001223_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93cf982117c3e15852761cb33624f6eeaadd76ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001223_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01322:0.159885,(GCF_005280335_PROKKA_01422:0.116651,(GCF_002008305_PROKKA_01480:0.00316617,(GCF_003691675_PROKKA_01212:0.00315761,GCF_023573625_PROKKA_01430:0.00315294)n3:5e-09)n2:0.101253)n1:0.159885)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001224_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001224_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e84a6dcbcaef001d39b2591fbaa09e48b1c37e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001224_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01321:0.073317,(GCF_005280335_PROKKA_01421:0.044161,((GCF_002008305_PROKKA_01481:0,GCF_023573625_PROKKA_01431:0)n3:0.00967769,GCF_003691675_PROKKA_01213:0.00672112)n2:0.0667849)n1:0.073317)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001228_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001228_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02f8b364664596b1d2f3a074c01d921e4448bdbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001228_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01317:0.220701,(GCF_005280335_PROKKA_01417:0.0779121,(GCF_003691675_PROKKA_01217:0.00844026,(GCF_002008305_PROKKA_01485:0.0256287,GCF_023573625_PROKKA_01435:5e-09)n3:0.0112895)n2:0.101961)n1:0.220701)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001229_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001229_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0027e627fc85b8fe4df4670e7cdabd7a202af827
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001229_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01316:0.0634561,(GCF_005280335_PROKKA_01416:0.0320204,(GCF_002008305_PROKKA_01486:0.00346085,(GCF_003691675_PROKKA_01218:0,GCF_023573625_PROKKA_01436:0)n3:5e-09)n2:0.0558882)n1:0.0634561)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001230_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001230_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..444fc0b7e8bdb4b5b23ded70a64716f7663432c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001230_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01314:0.0968057,(GCF_005280335_PROKKA_01415:0.0221547,(GCF_023573625_PROKKA_01437:5e-09,(GCF_002008305_PROKKA_01487:0.00636512,GCF_003691675_PROKKA_01219:6e-09)n3:0.00423135)n2:0.0538013)n1:0.0968057)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001231_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001231_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..33d1a8ff76e4fe75ebd56107449d07a6f82ffffe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001231_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01312:0.0974447,(GCF_005280335_PROKKA_01413:0.0581003,(GCF_002008305_PROKKA_01512:0.00476891,(GCF_003691675_PROKKA_01221:5e-09,GCF_023573625_PROKKA_01439:0.00381592)n3:0.00105101)n2:0.0522617)n1:0.0974447)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001232_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001232_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b5ae8df45ce3d44fa59ffdd4d91f38746abf5f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001232_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01311:0.224533,(GCF_005280335_PROKKA_01412:0.129864,(GCF_003691675_PROKKA_01222:0.00282115,(GCF_002008305_PROKKA_01513:0.00282486,GCF_023573625_PROKKA_01440:0.00565989)n3:5e-09)n2:0.0850486)n1:0.224533)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001233_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001233_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3cf0437164527c1755ca16537210868274d67205
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001233_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01309:0.244709,(GCF_005280335_PROKKA_01410:0.245573,((GCF_002008305_PROKKA_01515:0,GCF_003691675_PROKKA_01224:0)n3:0.0189718,GCF_023573625_PROKKA_01442:0.00340451)n2:0.0868144)n1:0.244709)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001234_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001234_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0767abeea2083f37a053f8bc00ad1c7a98cf0894
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001234_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01308:0.492356,(GCF_005280335_PROKKA_01409:0.263296,(GCF_023573625_PROKKA_01443:0.00680612,(GCF_002008305_PROKKA_01516:0.00411549,GCF_003691675_PROKKA_01225:5e-09)n3:0.0139095)n2:0.0749322)n1:0.492356)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001236_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001236_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c020f8d19407e155dee88eeeb163ccb5e77ec6ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001236_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01306:0.233527,(GCF_005280335_PROKKA_01407:0.0859592,(GCF_023573625_PROKKA_01445:0.0103926,(GCF_002008305_PROKKA_01518:0.00303067,GCF_003691675_PROKKA_01227:5e-09)n3:0.00531479)n2:0.0748953)n1:0.233527)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001240_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001240_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4dd0c95bb955efd8013632a32f40b9c081217004
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001240_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01302:0.233895,(GCF_005280335_PROKKA_01403:0.0364161,(GCF_023573625_PROKKA_01449:0.0152269,(GCF_002008305_PROKKA_01522:0.00754195,GCF_003691675_PROKKA_01231:0.00751967)n3:0.00767543)n2:0.250163)n1:0.233895)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001241_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001241_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96e7c561c3fba199dc8c8a3c8091555fcb55a367
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001241_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01301:0.11814,(GCF_005280335_PROKKA_01402:0.0389963,(GCF_003691675_PROKKA_01232:0.00857733,(GCF_002008305_PROKKA_01523:0.00842691,GCF_023573625_PROKKA_01450:0.00835917)n3:6e-09)n2:0.0424049)n1:0.11814)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001245_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001245_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a72889d0b248a39308a9092cec8e8414e5f3e949
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001245_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01289:0.172722,(GCF_005280335_PROKKA_01398:0.0107572,((GCF_002008305_PROKKA_01527:0,GCF_023573625_PROKKA_01454:0)n3:0.00757322,GCF_003691675_PROKKA_01237:0.000462712)n2:0.0150284)n1:0.172722)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001247_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001247_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c3ef1ee693ba6d7fa5797f4fefefdc0e58e3090
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001247_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01287:0.420259,(GCF_023573625_PROKKA_01456:0.0117578,(GCF_005280335_PROKKA_01396:0.018778,(GCF_002008305_PROKKA_01529:5e-09,GCF_003691675_PROKKA_01239:0.00365077)n3:0.00724442)n2:0.00694518)n1:0.420259)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001248_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001248_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d6a6038f97d1393720dcf5269d168cbf857fdb4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001248_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01286:0.0736094,(GCF_005280335_PROKKA_01395:0.0493442,(GCF_023573625_PROKKA_01457:0.0051813,(GCF_002008305_PROKKA_01530:0.00281859,GCF_003691675_PROKKA_01240:0.00497489)n3:0.00549746)n2:0.0322346)n1:0.0736094)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001249_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001249_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..148f053c9446f7dd46593ecaa3a68602538f078c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001249_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01285:0.0938247,(GCF_005280335_PROKKA_01394:0.0804961,((GCF_002008305_PROKKA_01531:0,GCF_023573625_PROKKA_01458:0)n3:5e-09,GCF_003691675_PROKKA_01241:0.00443924)n2:0.0379389)n1:0.0938247)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001253_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001253_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..706b54433b2e2c6357eb5c891a397d1ce080a689
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001253_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01281:0.111064,(GCF_005280335_PROKKA_01390:0.0910539,(GCF_023573625_PROKKA_01462:0.00656219,(GCF_002008305_PROKKA_01535:0.00643736,GCF_003691675_PROKKA_01245:5e-09)n3:0.00205737)n2:0.0731624)n1:0.111064)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001255_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001255_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f29a36e3c9044b251d36546a7ab694f42e8b48dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001255_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01279:0.102529,(GCF_005280335_PROKKA_01388:0.0401684,(GCF_023573625_PROKKA_01464:0.0128978,(GCF_002008305_PROKKA_01537:0.0128952,GCF_003691675_PROKKA_01247:5e-09)n3:5e-09)n2:0.0408354)n1:0.102529)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001256_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001256_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..280723f6f74d0f6ca4767bdd12d43232cea72f71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001256_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01278:0.128127,(GCF_005280335_PROKKA_01387:0.10818,(GCF_002008305_PROKKA_01538:0.013615,(GCF_003691675_PROKKA_01248:0.0191835,GCF_023573625_PROKKA_01465:5e-09)n3:0.0131957)n2:0.120908)n1:0.128127)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001257_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001257_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fcf1866bf5fee571a669ac0f5d20232968783e28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001257_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01276:0.0705246,(GCF_005280335_PROKKA_01385:0.139423,(GCF_002008305_PROKKA_01540:0.00484267,(GCF_003691675_PROKKA_01250:0,GCF_023573625_PROKKA_01467:0)n3:0.00894414)n2:0.120022)n1:0.0705246)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001258_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001258_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..825557f336bbf9ccbc5d3030e41a4d9914efad8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001258_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01275:0.0672452,(GCF_005280335_PROKKA_01384:0.0446183,(GCF_023573625_PROKKA_01468:0.00930505,(GCF_002008305_PROKKA_01541:0.00183997,GCF_003691675_PROKKA_01251:0.00369593)n3:0.00372047)n2:0.0525195)n1:0.0672452)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001260_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001260_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..434a7850ddb21dd591b2f2f0aadbac1754f73e01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001260_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01273:0.182235,(GCF_005280335_PROKKA_01382:0.123217,(GCF_003691675_PROKKA_01253:0.00754044,(GCF_002008305_PROKKA_01543:5e-09,GCF_023573625_PROKKA_01470:0.00393176)n3:0.0376491)n2:0.119333)n1:0.182235)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001267_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001267_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9f08e4c4601e8eaa1294f533c9e36bf82c1d842
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001267_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01265:0.223432,(GCF_005280335_PROKKA_01374:0.114153,(GCF_002008305_PROKKA_01551:0.00476888,(GCF_023573625_PROKKA_01478:0.0498768,GCF_003691675_PROKKA_01261:5e-09)n3:0.0116179)n2:0.222254)n1:0.223432)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001268_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001268_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea4781a71298e070b6447852a4ca6f632631c6da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001268_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01264:0.143603,(GCF_005280335_PROKKA_01373:0.132515,(GCF_002008305_PROKKA_01552:0.0236145,(GCF_003691675_PROKKA_01262:0.0312865,GCF_023573625_PROKKA_01479:6e-09)n3:0.0111074)n2:0.0834532)n1:0.143603)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001269_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001269_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5bdf36df77382e419631070718f2a2d1eba294e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001269_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01263:0.0770067,(GCF_005280335_PROKKA_01372:0.0329244,(GCF_023573625_PROKKA_01480:0.00362682,(GCF_003691675_PROKKA_01263:0.00364378,GCF_002008305_PROKKA_01553:6e-09)n3:6e-09)n2:0.0628322)n1:0.0770067)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001271_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001271_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4f7d9d116152d6565d3b27a550d3d9b530aae6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001271_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01261:0.0746407,(GCF_005280335_PROKKA_01370:0.0152052,(GCF_002008305_PROKKA_01555:0.0029587,(GCF_003691675_PROKKA_01265:0,GCF_023573625_PROKKA_01482:0)n3:0.00574652)n2:0.0169887)n1:0.0746407)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001275_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001275_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b860db08f8ddc42a81af8faeadec6ad1acc8e2b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001275_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01257:0.0393277,(GCF_005280335_PROKKA_01366:0.0164126,(GCF_023573625_PROKKA_01487:5e-09,(GCF_002008305_PROKKA_01560:0.00472911,GCF_003691675_PROKKA_01270:0.00235869)n3:0.00236705)n2:0.0152807)n1:0.0393277)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001276_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001276_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69724b435ae67f923e650cc91cad335800e4c1bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001276_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01256:0.0874122,(GCF_005280335_PROKKA_01365:0.0489164,(GCF_002008305_PROKKA_01561:0.00671362,(GCF_003691675_PROKKA_01271:0.00258094,GCF_023573625_PROKKA_01488:5e-09)n3:0.00635232)n2:0.0531238)n1:0.0874122)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001277_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001277_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b66f3e9ebd3956560388ba40a7e3bc90d3d3bd48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001277_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01255:0.0314697,(GCF_005280335_PROKKA_01364:0.00909645,((GCF_002008305_PROKKA_01562:0,GCF_003691675_PROKKA_01272:0)n3:5e-09,GCF_023573625_PROKKA_01489:0.00962633)n2:0.0304963)n1:0.0314697)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001278_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001278_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9592b8ec516202f8bec6ef831eb06aae02a08139
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001278_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01253:0.0194341,(GCF_005280335_PROKKA_01362:0.0653074,(GCF_023573625_PROKKA_01491:5e-09,(GCF_002008305_PROKKA_01564:0.00153367,GCF_003691675_PROKKA_01274:0.00153424)n3:0.00153166)n2:0.0190284)n1:0.0194341)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001279_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001279_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..240647375eea4fa12eca22c38b474ce2806b84cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001279_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01252:0.0817345,(GCF_005280335_PROKKA_01361:0.0467481,(GCF_003691675_PROKKA_01275:5e-09,(GCF_002008305_PROKKA_01565:0.00627287,GCF_023573625_PROKKA_01492:0.00311334)n3:0.00310511)n2:0.0319498)n1:0.0817345)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001280_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001280_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f673b759bd5a6f6ca9f3f517017f1eb500b9825f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001280_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01251:0.134551,(GCF_005280335_PROKKA_01360:0.0450926,(GCF_023573625_PROKKA_01493:5e-09,(GCF_002008305_PROKKA_01566:0.00753821,GCF_003691675_PROKKA_01276:0.00250026)n3:0.00499833)n2:0.050253)n1:0.134551)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001283_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001283_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..811a094beb5dcdc698f5e199927395ea5ea23525
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001283_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01247:0.325294,(GCF_005280335_PROKKA_01354:0.105035,(GCF_003691675_PROKKA_01280:0.016298,(GCF_002008305_PROKKA_01570:0.0035946,GCF_023573625_PROKKA_01497:0.00438574)n3:0.0112567)n2:0.0906756)n1:0.325294)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001284_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001284_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9914a97992629f460b36dd33334d246657ba7568
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001284_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01246:0.195866,(GCF_005280335_PROKKA_01353:0.153487,(GCF_003691675_PROKKA_01281:0.0173975,(GCF_002008305_PROKKA_01571:0.00245108,GCF_023573625_PROKKA_01498:0.00245133)n3:0.00507286)n2:0.0881036)n1:0.195866)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001285_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001285_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a81a1e4b0ce1b09de836ac99f996d448aad55ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001285_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01245:0.139693,(GCF_005280335_PROKKA_01352:0.0433539,(GCF_003691675_PROKKA_01282:0.00543846,(GCF_002008305_PROKKA_01572:0.0175932,GCF_023573625_PROKKA_01499:0.00581432)n3:0.00622622)n2:0.0680141)n1:0.139693)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001286_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001286_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e4c89fab393f76094c9f29a9b0d74a293a719b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001286_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01244:0.0634993,(GCF_005280335_PROKKA_01351:0.0406934,(GCF_003691675_PROKKA_01283:0.00334666,(GCF_002008305_PROKKA_01573:5e-09,GCF_023573625_PROKKA_01500:0.0100142)n3:0.00661329)n2:0.0614784)n1:0.0634993)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001288_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001288_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..331361313b994ed2dbeea81ef4cc13bd340689eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001288_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01242:0.0676714,(GCF_005280335_PROKKA_01349:0.135904,((GCF_002008305_PROKKA_01575:0,GCF_003691675_PROKKA_01285:0)n3:5e-09,GCF_023573625_PROKKA_01502:0.00571433)n2:0.141086)n1:0.0676714)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001289_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001289_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..285371ceaa5eb16c14a8747a78ed834093662723
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001289_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01241:0.0850642,(GCF_005280335_PROKKA_01348:0.0855369,(GCF_002008305_PROKKA_01576:0.00333276,(GCF_003691675_PROKKA_01286:0.0031847,GCF_023573625_PROKKA_01503:5e-09)n3:0.00304149)n2:0.134237)n1:0.0850642)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001290_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001290_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1829a84352b5995f70f6753f60b85e336970a8f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001290_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01239:0.0647066,(GCF_005280335_PROKKA_01346:0.100699,(GCF_023573625_PROKKA_01504:0.0108372,(GCF_002008305_PROKKA_01577:0.003606,GCF_003691675_PROKKA_01287:0.0107533)n3:6e-09)n2:0.058401)n1:0.0647066)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001293_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001293_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..171f5ba7b5872905926cc3f506e8b37546441cdc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001293_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01236:2.5e-09,(GCF_005280335_PROKKA_01343:0.169446,(GCF_002008305_PROKKA_01580:0.00935222,(GCF_003691675_PROKKA_01290:5e-09,GCF_023573625_PROKKA_01507:0.00311685)n3:0.00936661)n2:0.00935409)n1:2.5e-09)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001294_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001294_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cab707d12bfab57461acf44ea0cc19bf0a4bba03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001294_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01233:0.191818,(GCF_005280335_PROKKA_01335:0.0346778,(GCF_002008305_PROKKA_01587:0.00463783,(GCF_003691675_PROKKA_01298:0.00232032,GCF_023573625_PROKKA_01514:5e-09)n3:6e-09)n2:0.0333132)n1:0.191818)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001295_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001295_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..af62b82b857b2f8de132848e3268d4bc0de45c93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001295_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01231:0.191772,(GCF_005280335_PROKKA_01333:0.0204634,(GCF_003691675_PROKKA_01300:0.0143808,(GCF_002008305_PROKKA_01589:0.00172258,GCF_023573625_PROKKA_01516:0.00171604)n3:0.0115931)n2:0.0318377)n1:0.191772)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001296_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001296_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56d7ab3657e13a3219b648570578ea331226a391
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001296_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01219:0.0708366,(GCF_005280335_PROKKA_01300:0.122236,((GCF_002008305_PROKKA_01591:0,GCF_003691675_PROKKA_01303:0)n3:0.0061057,GCF_023573625_PROKKA_01518:0.0198563)n2:0.0843595)n1:0.0708366)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001298_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001298_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f52de944f8cdba7794688eeb81a55f6a9f8bcd11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001298_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01214:0.0100194,(GCF_023573625_PROKKA_01522:0.0245307,(GCF_003691675_PROKKA_01307:0.00282463,(GCF_002008305_PROKKA_01595:0.00906148,GCF_005280335_PROKKA_01301:0.390601)n3:0.0105006)n2:0.00748229)n1:0.0100194)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001300_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001300_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45e170a1ac9378bee1d796ff895270f31dcebe5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001300_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01204:2.5e-09,(GCF_005280335_PROKKA_01295:6e-09,((GCF_002008305_PROKKA_01598:0,GCF_003691675_PROKKA_01310:0)n3:0.014878,GCF_023573625_PROKKA_01525:0.0148145)n2:0.0148617)n1:2.5e-09)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001307_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001307_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3dfaf6404b0256746ea6e60487c14858e26675f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001307_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01191:0.022789,(GCF_003691675_PROKKA_01323:0.0345515,((GCF_002008305_PROKKA_01612:0.0436265,GCF_005280335_PROKKA_01286:0.028456)n3:0.0135945,GCF_023573625_PROKKA_01538:0.0350076)n2:0.00833802)n1:0.022789)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001308_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001308_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5a3dec4e14b6b6cc2f94f424ba713c2fd11a64c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001308_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00838:0.00890765,(GCF_003691675_PROKKA_01648:0.0141912,(GCF_005280335_PROKKA_00900:0.0164974,(GCF_002008305_PROKKA_01620:1.5622,GCF_023573625_PROKKA_01879:0.0102557)n3:0.00931413)n2:0.00539971)n1:0.00890765)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001310_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001310_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ad44a8bf3ef165a9b4c29942611bfa730b04dc6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001310_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01176:0.0214355,(GCF_005280335_PROKKA_01268:0.163187,(GCF_003691675_PROKKA_01333:0.024967,(GCF_002008305_PROKKA_01628:0.0108103,GCF_023573625_PROKKA_01557:0.0160486)n3:0.0255577)n2:0.0646843)n1:0.0214355)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001311_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001311_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ba000677c75cf07fc66c7c0e59a2800e88e5210
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001311_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01175:0.170201,(GCF_005280335_PROKKA_01267:0.0720617,(GCF_023573625_PROKKA_01558:0.0067848,(GCF_002008305_PROKKA_01629:0.0136182,GCF_003691675_PROKKA_01334:0.00681012)n3:5e-09)n2:0.0714778)n1:0.170201)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001313_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001313_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54250bad62df22e6f3bfab057f517deac1d3e773
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001313_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00143:0.85591,GCF_005280335_PROKKA_01265:0.035196)n1:0.0208604,(GCF_003691675_PROKKA_01336:0.0081715,(GCF_002008305_PROKKA_01631:0.00965706,GCF_023573625_PROKKA_01560:0.0069874)n3:0.0175218)n2:0.0208604)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001315_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001315_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b1bd563284afc6a5ec492e66392d836e72532405
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001315_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01171:0.172565,(GCF_005280335_PROKKA_01262:0.370657,(GCF_023573625_PROKKA_01562:0.0210122,(GCF_002008305_PROKKA_01633:0.0110665,GCF_003691675_PROKKA_01338:5e-09)n3:0.00424513)n2:0.337219)n1:0.172565)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001316_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001316_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f00552d2de1c87973ec1c126c85224e92f576cfd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001316_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01170:0.0730982,(GCF_005280335_PROKKA_01261:0.176779,(GCF_002008305_PROKKA_01634:5e-09,(GCF_003691675_PROKKA_01339:0.011085,GCF_023573625_PROKKA_01563:0.00660721)n3:0.00219545)n2:0.0997349)n1:0.0730982)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001321_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001321_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1cf0ef3a4d257d4087d81530597876f8a01b281a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001321_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01164:0.13395,(GCF_005280335_PROKKA_01255:0.0891127,(GCF_003691675_PROKKA_01345:5e-09,(GCF_002008305_PROKKA_01640:5e-09,GCF_023573625_PROKKA_01569:0.00643902)n3:0.0195746)n2:0.0561275)n1:0.13395)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001322_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001322_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89bf0868c2b4986467aa59add53595390473f2ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001322_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01163:0.26117,(GCF_005280335_PROKKA_01254:0.0808459,(GCF_002008305_PROKKA_01641:5e-09,(GCF_003691675_PROKKA_01346:0.0166001,GCF_023573625_PROKKA_01571:0.00496055)n3:0.00163417)n2:0.105365)n1:0.26117)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001324_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001324_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7eefeaaa59fd208d46edf020f4a9162200d01026
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001324_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01161:0.508917,(GCF_005280335_PROKKA_01250:0.185647,(GCF_003691675_PROKKA_01348:0.0290126,(GCF_002008305_PROKKA_01643:0.00630128,GCF_023573625_PROKKA_01573:0.00954301)n3:0.0105887)n2:0.170495)n1:0.508917)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001328_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001328_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66a52028a4dad649f1a22f5771cd712291b15998
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001328_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01157:0.26835,(GCF_005280335_PROKKA_01246:0.156547,(GCF_023573625_PROKKA_01577:0.0147236,(GCF_002008305_PROKKA_01647:0.0396981,GCF_003691675_PROKKA_01352:0.0313445)n3:0.0134367)n2:0.318642)n1:0.26835)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001329_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001329_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c1c92030544e231bca4f98cdd3293de790120be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001329_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01156:0.134863,(GCF_005280335_PROKKA_01245:0.059677,(GCF_003691675_PROKKA_01353:0.00355935,(GCF_002008305_PROKKA_01648:0.00306587,GCF_023573625_PROKKA_01578:0.00949883)n3:0.00513881)n2:0.0531638)n1:0.134863)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001330_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001330_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cecd29767ac39d58e07fff453394749bbba3be57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001330_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01155:0.047574,(GCF_005280335_PROKKA_01244:0.0159765,(GCF_002008305_PROKKA_01649:0.0018602,(GCF_003691675_PROKKA_01354:0.00370881,GCF_023573625_PROKKA_01579:0.0110448)n3:0.00370772)n2:0.0128021)n1:0.047574)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001332_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001332_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86020197766f9c689149e6e05a330614c3c6165e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001332_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01153:0.147558,(GCF_005280335_PROKKA_01242:0.126381,(GCF_003691675_PROKKA_01356:5e-09,(GCF_002008305_PROKKA_01651:0.0126926,GCF_023573625_PROKKA_01581:5e-09)n3:0.0126986)n2:0.102079)n1:0.147558)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001333_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001333_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..538527b8d2dae99e5b12e8b9232877cdeb95e186
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001333_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01152:0.0469309,(GCF_005280335_PROKKA_01241:0.0180416,(GCF_003691675_PROKKA_01357:0.00521568,(GCF_002008305_PROKKA_01652:0.00782719,GCF_023573625_PROKKA_01582:0.00260776)n3:6e-09)n2:0.027603)n1:0.0469309)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001335_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001335_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..303296caf775c02bee07ecbc0530d006131566f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001335_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01150:0.0609631,(GCF_005280335_PROKKA_01239:0.0730421,(GCF_003691675_PROKKA_01359:5e-09,(GCF_002008305_PROKKA_01654:0.0123661,GCF_023573625_PROKKA_01584:5e-09)n3:0.00204321)n2:0.0606432)n1:0.0609631)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001337_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001337_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..078867d878251c016823e2b17ab4ecae2229fa82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001337_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01146:0.00197112,(GCF_023573625_PROKKA_01589:0.00394731,((GCF_002008305_PROKKA_01659:5e-09,GCF_005280335_PROKKA_01235:0.0525677)n3:0.00393635,GCF_003691675_PROKKA_01364:0.00394732)n2:5e-09)n1:0.00197112)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001339_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001339_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2233de0bc51477589d5c3dfcd87e511c3709cb6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001339_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01144:0.0034898,(GCF_002008305_PROKKA_01661:0.00438629,(GCF_023573625_PROKKA_01591:0.0069951,(GCF_003691675_PROKKA_01366:0.0021366,GCF_005280335_PROKKA_01233:0.101592)n3:0.0108042)n2:0.00283103)n1:0.0034898)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001342_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001342_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b50a7ad18f5529e35116ad933d921fe2930591c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001342_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01141:0.0602431,(GCF_005280335_PROKKA_01230:0.0706628,(GCF_002008305_PROKKA_01664:6e-09,(GCF_023573625_PROKKA_01594:0.0074246,GCF_003691675_PROKKA_01369:0.00991095)n3:0.00242944)n2:0.256596)n1:0.0602431)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001344_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001344_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64bcce354debebf3dd80897e7df3d5a0c561d0c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001344_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01139:0.0799094,(GCF_005280335_PROKKA_01228:0.0171285,(GCF_002008305_PROKKA_01666:0.00389106,(GCF_003691675_PROKKA_01371:0.00857961,GCF_023573625_PROKKA_01596:0.00288942)n3:0.0134787)n2:0.0182601)n1:0.0799094)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001346_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001346_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..319128c7c962bca63f822b6a53128c69e777ef75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001346_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01137:0.0522379,(GCF_005280335_PROKKA_01226:0.123083,(GCF_023573625_PROKKA_01598:0.00590887,(GCF_003691675_PROKKA_01373:0.014287,GCF_002008305_PROKKA_01668:0.00591196)n3:0.00285271)n2:0.0582038)n1:0.0522379)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001349_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001349_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea8f4761fb61e810b993f977806663811e672bbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001349_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01134:0.118183,(GCF_005280335_PROKKA_01206:0.0169284,(GCF_023573625_PROKKA_01602:0.0140658,(GCF_002008305_PROKKA_01672:0.00449376,GCF_003691675_PROKKA_01377:0.00903995)n3:0.00398435)n2:0.056434)n1:0.118183)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001350_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001350_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf2f7ff2d098875a75fd843dba93880c2243315d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001350_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01133:0.13277,(GCF_005280335_PROKKA_01205:0.0290724,(GCF_023573625_PROKKA_01603:0.0109244,(GCF_002008305_PROKKA_01673:5e-09,GCF_003691675_PROKKA_01378:0.00947935)n3:0.0135682)n2:0.0643532)n1:0.13277)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001351_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001351_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4be335004dedb21c86b557dda27a900fdbf1627
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001351_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01132:0.164251,(GCF_005280335_PROKKA_01204:0.105729,(GCF_023573625_PROKKA_01604:6e-09,(GCF_002008305_PROKKA_01674:0.00748748,GCF_003691675_PROKKA_01379:0.00736767)n3:0.0148064)n2:0.110484)n1:0.164251)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001352_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001352_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..876b2bf20d51d1c547b8faa580a19d667aa1a19f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001352_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01131:0.20364,(GCF_005280335_PROKKA_01203:0.100988,(GCF_002008305_PROKKA_01675:0.012573,(GCF_003691675_PROKKA_01380:0.0133499,GCF_023573625_PROKKA_01605:0.00933919)n3:0.00668585)n2:0.110854)n1:0.20364)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001353_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001353_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..929a8cc103314f9da725d0a74642ecfc1baec61e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001353_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01130:0.106361,(GCF_005280335_PROKKA_01202:0.0343416,((GCF_002008305_PROKKA_01676:0,GCF_003691675_PROKKA_01381:0)n3:5e-09,GCF_023573625_PROKKA_01606:0.00777584)n2:0.0224525)n1:0.106361)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001354_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001354_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4006d54b14dbe97b18b3c665d4febc871008f1f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001354_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01129:0.274659,(GCF_005280335_PROKKA_01201:0.159068,(GCF_023573625_PROKKA_01607:0.0244747,(GCF_002008305_PROKKA_01677:0.00477564,GCF_003691675_PROKKA_01382:0.0037408)n3:0.0232349)n2:0.131586)n1:0.274659)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001357_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001357_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e6b2d367aaa09f4a04df751ce9bf3b281e377ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001357_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01125:0.0993954,(GCF_005280335_PROKKA_01196:0.0347094,((GCF_002008305_PROKKA_01682:0,GCF_023573625_PROKKA_01611:0)n3:5e-09,GCF_003691675_PROKKA_01386:0.00285287)n2:0.0701392)n1:0.0993954)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001360_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001360_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e9a30f7ba7a0061f7358481dbf12b49e5e3fa538
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001360_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01122:0.0576356,(GCF_005280335_PROKKA_01192:0.0233384,(GCF_023573625_PROKKA_01615:5e-09,(GCF_002008305_PROKKA_01686:5e-09,GCF_003691675_PROKKA_01390:0.00218236)n3:0.00218198)n2:0.025086)n1:0.0576356)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001361_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001361_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e419f30c18210fa4691f789cdef2790dcc2dda1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001361_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01120:0.0687307,(GCF_005280335_PROKKA_01190:0.522321,(GCF_002008305_PROKKA_01688:0.0110246,(GCF_003691675_PROKKA_01392:6e-09,GCF_023573625_PROKKA_01617:0.0353146)n3:0.0387841)n2:0.0139071)n1:0.0687307)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001365_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001365_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..455ca12f93153eef370198f22c4284881dc0f60e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001365_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01116:0.0201951,(GCF_005280335_PROKKA_01186:0.021322,((GCF_002008305_PROKKA_01692:0,GCF_023573625_PROKKA_01621:0)n3:0.0039184,GCF_003691675_PROKKA_01399:5e-09)n2:0.0307359)n1:0.0201951)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001367_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001367_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a66fc959c735631639ad34b988e67bb8b677dfa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001367_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01114:0.00710484,((GCF_002008305_PROKKA_01694:0,GCF_003691675_PROKKA_01401:0,GCF_023573625_PROKKA_01623:0)n2:0.0140217,GCF_005280335_PROKKA_01184:5e-09)n1:0.00710484)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001369_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001369_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21b7a9efc60e4897b195c9b9c222f44a066184cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001369_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01696:0,GCF_003691675_PROKKA_01403:0,GCF_005280335_PROKKA_01182:0,GCF_023573625_PROKKA_01625:0)n1:0.014731,GCF_020097155_PROKKA_01112:0.014731)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001373_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001373_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8bed9e4a1a042cbe83f62b64df402b54ddfa685
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001373_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01108:0.0526976,(GCF_005280335_PROKKA_01178:0.0301225,((GCF_002008305_PROKKA_01700:0,GCF_003691675_PROKKA_01407:0)n3:0.00677242,GCF_023573625_PROKKA_01629:0.00245735)n2:0.0446285)n1:0.0526976)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001374_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001374_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1849839ae2f42193eedf52b2208acf28aad87d3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001374_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01107:0.0456382,((GCF_002008305_PROKKA_01701:0,GCF_003691675_PROKKA_01408:0,GCF_023573625_PROKKA_01630:0)n2:0.0134138,GCF_005280335_PROKKA_01177:0.00649181)n1:0.0456382)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001379_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001379_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ea6855183eb36a752f8289f77b1f728d13c972c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001379_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01102:0.0191937,((GCF_002008305_PROKKA_01706:0,GCF_003691675_PROKKA_01413:0,GCF_023573625_PROKKA_01635:0)n2:5e-09,GCF_005280335_PROKKA_01172:0.00748055)n1:0.0191937)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001380_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001380_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e5d4f329a90e0c8632efa2441f2af648ecadc11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001380_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01101:0.015316,((GCF_002008305_PROKKA_01707:0,GCF_003691675_PROKKA_01414:0,GCF_023573625_PROKKA_01636:0)n2:0.0137867,GCF_005280335_PROKKA_01171:0.0131278)n1:0.015316)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001381_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001381_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d649d09f90d1da30d52c96e1ed70daa67f2e8947
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001381_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01100:0.0181405,((GCF_002008305_PROKKA_01708:0,GCF_003691675_PROKKA_01415:0,GCF_023573625_PROKKA_01637:0)n2:0.0174217,GCF_005280335_PROKKA_01170:0.0174001)n1:0.0181405)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001382_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001382_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c874798170fd08b6489746109ab24cfdf243c31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001382_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01709:0,GCF_003691675_PROKKA_01416:0,GCF_005280335_PROKKA_01169:0,GCF_023573625_PROKKA_01638:0)n1:0.00803552,GCF_020097155_PROKKA_01099:0.00803552)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001384_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001384_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb903cc5fdc33aa9f46fb262d69613007913d8b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001384_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01097:0.0290774,((GCF_002008305_PROKKA_01711:0,GCF_003691675_PROKKA_01418:0,GCF_023573625_PROKKA_01640:0)n2:0.0107794,GCF_005280335_PROKKA_01167:0.0219622)n1:0.0290774)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001385_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001385_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8fd1367d009a69490e1f14fe824d2850427c07f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001385_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01096:0.00752911,((GCF_002008305_PROKKA_01712:0,GCF_003691675_PROKKA_01419:0,GCF_023573625_PROKKA_01641:0)n2:0.0147647,GCF_005280335_PROKKA_01166:0.00722957)n1:0.00752911)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001389_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001389_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9abdce790711c05a9811f4d264a977446f4b63e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001389_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01716:0,GCF_003691675_PROKKA_01423:0,GCF_005280335_PROKKA_01162:0,GCF_023573625_PROKKA_01645:0)n1:0.0107628,GCF_020097155_PROKKA_01092:0.0107628)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001391_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001391_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..471e0aff9669d161d13c8508a2e169c49759eece
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001391_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01090:0.0183637,((GCF_002008305_PROKKA_01718:0,GCF_003691675_PROKKA_01425:0,GCF_023573625_PROKKA_01647:0)n2:0.0136414,GCF_005280335_PROKKA_01160:5e-09)n1:0.0183637)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001394_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001394_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1f381fe9bb176689e311c0da9d29b8554ec4608
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001394_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01087:0.165641,(GCF_005280335_PROKKA_01157:0.0991567,((GCF_002008305_PROKKA_01721:0,GCF_023573625_PROKKA_01650:0)n3:5e-09,GCF_003691675_PROKKA_01428:0.0134996)n2:0.226143)n1:0.165641)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001396_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001396_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c3c23812bb0554dbd30ea4135b9ffe6f6a57def
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001396_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01085:0.00855744,(GCF_005280335_PROKKA_01155:0.00697376,((GCF_002008305_PROKKA_01723:0,GCF_023573625_PROKKA_01652:0)n3:5e-09,GCF_003691675_PROKKA_01430:0.00247049)n2:0.0109407)n1:0.00855744)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001398_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001398_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f482c7e4a80100b063166188bdf6ba522ca4e616
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001398_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01083:0.00318706,((GCF_002008305_PROKKA_01725:0,GCF_003691675_PROKKA_01432:0,GCF_023573625_PROKKA_01654:0)n2:0.00636814,GCF_005280335_PROKKA_01153:5e-09)n1:0.00318706)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001399_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001399_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05a21e3ff5dff34b91cdd2a0132ac26f99506ff7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001399_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01082:0.00805553,(GCF_005280335_PROKKA_01152:5e-09,(GCF_002008305_PROKKA_01726:5e-09,(GCF_003691675_PROKKA_01433:0,GCF_023573625_PROKKA_01655:0)n3:0.00800405)n2:0.00802023)n1:0.00805553)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001400_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001400_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7df5d413fa7cb3552061a1f9deea706e160b779
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001400_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01080:0.0231785,(GCF_005280335_PROKKA_01151:0.0185099,((GCF_002008305_PROKKA_01727:0,GCF_023573625_PROKKA_01656:0)n3:0.0007615,GCF_003691675_PROKKA_01434:0.00076739)n2:0.0100749)n1:0.0231785)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001401_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001401_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cfaac29ffb054fda4032a7be59d8984627529bb2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001401_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01079:0.016172,((GCF_002008305_PROKKA_01728:0,GCF_003691675_PROKKA_01435:0,GCF_023573625_PROKKA_01657:0)n2:0.010106,GCF_005280335_PROKKA_01150:0.0151444)n1:0.016172)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001402_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001402_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..593f54aca4479b601a7baa2394b87babd91a1864
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001402_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01078:0.0159406,(GCF_005280335_PROKKA_01149:0.0158221,(GCF_002008305_PROKKA_01729:0.0077003,(GCF_003691675_PROKKA_01436:0,GCF_023573625_PROKKA_01658:0)n3:5e-09)n2:0.00762115)n1:0.0159406)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001403_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001403_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b399fc7144659d8383032b55143b8aa20766b48b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001403_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01077:0.0352705,(GCF_005280335_PROKKA_01148:0.0110735,(GCF_002008305_PROKKA_01730:0.00562383,(GCF_003691675_PROKKA_01437:0,GCF_023573625_PROKKA_01659:0)n3:5e-09)n2:0.0173436)n1:0.0352705)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001405_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001405_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b158673f87eb25b5d1d65bc42dcb9ea33d8c6e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001405_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01075:0.0235205,((GCF_002008305_PROKKA_01732:0,GCF_003691675_PROKKA_01439:0,GCF_023573625_PROKKA_01661:0)n2:0.0174227,GCF_005280335_PROKKA_01146:0.0100587)n1:0.0235205)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001406_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001406_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e141a46b5b64af7dc4fe534ff7b019c89687f49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001406_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01074:0.0735912,(GCF_005280335_PROKKA_01145:0.0781166,(GCF_003691675_PROKKA_01440:0.0070265,(GCF_002008305_PROKKA_01733:0.00283083,GCF_023573625_PROKKA_01662:0.00304724)n3:0.00474651)n2:0.03243)n1:0.0735912)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001408_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001408_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22ebc6cbc27e403f554f6b4bfb01573191de4d49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001408_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01071:0.0312759,(GCF_005280335_PROKKA_01142:0.0574975,(GCF_023573625_PROKKA_01665:0.00299714,(GCF_002008305_PROKKA_01736:0.00483115,GCF_003691675_PROKKA_01443:5e-09)n3:0.00912154)n2:0.0448412)n1:0.0312759)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001410_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001410_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f08a01a760a76d0b811b64db6c4eed98773014f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001410_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01069:0.110291,(GCF_005280335_PROKKA_01140:0.10962,(GCF_003691675_PROKKA_01445:0.0133082,(GCF_002008305_PROKKA_01738:0.00960326,GCF_023573625_PROKKA_01667:0.0119071)n3:0.0157528)n2:0.102445)n1:0.110291)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001411_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001411_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6fbcc9379bd80205a1fc25d8eb964727e336ba66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001411_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01068:0.210395,(GCF_005280335_PROKKA_01139:0.183206,(GCF_003691675_PROKKA_01446:0.0128291,(GCF_002008305_PROKKA_01739:0.00578693,GCF_023573625_PROKKA_01668:0.00284663)n3:0.0045632)n2:0.242818)n1:0.210395)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001414_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001414_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ccacbce5bfa1753d1fbb41a3cc0dc76d0c4b567b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001414_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01064:0.131339,(GCF_005280335_PROKKA_01135:0.0768288,((GCF_002008305_PROKKA_01742:0,GCF_003691675_PROKKA_01449:0)n3:0.00526125,GCF_023573625_PROKKA_01671:0.00233347)n2:0.0465323)n1:0.131339)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001417_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001417_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1470bf790e052c40198f30a70d6ba832990dd69b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001417_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01061:0.189191,(GCF_005280335_PROKKA_01132:0.10477,((GCF_002008305_PROKKA_01745:0,GCF_003691675_PROKKA_01452:0)n3:0.00772435,GCF_023573625_PROKKA_01674:0.00378359)n2:0.0467711)n1:0.189191)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001421_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001421_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4256206509d40b35db5269321dcb53174cff819c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001421_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01053:0.0506444,((GCF_002008305_PROKKA_01749:0,GCF_003691675_PROKKA_01456:0,GCF_023573625_PROKKA_01678:0)n2:0.00399409,GCF_005280335_PROKKA_01128:0.0303528)n1:0.0506444)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001422_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001422_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2c9dabfc9b2f9036861062750ff89dabb386b08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001422_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01052:0.14964,(GCF_005280335_PROKKA_01127:0.00954061,((GCF_002008305_PROKKA_01750:0,GCF_003691675_PROKKA_01457:0)n3:0.00970219,GCF_023573625_PROKKA_01679:0.00608392)n2:0.0108529)n1:0.14964)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001423_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001423_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ef5edeff7f9a1f2418b99d0d053537e920297a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001423_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01051:0.166208,(GCF_005280335_PROKKA_01126:0.0584212,((GCF_002008305_PROKKA_01751:0,GCF_003691675_PROKKA_01458:0)n3:0.00495213,GCF_023573625_PROKKA_01680:0.0353634)n2:0.0997258)n1:0.166208)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001426_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001426_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8469de4fb488b2551d215375ed93b458b09bc1f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001426_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01048:0.138738,(GCF_005280335_PROKKA_01123:0.0422238,((GCF_002008305_PROKKA_01754:0,GCF_003691675_PROKKA_01461:0)n3:5e-09,GCF_023573625_PROKKA_01683:0.0117601)n2:0.0590642)n1:0.138738)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001427_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001427_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1dcd3f4cc99aa392efd6bc4d2f21ad9c6a4db08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001427_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01047:0.0964928,(GCF_005280335_PROKKA_01122:0.0515108,((GCF_002008305_PROKKA_01755:0,GCF_003691675_PROKKA_01462:0)n3:0.00631711,GCF_023573625_PROKKA_01684:5e-09)n2:0.0315166)n1:0.0964928)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001429_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001429_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc7ab574953deb4600cc95fa2c2f4e0f53d16d99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001429_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01043:0.104502,(GCF_005280335_PROKKA_01118:0.041461,((GCF_002008305_PROKKA_01759:0,GCF_003691675_PROKKA_01466:0)n3:0.00299256,GCF_023573625_PROKKA_01688:0.00265238)n2:0.0442249)n1:0.104502)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001430_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001430_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4b07a9e17f76f396dab673ea1f8ccd14bc41315
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001430_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01042:0.314184,(GCF_005280335_PROKKA_01117:0.130966,((GCF_002008305_PROKKA_01760:0,GCF_003691675_PROKKA_01467:0)n3:0.0140853,GCF_023573625_PROKKA_01689:0.0048041)n2:0.032725)n1:0.314184)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001431_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001431_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5972b3848b4b82e676a97047077e6a374fb1d2fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001431_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01041:0.0440241,(GCF_005280335_PROKKA_01116:0.0527297,((GCF_002008305_PROKKA_01761:0,GCF_003691675_PROKKA_01468:0)n3:0.0051896,GCF_023573625_PROKKA_01690:0.0022394)n2:0.0456834)n1:0.0440241)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001434_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001434_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e81516c055c4dcb6c670e3127127bb0116fec26e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001434_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01038:0.150097,(GCF_005280335_PROKKA_01113:0.0679992,(GCF_002008305_PROKKA_01764:0.0249935,(GCF_003691675_PROKKA_01471:0.0159561,GCF_023573625_PROKKA_01693:0.0103841)n3:0.00572682)n2:0.0571166)n1:0.150097)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001436_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001436_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..72e950812fa4ce18e734a3b58c2582b3b607453c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001436_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01035:0.0460569,(GCF_005280335_PROKKA_01109:5e-09,(GCF_003691675_PROKKA_01475:0.00587951,(GCF_002008305_PROKKA_01768:0.00587723,GCF_023573625_PROKKA_01697:5e-09)n3:5e-09)n2:0.0119846)n1:0.0460569)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001438_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001438_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37e5d408ad349cbd3f49249ccb3e31e9cf533dd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001438_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01033:0.110676,(GCF_005280335_PROKKA_01107:0.0534278,(GCF_002008305_PROKKA_01770:0.0118974,(GCF_003691675_PROKKA_01477:0.00949621,GCF_023573625_PROKKA_01699:0.00236989)n3:5e-09)n2:0.0790075)n1:0.110676)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001442_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001442_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e954d1fead06b895722cbc06bae982039089e0f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001442_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01026:0.0989543,(GCF_005280335_PROKKA_01102:0.0819327,(GCF_023573625_PROKKA_01704:0.00497214,(GCF_002008305_PROKKA_01775:5e-09,GCF_003691675_PROKKA_01482:0.005576)n3:0.00624373)n2:0.0356516)n1:0.0989543)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001443_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001443_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..062f72f6d8a5394a0faab1f58e1475b30323174b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001443_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01025:0.0887011,(GCF_005280335_PROKKA_01101:0.0418414,(GCF_002008305_PROKKA_01776:0.0065087,(GCF_003691675_PROKKA_01483:0.00216206,GCF_023573625_PROKKA_01705:0.00431476)n3:6e-09)n2:0.0729685)n1:0.0887011)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001445_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001445_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4302e14984645543cc64962dab91dd320e24fe2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001445_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01020:0.370727,(GCF_005280335_PROKKA_01097:0.169566,(GCF_003691675_PROKKA_01488:0.00435101,(GCF_002008305_PROKKA_01781:5e-09,GCF_023573625_PROKKA_01710:0.00352199)n3:0.00992183)n2:0.0860004)n1:0.370727)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001448_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001448_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c19c07beac45e0aabfae5feaaa985232e0bdd91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001448_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01017:0.0490157,(GCF_005280335_PROKKA_01094:0.0398888,(GCF_002008305_PROKKA_01784:5e-09,(GCF_003691675_PROKKA_01491:0.0049679,GCF_023573625_PROKKA_01713:0.00247638)n3:0.00247495)n2:0.0263908)n1:0.0490157)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001450_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001450_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9bc44f8dea1d411b169fea05b431eb5f69598ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001450_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01015:0.134621,((GCF_003691675_PROKKA_01494:0.00200052,GCF_023573625_PROKKA_01716:5e-09)n2:5e-09,(GCF_002008305_PROKKA_01787:0.00602665,GCF_005280335_PROKKA_01089:0.00435728)n3:0.00199761)n1:0.134621)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001451_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001451_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fbed9dbd28f4de3a654ecaf9f3ded884906eaacc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001451_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01013:0.115939,(GCF_005280335_PROKKA_01078:0.0521519,(GCF_003691675_PROKKA_01495:0.00447902,(GCF_023573625_PROKKA_01717:0.0133306,GCF_002008305_PROKKA_01798:0.00266762)n3:0.00218414)n2:0.0377683)n1:0.115939)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001454_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001454_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39b3ba3b674a3f7275128da08875c3fa86d477a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001454_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01008:0.00189306,((GCF_003691675_PROKKA_01498:0.0143403,GCF_005280335_PROKKA_01072:0.0160972)n2:0.0393309,(GCF_002008305_PROKKA_01801:0.0203861,GCF_023573625_PROKKA_01722:0.0154193)n3:0.00363735)n1:0.00189306)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001456_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001456_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c24b3b95078daa6dfe74b95709a10a10cf976265
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001456_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01006:0.147925,((GCF_003691675_PROKKA_01500:0.0120144,GCF_005280335_PROKKA_01070:5e-09)n2:0.194549,(GCF_002008305_PROKKA_01803:0.0433827,GCF_023573625_PROKKA_01724:0.0398436)n3:0.127672)n1:0.147925)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001457_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001457_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..32b3e212f7781c410f76d55598c016dd43f05eff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001457_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01005:0.196099,((GCF_002008305_PROKKA_01804:5e-09,GCF_023573625_PROKKA_01725:0.0237392)n2:0.161956,(GCF_003691675_PROKKA_01501:5e-09,GCF_005280335_PROKKA_01069:0.00775009)n3:0.098726)n1:0.196099)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001459_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001459_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd264d3c10880a04a5ffc7ce3a72dd4e7db6403b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001459_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00999:0.316629,(GCF_005280335_PROKKA_01064:0.303659,(GCF_003691675_PROKKA_01507:0.00839226,(GCF_023573625_PROKKA_01731:0.0168585,GCF_002008305_PROKKA_01810:0.0253582)n3:5e-09)n2:0.345084)n1:0.316629)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001460_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001460_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c678c10e0c014e887f376492cad340b273ac1735
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001460_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00998:0.1048,(GCF_005280335_PROKKA_01063:0.0937422,(GCF_002008305_PROKKA_01811:0.0134533,(GCF_003691675_PROKKA_01508:5e-09,GCF_023573625_PROKKA_01732:0.02273)n3:0.0208734)n2:0.0361593)n1:0.1048)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001465_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001465_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de1109247a4ed9d7cf7cc77d4cc427384886b725
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001465_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00992:0.120287,(GCF_005280335_PROKKA_01054:0.186738,(GCF_003691675_PROKKA_01513:0.00457048,(GCF_002008305_PROKKA_01816:0.0103953,GCF_023573625_PROKKA_01737:5e-09)n3:0.00583528)n2:0.23644)n1:0.120287)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001466_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001466_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c253c0abd5fcd3fc910d342150a20167eef2d93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001466_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00991:0.0977051,(GCF_005280335_PROKKA_01053:0.0687596,(GCF_002008305_PROKKA_01817:0.003338,(GCF_003691675_PROKKA_01514:0.0375483,GCF_023573625_PROKKA_01738:5e-09)n3:0.00330913)n2:0.0677131)n1:0.0977051)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001467_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001467_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5da79355522e714379e8e8faa7f478898f12b6bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001467_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00990:0.0764292,(GCF_005280335_PROKKA_01052:0.0319671,(GCF_002008305_PROKKA_01818:0.00524434,(GCF_003691675_PROKKA_01515:5e-09,GCF_023573625_PROKKA_01739:0.00291239)n3:0.00943901)n2:0.0604158)n1:0.0764292)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001468_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001468_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd9bd7f1fd56d2f97288eeebd450d3299bd8e321
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001468_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00989:0.0427039,(GCF_005280335_PROKKA_01051:0.0366541,(GCF_002008305_PROKKA_01819:0.0031521,(GCF_003691675_PROKKA_01516:5e-09,GCF_023573625_PROKKA_01740:0.00208353)n3:0.0010177)n2:0.0297437)n1:0.0427039)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001469_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001469_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2d4ba31a8ce9f691668f0cb5fb847585d7ec0bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001469_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00988:0.0428587,(GCF_005280335_PROKKA_01049:0.10059,(GCF_023573625_PROKKA_01741:0.00376361,(GCF_003691675_PROKKA_01517:0.0184587,GCF_002008305_PROKKA_01820:0.00713136)n3:0.00180664)n2:0.0869942)n1:0.0428587)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001472_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001472_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71f9be8159007ab635ce69c9c5988e9d71fa6e16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001472_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00985:0.0724627,(GCF_005280335_PROKKA_01046:0.103729,(GCF_003691675_PROKKA_01520:0.0108004,(GCF_002008305_PROKKA_01823:0.00785112,GCF_023573625_PROKKA_01744:0.0045259)n3:0.0025311)n2:0.0579309)n1:0.0724627)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001473_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001473_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf6e29c577985ffc6797fcb263a07bbe3994ab33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001473_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00984:0.28559,(GCF_005280335_PROKKA_01045:0.247233,(GCF_003691675_PROKKA_01521:0.0193479,(GCF_002008305_PROKKA_01824:0.00636459,GCF_023573625_PROKKA_01745:0.0132211)n3:0.0201688)n2:0.0619865)n1:0.28559)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001474_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001474_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0898d2cdc559f452080e69c1d03e9e72f17a1db6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001474_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00983:0.254462,(GCF_005280335_PROKKA_01044:0.219477,(GCF_003691675_PROKKA_01522:0.0142531,(GCF_002008305_PROKKA_01825:0.00636345,GCF_023573625_PROKKA_01746:0.0191885)n3:0.0113411)n2:0.0612688)n1:0.254462)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001479_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001479_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b515c1799935f1fd808ae93a629725263832586b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001479_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00977:0.0722761,(GCF_005280335_PROKKA_01037:0.0645885,(GCF_003691675_PROKKA_01528:5e-09,(GCF_023573625_PROKKA_01752:0.0189709,GCF_002008305_PROKKA_01831:0.00377753)n3:0.00379003)n2:0.0655835)n1:0.0722761)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001481_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001481_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57d59eed16507e2c6b9fef8ccf89ef58c408b6c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001481_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01055:0.476591,(GCF_023573625_PROKKA_01754:0.036824,((GCF_005280335_PROKKA_01035:0.122953,GCF_003691675_PROKKA_01530:5e-09)n3:0.00588151,GCF_002008305_PROKKA_01833:0.0301716)n2:0.00762276)n1:0.476591)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001484_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001484_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..772275d8019a99293c3a480fcdf32382cd96acac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001484_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00972:0.00660554,((GCF_002008305_PROKKA_01837:0,GCF_003691675_PROKKA_01534:0,GCF_023573625_PROKKA_01758:0)n2:0.00435065,GCF_005280335_PROKKA_01031:0.00439085)n1:0.00660554)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001489_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001489_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d66140cbc4859d11ef21aaf702b04f3b4644f863
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001489_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00967:0.167404,(GCF_005280335_PROKKA_01026:0.108721,((GCF_002008305_PROKKA_01842:0,GCF_003691675_PROKKA_01539:0)n3:0.0127366,GCF_023573625_PROKKA_01763:0.0259337)n2:0.0720573)n1:0.167404)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001493_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001493_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c72bd98b2ece88d12db78e87d81d116949bd073
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001493_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00961:0.128098,(GCF_005280335_PROKKA_01019:0.0532312,(GCF_003691675_PROKKA_01545:0.00452582,(GCF_002008305_PROKKA_01849:5e-09,GCF_023573625_PROKKA_01769:0.0045208)n3:0.00452212)n2:0.0595122)n1:0.128098)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001495_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001495_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..529920e8dfa376729592fb337e714e9f1065affd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001495_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00959:0.220692,(GCF_005280335_PROKKA_01017:0.103401,(GCF_003691675_PROKKA_01547:0.00929309,(GCF_002008305_PROKKA_01851:0.00767083,GCF_023573625_PROKKA_01771:0.00768835)n3:0.00627446)n2:0.0478233)n1:0.220692)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001496_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001496_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..badbc7baac6b3d81403077f2db4b0921a987e5da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001496_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00957:0.0805046,(GCF_005280335_PROKKA_01015:0.193816,(GCF_023573625_PROKKA_01773:0.00323124,(GCF_002008305_PROKKA_01853:0.005389,GCF_003691675_PROKKA_01549:0.00830784)n3:0.00507813)n2:0.135992)n1:0.0805046)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001497_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001497_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0726ea8cde156bb17c8d8b9f7c637fc37389009
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001497_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00956:0.029765,(GCF_005280335_PROKKA_01014:0.108427,(GCF_002008305_PROKKA_01854:6e-09,(GCF_003691675_PROKKA_01550:0.0222434,GCF_023573625_PROKKA_01774:5e-09)n3:0.00738121)n2:0.0657596)n1:0.029765)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001499_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001499_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c9d864ff6ddda8afef68e8e1be4a2cb117b9f24
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001499_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00952:0.038693,(GCF_005280335_PROKKA_01008:0.0540753,(GCF_003691675_PROKKA_01552:0.00643967,(GCF_002008305_PROKKA_01856:0.00367731,GCF_023573625_PROKKA_01776:0.00184209)n3:0.000930012)n2:0.0781361)n1:0.038693)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001500_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001500_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea3c61fdf1e1550ceac8f5793bdac9469b9b118f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001500_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00951:0.0937729,(GCF_005280335_PROKKA_01007:0.0602797,(GCF_003691675_PROKKA_01553:0.00252671,(GCF_002008305_PROKKA_01857:0.00253226,GCF_023573625_PROKKA_01777:0.00758414)n3:0.00253609)n2:0.0285645)n1:0.0937729)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001503_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001503_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfe40eddd4c87d23c8051f7b5d3900dd2646f3a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001503_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00946:0.10113,(GCF_005280335_PROKKA_01003:0.0317419,((GCF_002008305_PROKKA_01860:0,GCF_003691675_PROKKA_01556:0)n3:0.0280713,GCF_023573625_PROKKA_01780:0.023954)n2:0.0232088)n1:0.10113)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001504_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001504_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e44cf63a141dc2d6a8a1a0aad33764c00642bd99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001504_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00999:0.201528,GCF_005280335_PROKKA_01510:1.43348)n1:0.0957332,(GCF_023573625_PROKKA_01781:0.00249237,(GCF_003691675_PROKKA_01557:0.015761,GCF_002008305_PROKKA_01861:0.00746158)n3:0.00678457)n2:0.0957332)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001505_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001505_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2bd256185897db67f9516e4fc7f1992511caccbe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001505_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00945:0.0805853,(GCF_005280335_PROKKA_00998:0.000400395,((GCF_002008305_PROKKA_01862:0,GCF_023573625_PROKKA_01782:0)n3:0.0151196,GCF_003691675_PROKKA_01558:0.0096625)n2:0.00879936)n1:0.0805853)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001507_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001507_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..701b6327bf429dba9084e06d3ff578e16a469b2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001507_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00935:0.523686,(GCF_005280335_PROKKA_00996:0.0219782,(GCF_003691675_PROKKA_01560:0.0257746,(GCF_002008305_PROKKA_01864:0.00463955,GCF_023573625_PROKKA_01784:0.016788)n3:0.0260216)n2:5e-09)n1:0.523686)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001508_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001508_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d4fa0c8fc0a715fe7f91d388762af1c4a271e02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001508_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00933:0.133215,(GCF_005280335_PROKKA_00995:0.081023,(GCF_003691675_PROKKA_01561:0.00491776,(GCF_002008305_PROKKA_01865:5e-09,GCF_023573625_PROKKA_01785:0.00722093)n3:0.0022837)n2:0.0699369)n1:0.133215)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001509_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001509_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a96eb066c542530c13ef55852249e520b346ef99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001509_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00932:0.0657472,(GCF_005280335_PROKKA_00994:0.0616671,(GCF_003691675_PROKKA_01562:5e-09,(GCF_002008305_PROKKA_01866:5e-09,GCF_023573625_PROKKA_01786:0.00726377)n3:0.00362611)n2:0.0364805)n1:0.0657472)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001510_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001510_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..602ecdb745cf15dc89803b7e94e54211ed83f8ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001510_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00931:0.0739883,(GCF_005280335_PROKKA_00993:0.0514349,(GCF_002008305_PROKKA_01867:0.00365852,(GCF_003691675_PROKKA_01563:5e-09,GCF_023573625_PROKKA_01787:0.00366722)n3:5e-09)n2:0.0479323)n1:0.0739883)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001512_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001512_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ba3cd7c0ee1de592f1441b60af12610390d4d66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001512_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00929:0.115833,(GCF_005280335_PROKKA_00991:0.101741,((GCF_002008305_PROKKA_01869:0,GCF_003691675_PROKKA_01565:0)n3:5e-09,GCF_023573625_PROKKA_01789:0.00402861)n2:0.0639693)n1:0.115833)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001513_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001513_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cfecdbaaa16590a6871f337654f77a07a2b1e2d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001513_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00928:0.268967,(GCF_005280335_PROKKA_00990:0.395322,(GCF_023573625_PROKKA_01790:0.0331953,(GCF_002008305_PROKKA_01870:0.0102537,GCF_003691675_PROKKA_01566:5e-09)n3:0.0107783)n2:0.132383)n1:0.268967)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001515_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001515_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f2c69167360c644a53cf0423f4feda7d0fb4194b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001515_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00925:0.314847,(GCF_005280335_PROKKA_00988:0.100207,(GCF_023573625_PROKKA_01792:0.0160046,(GCF_002008305_PROKKA_01872:0.0150223,GCF_003691675_PROKKA_01568:0.0242825)n3:0.0210339)n2:0.0727183)n1:0.314847)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001516_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001516_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ccaf2b469b2527d38c81834d9a793d3588c09ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001516_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00924:0.21835,((GCF_002008305_PROKKA_01873:0,GCF_003691675_PROKKA_01569:0)n2:0.0713297,(GCF_005280335_PROKKA_00987:0.00559964,GCF_023573625_PROKKA_01793:0.0104016)n3:0.0413788)n1:0.21835)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001518_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001518_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e5a45f863be8b779ee5c29de453609281c8be54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001518_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00922:0.130848,(GCF_005280335_PROKKA_00984:0.0190082,(GCF_003691675_PROKKA_01571:0.0269344,(GCF_002008305_PROKKA_01875:5e-09,GCF_023573625_PROKKA_01795:0.0176863)n3:0.00855212)n2:0.00854038)n1:0.130848)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001520_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001520_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e4eeb15a9491a3589c3af4f046fd93b86f9de7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001520_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00919:0.173444,(GCF_005280335_PROKKA_00979:0.0916472,((GCF_002008305_PROKKA_01880:0,GCF_003691675_PROKKA_01576:0)n3:0.0162062,GCF_023573625_PROKKA_01800:0.00709532)n2:0.146358)n1:0.173444)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001521_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001521_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..366a8955aec8ce21017333416bce9bf37aa57d26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001521_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00915:0.147562,(GCF_005280335_PROKKA_00977:0.0583976,(GCF_003691675_PROKKA_01577:0.0026697,(GCF_023573625_PROKKA_01801:0.0191495,GCF_002008305_PROKKA_01881:5e-09)n3:0.00816706)n2:0.0714193)n1:0.147562)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001523_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001523_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04ed392e5c95ec8f75e3309f4ddb01cef3ae807d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001523_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00913:0.199482,(GCF_005280335_PROKKA_00975:0.0295591,((GCF_002008305_PROKKA_01883:0,GCF_023573625_PROKKA_01803:0)n3:0.0224066,GCF_003691675_PROKKA_01579:0.00857464)n2:0.0723861)n1:0.199482)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001525_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001525_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a3bf2ef9c9f6ad4b79111dfa3037a5cb23a88f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001525_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00911:0.174782,(GCF_005280335_PROKKA_00973:0.0328679,((GCF_002008305_PROKKA_01885:0,GCF_023573625_PROKKA_01805:0)n3:0.0889941,GCF_003691675_PROKKA_01581:0.00767837)n2:0.0809452)n1:0.174782)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001526_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001526_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c38ce17f66cc6811ccb302f11fdc8c85a706d384
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001526_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00910:0.253324,(GCF_005280335_PROKKA_00972:0.0899985,((GCF_002008305_PROKKA_01886:0,GCF_023573625_PROKKA_01806:0)n3:0.112935,GCF_003691675_PROKKA_01582:0.00177466)n2:0.133061)n1:0.253324)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001529_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001529_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43b5edc1c98592e9fa1c080ece7bf46cea0a364c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001529_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00907:0.134195,(GCF_005280335_PROKKA_00969:0.0233625,(GCF_023573625_PROKKA_01809:0.00191752,(GCF_002008305_PROKKA_01889:0.00946837,GCF_003691675_PROKKA_01585:0.0229122)n3:0.0135213)n2:0.0349538)n1:0.134195)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001530_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001530_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..283fb50cd32de260fa0202ee2498e1723f7002e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001530_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00906:0.137887,(GCF_005280335_PROKKA_00968:0.0691011,(GCF_003691675_PROKKA_01586:0.0097337,(GCF_002008305_PROKKA_01890:0.00299367,GCF_023573625_PROKKA_01810:0.00377927)n3:0.0241759)n2:0.0495395)n1:0.137887)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001531_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001531_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74dc034ae69b5289f9327899c33334dde40046c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001531_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00905:0.070811,(GCF_005280335_PROKKA_00967:0.0244232,(GCF_003691675_PROKKA_01587:0.00526008,(GCF_002008305_PROKKA_01891:0.00522572,GCF_023573625_PROKKA_01811:5e-09)n3:5e-09)n2:0.0219858)n1:0.070811)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001532_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001532_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4ef83f0848721fb4bedacb165e0711a599a9a53f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001532_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00901:0.08551,(GCF_005280335_PROKKA_00962:0.106328,((GCF_002008305_PROKKA_01896:0,GCF_023573625_PROKKA_01816:0)n3:0.00302569,GCF_003691675_PROKKA_01592:0.00292646)n2:0.0835093)n1:0.08551)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001533_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001533_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6eb37e784b23b2c59c40c193904fa888b4e4a864
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001533_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00899:0.223679,(GCF_005280335_PROKKA_00959:0.0966268,(GCF_003691675_PROKKA_01595:5e-09,(GCF_002008305_PROKKA_01899:0.0250966,GCF_023573625_PROKKA_01819:0.00616292)n3:0.00622501)n2:0.0617822)n1:0.223679)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001535_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001535_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5221b1e1c9bef4c91ff1864be8538d0cc1289aa2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001535_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00897:0.263306,(GCF_005280335_PROKKA_00957:0.131825,((GCF_002008305_PROKKA_01901:0,GCF_023573625_PROKKA_01821:0)n3:0.0282498,GCF_003691675_PROKKA_01597:0.0101281)n2:0.0707996)n1:0.263306)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001536_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001536_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb3c43059c80a4e80a03bd0650dd71bd21f35f1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001536_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00896:0.0949595,(GCF_005280335_PROKKA_00956:0.0897455,(GCF_023573625_PROKKA_01822:5e-09,(GCF_003691675_PROKKA_01598:0.011987,GCF_002008305_PROKKA_01902:0.00132536)n3:0.00132365)n2:0.0705425)n1:0.0949595)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001537_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001537_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2fc906b58eeed8eb4f2924e6aa6bf40b51d8b16e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001537_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00895:0.105329,(GCF_005280335_PROKKA_00955:0.0544061,(GCF_003691675_PROKKA_01599:0.00651956,(GCF_002008305_PROKKA_01903:0.0138915,GCF_023573625_PROKKA_01823:0.00597738)n3:0.00593381)n2:0.0556631)n1:0.105329)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001538_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001538_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7aa45db9d2c43cd177b30142b27eeab0e0457a38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001538_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00894:0.209223,(GCF_005280335_PROKKA_00954:0.197316,(GCF_003691675_PROKKA_01600:5e-09,(GCF_002008305_PROKKA_01904:0.0146962,GCF_023573625_PROKKA_01824:0.00877494)n3:0.0108803)n2:0.158656)n1:0.209223)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001546_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001546_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8327ed6a6d2f7ac6d471ee52da02828bf9537ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001546_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00877:0.023034,((GCF_002008305_PROKKA_01918:0.00534546,GCF_003691675_PROKKA_01614:0.00266286)n2:0.00326335,(GCF_005280335_PROKKA_00942:0.0334068,GCF_023573625_PROKKA_01838:0.00745059)n3:0.00271499)n1:0.023034)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001549_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001549_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c31e66de1562cabf1106f536a4ed5b4e8e207b2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001549_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00873:0.0516527,(GCF_005280335_PROKKA_00938:0.0456696,((GCF_002008305_PROKKA_01922:0,GCF_023573625_PROKKA_01842:0)n3:0.00393241,GCF_003691675_PROKKA_01618:0.00274532)n2:0.0602356)n1:0.0516527)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001553_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001553_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f766077d777da7da0574adbf97995aa1abfdf054
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001553_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00865:0.0323267,(GCF_002008305_PROKKA_01927:5e-09,((GCF_003691675_PROKKA_01623:0,GCF_023573625_PROKKA_01846:0)n3:0.0135828,GCF_005280335_PROKKA_00934:0.024429)n2:0.00730515)n1:0.0323267)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001554_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001554_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..272c42b02662575d6bdbc4736fdb7492e5a343d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001554_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00863:0.11132,(GCF_005280335_PROKKA_00931:0.0627547,(GCF_023573625_PROKKA_01847:0.0073641,(GCF_002008305_PROKKA_01928:0.0123169,GCF_003691675_PROKKA_01624:0.00457607)n3:0.00264775)n2:0.103544)n1:0.11132)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001555_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001555_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4826101cd1d0ee53e47b54622ac9946ab51b02f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001555_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01592:0.566951,(GCF_005280335_PROKKA_00930:0.0690165,(GCF_003691675_PROKKA_01625:0.00232785,(GCF_002008305_PROKKA_01929:0.00757254,GCF_023573625_PROKKA_01848:0.00301803)n3:0.0052126)n2:0.0749497)n1:0.566951)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001556_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001556_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c64b22f81cc1c4526df5d5d867ce890318987fb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001556_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00862:0.0930104,(GCF_005280335_PROKKA_00928:0.159745,((GCF_002008305_PROKKA_01930:0,GCF_003691675_PROKKA_01626:0)n3:5e-09,GCF_023573625_PROKKA_01849:0.00522896)n2:0.197396)n1:0.0930104)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001560_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001560_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0627392a301c8600df62acdbf0b847252e2724d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001560_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00858:0.0749175,(GCF_005280335_PROKKA_00924:0.148813,(GCF_003691675_PROKKA_01631:5e-09,(GCF_023573625_PROKKA_01854:0.00344222,GCF_002008305_PROKKA_01935:0.00344484)n3:0.00171756)n2:0.119356)n1:0.0749175)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001563_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001563_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..185cfa2ab46e0b0c44756cb3dc23ad30acdf8d9f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001563_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00855:0.266874,(GCF_005280335_PROKKA_00921:0.117617,((GCF_002008305_PROKKA_01938:0,GCF_023573625_PROKKA_01857:0)n3:0.00540822,GCF_003691675_PROKKA_01634:0.00537842)n2:0.0537362)n1:0.266874)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001564_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001564_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd193d9683cc24d30c692804ffbc17581fd75f21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001564_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00853:0.156087,(GCF_005280335_PROKKA_00918:0.352323,((GCF_002008305_PROKKA_01941:0,GCF_023573625_PROKKA_01860:0)n3:6e-09,GCF_003691675_PROKKA_01637:0.036151)n2:0.147973)n1:0.156087)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001566_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001566_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6770273ac0ea7ffe5fd97adfb6c68afd4bbf3fb4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001566_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00851:0.0046209,((GCF_003691675_PROKKA_01639:5e-09,GCF_023573625_PROKKA_01862:0.00371045)n2:0.0037767,(GCF_005280335_PROKKA_00913:0.0780708,GCF_002008305_PROKKA_01943:0.00863567)n3:0.0025639)n1:0.0046209)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001567_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001567_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a20ae68a7f5f6df9c2eaa84996d0001be66ebb65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001567_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00850:0.00629716,(GCF_003691675_PROKKA_01640:5e-09,(GCF_002008305_PROKKA_01944:0.00248152,(GCF_023573625_PROKKA_01863:0.00499176,GCF_005280335_PROKKA_00912:0.02262)n3:5e-09)n2:0.00498353)n1:0.00629716)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001569_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001569_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bae5ea6d431214f8c745593b6542bc2e43af456f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001569_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00846:0,(GCF_002008305_PROKKA_01948:0,GCF_003691675_PROKKA_01642:0,(GCF_005280335_PROKKA_00907:5e-09,GCF_023573625_PROKKA_01871:0.0638897)n2:0.0149691)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001570_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001570_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..272fc378d05310e42d77f7ce759661ebec099b4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001570_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01951:1.51696,(GCF_020097155_PROKKA_00292:1.63256,GCF_020097155_PROKKA_00845:4.5e-09)n2:5e-10)n1:2.5e-09,(GCF_023573625_PROKKA_01872:0.0191164,GCF_005280335_PROKKA_00906:0.0119095)n3:0.0106857)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001572_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001572_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de853d4c35c89838857f9607e8d0c66d793cf019
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001572_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00833:0.431785,(GCF_002008305_PROKKA_01966:0.00624374,(GCF_023573625_PROKKA_01892:0.00502162,(GCF_003691675_PROKKA_01660:0.0201481,GCF_005280335_PROKKA_00893:0.0181492)n3:0.0158424)n2:0.00785108)n1:0.431785)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001574_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001574_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5811701f0f849b1ff328cb2d3022e22f00b57ad3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001574_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00831:0.266025,(GCF_005280335_PROKKA_00890:0.0343426,(GCF_002008305_PROKKA_01969:0.0111742,(GCF_003691675_PROKKA_01663:0.00540029,GCF_023573625_PROKKA_01895:0.0054289)n3:0.00780461)n2:0.0279623)n1:0.266025)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001576_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001576_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b704a568514cc5d9fcbd73c0aaaa1da48e567ecf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001576_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00829:0.192366,(GCF_005280335_PROKKA_00888:0.0603378,(GCF_002008305_PROKKA_01971:0.00856567,(GCF_003691675_PROKKA_01665:0.00251471,GCF_023573625_PROKKA_01897:0.00553012)n3:0.0106341)n2:0.145812)n1:0.192366)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001577_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001577_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..488583333f4d0cc4ff426936132fa9e672876d96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001577_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00828:0.16598,(GCF_005280335_PROKKA_00887:0.0433351,(GCF_002008305_PROKKA_01972:0.00695773,(GCF_003691675_PROKKA_01666:0,GCF_023573625_PROKKA_01898:0)n3:0.00352355)n2:0.0345751)n1:0.16598)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001578_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001578_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34ff1d827c2a74c178d91e1bc1500660c93633b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001578_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00826:0.310623,(GCF_005280335_PROKKA_00884:0.298027,(GCF_002008305_PROKKA_01974:0.0156224,(GCF_003691675_PROKKA_01668:0.0216271,GCF_023573625_PROKKA_01900:0.0216488)n3:0.00574648)n2:0.106898)n1:0.310623)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001579_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001579_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4de78583c494adfd381a6bf9ae3c6ae3daa4b46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001579_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00815:0,(GCF_003691675_PROKKA_01672:0,(GCF_002008305_PROKKA_01978:0.00817182,(GCF_005280335_PROKKA_00880:0.341481,GCF_023573625_PROKKA_01904:0.00408025)n3:5.14e-07)n2:5e-09)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001580_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001580_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..220892e55f78f250404676a22da8faf052404f19
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001580_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00814:0.00916695,(GCF_003691675_PROKKA_01673:0.00723567,(GCF_002008305_PROKKA_01979:0.00359863,(GCF_005280335_PROKKA_00879:0.24992,GCF_023573625_PROKKA_01905:5e-09)n3:0.00902247)n2:0.00177752)n1:0.00916695)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001581_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001581_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c54703f06ba6aefeb0a2d71fad9bb444bd4f33e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001581_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00813:0.00625746,(GCF_005280335_PROKKA_00878:0.249999,((GCF_002008305_PROKKA_01980:0,GCF_023573625_PROKKA_01906:0)n3:0.00345424,GCF_003691675_PROKKA_01674:0.00689508)n2:0.0122237)n1:0.00625746)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001582_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001582_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a42e7d52616e3297a66f7df09a545f5732e96438
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001582_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00812:0.00356751,((GCF_005280335_PROKKA_00877:0.342412,GCF_002008305_PROKKA_01981:6e-09)n2:0.00177257,(GCF_003691675_PROKKA_01675:0.00177863,GCF_023573625_PROKKA_01907:5e-09)n3:0.00178198)n1:0.00356751)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001583_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001583_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..365b39d653d01c2a5265aee843fd2828ab8cf619
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001583_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00811:0.00589971,((GCF_002008305_PROKKA_01982:0,GCF_003691675_PROKKA_01676:0,GCF_023573625_PROKKA_01908:0)n2:5e-09,GCF_005280335_PROKKA_00876:0.543698)n1:0.00589971)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001584_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001584_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cba7bde1e294701ec3e843fd0e45f1e8352cb7f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001584_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00809:0.00277299,(GCF_005280335_PROKKA_00873:0.0942669,((GCF_002008305_PROKKA_01984:0,GCF_023573625_PROKKA_01910:0)n3:0.00536787,GCF_003691675_PROKKA_01678:0.00235617)n2:0.00508651)n1:0.00277299)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001587_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001587_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d993abca4cede4709677ebef91c8e344cb388a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001587_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00805:0.432367,(GCF_005280335_PROKKA_00868:0.198245,(GCF_002008305_PROKKA_01989:0.0180991,(GCF_023573625_PROKKA_01915:0.0358921,GCF_003691675_PROKKA_01683:0.0212827)n3:0.0149932)n2:0.282663)n1:0.432367)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001589_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001589_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60728d522b24172c013d85955834a98b57506d0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001589_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00804:0.00848506,(GCF_005280335_PROKKA_00866:0.0196275,(GCF_023573625_PROKKA_01917:0.00939395,(GCF_002008305_PROKKA_01991:0.0130736,GCF_003691675_PROKKA_01685:0.00367198)n3:0.00179419)n2:0.0681649)n1:0.00848506)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001590_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001590_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb33168929e4fe4335e8a1accef927fd3bda840f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001590_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00803:0.00615878,(GCF_005280335_PROKKA_00865:0.0298204,(GCF_023573625_PROKKA_01918:0.00608202,(GCF_002008305_PROKKA_01992:0.00825509,GCF_003691675_PROKKA_01686:0.00821886)n3:0.00356145)n2:0.0152502)n1:0.00615878)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001591_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001591_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb407e5f0c089f0e94af21b207383d680845397a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001591_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00802:0.0131461,(GCF_005280335_PROKKA_00864:0.0565444,(GCF_003691675_PROKKA_01687:0.00194083,(GCF_002008305_PROKKA_01993:0.00583465,GCF_023573625_PROKKA_01919:0.00387093)n3:5e-09)n2:0.0165515)n1:0.0131461)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001593_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001593_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa4a3a94f48d4a3edf86498f94d719cdacad556a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001593_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00798:0.0164524,(GCF_005280335_PROKKA_00860:0.0225519,(GCF_002008305_PROKKA_01995:0.00515384,(GCF_003691675_PROKKA_01689:0.0114571,GCF_023573625_PROKKA_01921:5e-09)n3:0.00633693)n2:0.216666)n1:0.0164524)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001596_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001596_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70d66cc04e0446bcbb16305f139fbb3e621ba10c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001596_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00793:0.229723,((GCF_002008305_PROKKA_02000:0,GCF_003691675_PROKKA_01694:0,GCF_023573625_PROKKA_01926:0)n2:0.12182,GCF_005280335_PROKKA_00857:0.099087)n1:0.229723)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001597_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001597_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..877d6ca347d5e1c7354e8d34d91098dd0fe9f683
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001597_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00776:0.100741,(GCF_005280335_PROKKA_00839:0.0319421,(GCF_002008305_PROKKA_02003:0.000341227,(GCF_003691675_PROKKA_01713:0.0126149,GCF_023573625_PROKKA_01941:0.0125553)n3:0.00700393)n2:0.0485822)n1:0.100741)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001601_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001601_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..936a83ba4357cf51c2c1a9dd433b42ee05d0905b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001601_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00771:0.0115535,(GCF_005280335_PROKKA_00834:0.0352938,(GCF_023573625_PROKKA_01946:0.00897213,(GCF_002008305_PROKKA_02008:0.00298368,GCF_003691675_PROKKA_01718:5e-09)n3:5e-09)n2:0.0179016)n1:0.0115535)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001603_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001603_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d7dc25c558cae930c84826e91501de35b0be24c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001603_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00769:0.05807,(GCF_005280335_PROKKA_00832:0.0423688,(GCF_003691675_PROKKA_01720:5e-09,(GCF_002008305_PROKKA_02010:0.010869,GCF_023573625_PROKKA_01948:0.00359269)n3:0.00360198)n2:0.0682384)n1:0.05807)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001604_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001604_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5a3970bb97719d0a3b92a078965c5f7fb04b32e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001604_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00768:0.0729089,(GCF_002008305_PROKKA_02011:0.00668345,(GCF_023573625_PROKKA_01949:0.0115586,(GCF_003691675_PROKKA_01721:0.00570164,GCF_005280335_PROKKA_00831:0.0495597)n3:0.0118539)n2:0.0110794)n1:0.0729089)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001606_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001606_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9dedfd594f4f96967be49e38f0ef759086b74136
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001606_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00766:0.0602502,(GCF_005280335_PROKKA_00829:0.0754931,(GCF_002008305_PROKKA_02013:0.00403946,(GCF_003691675_PROKKA_01723:0,GCF_023573625_PROKKA_01951:0)n3:0.00356287)n2:0.0713773)n1:0.0602502)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001607_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001607_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5a4b6e988509e9bb0db81befe4a8a089cfcfec6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001607_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00764:0.00481378,(GCF_002008305_PROKKA_02016:0.00237448,(GCF_003691675_PROKKA_01725:5e-09,(GCF_005280335_PROKKA_00805:0.0395139,GCF_023573625_PROKKA_01953:0.00608781)n3:0.00369008)n2:0.0047956)n1:0.00481378)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001608_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001608_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c400e40a3638d19549fc49b6646fc007ea8db43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001608_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00763:0.00811437,(GCF_005280335_PROKKA_00804:0.0225843,(GCF_003691675_PROKKA_01726:0.0108441,(GCF_002008305_PROKKA_02017:0.0153002,GCF_023573625_PROKKA_01954:6e-09)n3:0.00464099)n2:0.00378446)n1:0.00811437)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001609_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001609_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58210df0ebf78a3529735f79b1a17cfc9763060e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001609_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00761:2.5e-09,(GCF_005280335_PROKKA_02537:0.656441,((GCF_002008305_PROKKA_02019:0,GCF_003691675_PROKKA_01728:0)n3:0.41312,GCF_023573625_PROKKA_01956:0.0245429)n2:0.0152347)n1:2.5e-09)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001610_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001610_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed5aae0648964a8664e101628c6ec8aab728b9f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001610_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00760:0.0185899,((GCF_002008305_PROKKA_02020:0.0063762,GCF_003691675_PROKKA_01729:0.0213582)n2:0.0144764,(GCF_005280335_PROKKA_00802:0.453848,GCF_023573625_PROKKA_01957:0.0167494)n3:0.0201204)n1:0.0185899)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001612_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001612_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b50be1996d7254d1896862f56cd612575dd9749
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001612_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00758:0.00939218,(GCF_023573625_PROKKA_01959:0.00657845,(GCF_002008305_PROKKA_02022:0.00660735,(GCF_005280335_PROKKA_00797:0.386035,GCF_003691675_PROKKA_01731:0.011281)n3:0.00752767)n2:0.00937843)n1:0.00939218)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001613_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001613_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7abf44a21b39914190059f2ab9119783b7e7c18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001613_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00757:0.0525974,(GCF_005280335_PROKKA_00796:0.0429575,(GCF_003691675_PROKKA_01732:0.00658772,(GCF_002008305_PROKKA_02023:0.00173097,GCF_023573625_PROKKA_01960:0.00518585)n3:0.00139252)n2:0.00809137)n1:0.0525974)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001614_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001614_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f2c00bc989cd7d9d058a463dff6b6e397b67d11e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001614_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02090:0.334611,(GCF_005280335_PROKKA_00795:5e-09,(GCF_023573625_PROKKA_01961:5e-09,(GCF_002008305_PROKKA_02024:0.0165067,GCF_003691675_PROKKA_01733:6e-09)n3:0.00656868)n2:0.00658325)n1:0.334611)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001618_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001618_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..59fe303ec35db76ce4977007f8b2adecf15f4ef2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001618_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00752:0.0591661,((GCF_002008305_PROKKA_02028:0,GCF_003691675_PROKKA_01737:0,GCF_023573625_PROKKA_01965:0)n2:0.0349055,GCF_005280335_PROKKA_00791:0.0296895)n1:0.0591661)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001619_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001619_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40b9337370e9439effb330b92c0b15d80b24bda7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001619_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01226:0.280526,((GCF_002008305_PROKKA_02033:0,GCF_003691675_PROKKA_01740:0,GCF_023573625_PROKKA_01968:0)n2:0.0534554,GCF_005280335_PROKKA_00787:5e-09)n1:0.280526)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001623_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001623_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..599a516f44b75092e7d19ccb000408f873f1dc01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001623_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00746:0.030953,(GCF_005280335_PROKKA_00778:0.119067,(GCF_002008305_PROKKA_02040:0.00374438,(GCF_003691675_PROKKA_01744:0,GCF_023573625_PROKKA_01972:0)n3:0.00196403)n2:0.00741447)n1:0.030953)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001624_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001624_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0839ba4da0a5b87ceeb8c8801c6470a935e72ab5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001624_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00735:0.0251802,GCF_020097155_PROKKA_00741:0.78908)n1:0.002324,(GCF_003691675_PROKKA_01751:0.0110803,(GCF_002008305_PROKKA_02045:0.00631454,GCF_023573625_PROKKA_01979:0.0210076)n3:0.00781843)n2:0.002324)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001627_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001627_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..59a60d62d7d9929b74cb87c785d6c0548d444ab7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001627_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00726:0.0529811,(GCF_005280335_PROKKA_00711:0.0903165,(GCF_002008305_PROKKA_02055:0.00627078,(GCF_003691675_PROKKA_01761:5e-09,GCF_023573625_PROKKA_01989:5e-09)n3:5e-09)n2:0.205656)n1:0.0529811)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001628_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001628_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..932271548eb439d7282283dfbfbfecda05368c28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001628_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00728:0.0761183,(GCF_005280335_PROKKA_00764:0.142388,(GCF_002008305_PROKKA_02056:0.0150448,(GCF_003691675_PROKKA_01762:0,GCF_023573625_PROKKA_01990:0)n3:0.00437415)n2:0.16793)n1:0.0761183)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001631_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001631_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8aa49c7bdea5d1bfa15ebe2795bd37889e72dff1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001631_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00487:0.16799,((GCF_002008305_PROKKA_02071:0.00479683,GCF_023573625_PROKKA_01999:0.00347983)n2:0.100728,(GCF_005280335_PROKKA_00559:0.10586,GCF_005280335_PROKKA_00742:0.0911515)n3:0.0101279)n1:0.0551715)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001633_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001633_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..572b5cba2b6d7b594bb49d5e451570ac72aa35c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001633_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00613:0.00498257,((GCF_002008305_PROKKA_02081:0,GCF_023573625_PROKKA_02019:0)n2:0.00495448,(GCF_005280335_PROKKA_00703:0.00993926,GCF_003691675_PROKKA_01785:5e-09)n3:5e-09)n1:0.00498257)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001634_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001634_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aab51ec08ff91a96cb1e0b1156df4f344d5995d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001634_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00611:0.00889803,((GCF_002008305_PROKKA_02082:0,GCF_003691675_PROKKA_01787:0)n2:5e-09,(GCF_005280335_PROKKA_00701:0.0178518,GCF_023573625_PROKKA_02021:5e-09)n3:0.00590013)n1:0.00889803)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001636_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001636_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98e646d154a9f81cbbfe82f9a32433b3ec9cb2af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001636_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00609:0.00292562,(GCF_023573625_PROKKA_02023:0.00586566,((GCF_002008305_PROKKA_02084:0,GCF_003691675_PROKKA_01789:0)n3:5e-09,GCF_005280335_PROKKA_00699:0.0146763)n2:0.00293117)n1:0.00292562)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001639_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001639_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..245c6e78e14c41d92c24f08a69ff6b80d8f1185a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001639_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00606:0.0031992,(GCF_023573625_PROKKA_02026:0.00463491,((GCF_002008305_PROKKA_02087:0,GCF_003691675_PROKKA_01792:0)n3:0.00242715,GCF_005280335_PROKKA_00696:0.0130723)n2:0.0044182)n1:0.0031992)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001640_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001640_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea7914fea7ae8fc543edec34247560330badefae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001640_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00586:0.201311,GCF_005280335_PROKKA_00695:0.00710466)n1:0.00154482,((GCF_002008305_PROKKA_02088:0,GCF_003691675_PROKKA_01793:0)n3:0.0137642,GCF_023573625_PROKKA_02027:0.00981911)n2:0.00154482)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001641_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001641_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4881db3a4b65b331a3ad516429fb1a01f42a8ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001641_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_02092:0.00956403,(GCF_020097155_PROKKA_00602:0.0276556,(GCF_020097155_PROKKA_00413:0.142612,GCF_020097155_PROKKA_00937:1.53012)n3:0.20696)n2:0.0229955)n1:0.00697788,GCF_005280335_PROKKA_00686:0.0116311)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001643_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001643_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f701502003cf35eaa37d09612d6a69c2f53cc8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001643_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00594:0.099658,(GCF_005280335_PROKKA_00680:0.0478032,((GCF_002008305_PROKKA_02099:0,GCF_003691675_PROKKA_01806:0)n3:5e-09,GCF_023573625_PROKKA_02039:0.00178943)n2:0.0476829)n1:0.099658)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001644_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001644_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d7336500ca1d55d893790856b01a1964c0de8b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001644_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00592:0.49996,(GCF_005280335_PROKKA_00677:0.0250423,((GCF_002008305_PROKKA_02102:0,GCF_003691675_PROKKA_01809:0)n3:5e-09,GCF_023573625_PROKKA_02042:0.00890499)n2:0.476136)n1:0.49996)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001645_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001645_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f80086bdc8f98d4df42b8088789550cbe826f2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001645_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00591:0.489316,(GCF_005280335_PROKKA_00676:0.186752,((GCF_002008305_PROKKA_02103:0,GCF_003691675_PROKKA_01810:0)n3:0.00818516,GCF_023573625_PROKKA_02043:0.0101711)n2:0.167679)n1:0.489316)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001646_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001646_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98bd10b6eb3377c040c0fc7c19d78ee0e7a2284c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001646_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00593:0.0596395,(GCF_005280335_PROKKA_00675:0.0696917,((GCF_002008305_PROKKA_02104:0,GCF_003691675_PROKKA_01811:0)n3:0.00346965,GCF_023573625_PROKKA_02044:5e-09)n2:0.0710451)n1:0.0596395)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001647_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001647_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c18b3821d88ed9618ba0b882259ede8d658c4551
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001647_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00590:0.154457,(GCF_005280335_PROKKA_00674:0.109146,((GCF_002008305_PROKKA_02105:0,GCF_003691675_PROKKA_01812:0)n3:0.00139466,GCF_023573625_PROKKA_02045:0.00217604)n2:0.0670327)n1:0.154457)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001649_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001649_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4907f6ddcc4cd469f36aacf6e341a17c721c5efb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001649_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00588:0.321309,(GCF_005280335_PROKKA_00672:0.517615,((GCF_002008305_PROKKA_02107:0,GCF_003691675_PROKKA_01814:0)n3:0.00267476,GCF_023573625_PROKKA_02047:5e-09)n2:0.0545039)n1:0.321309)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001650_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001650_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..166b1180f75f90600c8720326034dfd0d58d8d42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001650_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00586:0.175237,(GCF_005280335_PROKKA_00669:0.0449975,(GCF_002008305_PROKKA_02109:0.00504642,(GCF_023573625_PROKKA_02049:0.0239312,GCF_003691675_PROKKA_01816:0.0149138)n3:0.0049039)n2:0.0200568)n1:0.175237)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001651_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001651_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dac4821fe44a97d3b0b3c93eed195939f20b199b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001651_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00585:0.066722,(GCF_005280335_PROKKA_00668:0.0584103,(GCF_003691675_PROKKA_01817:0.0136677,(GCF_023573625_PROKKA_02050:0.0275729,GCF_002008305_PROKKA_02110:6e-09)n3:5e-09)n2:0.0897368)n1:0.066722)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001655_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001655_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75af44a41908f5534417d792e94e2558512e9063
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001655_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00580:0.326575,(GCF_005280335_PROKKA_00663:0.175045,(GCF_003691675_PROKKA_01825:0.0100068,(GCF_023573625_PROKKA_02055:0.0100385,GCF_002008305_PROKKA_02117:5e-09)n3:5e-09)n2:0.0981643)n1:0.326575)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001656_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001656_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e48da02fbd4e0261c14c099f98074ae8bed8c40c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001656_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00579:0.172603,(GCF_005280335_PROKKA_00662:0.0861678,(GCF_002008305_PROKKA_02118:5e-09,(GCF_003691675_PROKKA_01826:0.009557,GCF_023573625_PROKKA_02056:0.0144283)n3:0.00979462)n2:0.0671756)n1:0.172603)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001657_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001657_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4ee01d713ee793bf141c5b98d6bd355b2890c6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001657_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00578:0.168478,(GCF_005280335_PROKKA_00661:0.133788,(GCF_023573625_PROKKA_02057:0.0132598,(GCF_002008305_PROKKA_02119:0.0113442,GCF_003691675_PROKKA_01827:5e-09)n3:0.0299636)n2:0.141374)n1:0.168478)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001659_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001659_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..450d845c62bf146c77c454e46eb9ca3312f6a856
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001659_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00576:0.0121132,((GCF_003691675_PROKKA_01829:0,GCF_023573625_PROKKA_02059:0)n2:0.0157267,(GCF_002008305_PROKKA_02121:0.0216406,GCF_005280335_PROKKA_00659:0.0632824)n3:0.0230547)n1:0.0121132)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001660_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001660_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18aacf3cf995d04fed5176d79f2a0193fed19f24
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001660_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00574:2.5e-09,(GCF_005280335_PROKKA_00656:0.1112,((GCF_003691675_PROKKA_01831:0,GCF_023573625_PROKKA_02061:0)n3:0.0224573,GCF_002008305_PROKKA_02123:0.0151347)n2:0.0074227)n1:2.5e-09)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001663_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001663_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b6f9852e2329c2c87404f5307e90366a6bf6b84f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001663_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00569:0.0170439,((GCF_002008305_PROKKA_02127:0.0133634,GCF_023573625_PROKKA_02065:0.0103962)n2:0.0179826,(GCF_003691675_PROKKA_01835:0.0107767,GCF_005280335_PROKKA_00653:0.0266426)n3:0.00351498)n1:0.0170439)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001664_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001664_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22c2d546e1d38d6d34c9c8384f4823389aee7bd2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001664_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00568:0.00843566,(GCF_005280335_PROKKA_00652:0.00279141,(GCF_002008305_PROKKA_02128:0.00291319,(GCF_003691675_PROKKA_01836:0,GCF_023573625_PROKKA_02066:0)n3:5e-09)n2:0.00984367)n1:0.00843566)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001665_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001665_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c51cfba6d6177a60e71f223b23f157a02242bb4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001665_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00567:0.00296408,(GCF_005280335_PROKKA_00651:0.00197205,(GCF_002008305_PROKKA_02129:0.00591124,(GCF_003691675_PROKKA_01837:6e-09,GCF_023573625_PROKKA_02067:0.00394418)n3:0.00198084)n2:0.00196844)n1:0.00296408)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001666_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001666_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5348b01e862121e97600dfedfc4da4d5b1f1755
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001666_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00566:0.0110741,((GCF_003691675_PROKKA_01838:0.00626165,GCF_023573625_PROKKA_02068:0.0021247)n2:0.0132123,(GCF_002008305_PROKKA_02130:0.0200458,GCF_005280335_PROKKA_00650:0.0168792)n3:0.00606869)n1:0.0110741)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001671_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001671_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5a2e1eb064b998fdef0a3839af3ef5a65b715374
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001671_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00560:0.0959607,(GCF_005280335_PROKKA_00636:0.0348779,(GCF_002008305_PROKKA_02136:5e-09,(GCF_003691675_PROKKA_01844:0,GCF_023573625_PROKKA_02074:0)n3:0.0146987)n2:0.0344068)n1:0.0959607)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001675_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001675_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a90c349faec7816986fb26966a1fee0b0e13182
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001675_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00556:0.149694,(GCF_005280335_PROKKA_00632:0.0183874,((GCF_002008305_PROKKA_02140:0,GCF_003691675_PROKKA_01848:0)n3:5e-09,GCF_023573625_PROKKA_02078:0.00699099)n2:0.0713705)n1:0.149694)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001678_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001678_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..427ba26b1152fa67688469b252296c89e7cadba4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001678_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00552:0.0065485,((GCF_002008305_PROKKA_02144:0.0246025,GCF_005280335_PROKKA_00628:0.00961026)n2:0.117857,(GCF_003691675_PROKKA_01851:5e-09,GCF_023573625_PROKKA_02081:0.00428591)n3:5e-09)n1:0.0065485)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001681_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001681_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0480e13163dd00db4c5d540f2de2e0532e916bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001681_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00547:0.0275999,(GCF_005280335_PROKKA_00622:0.078663,(GCF_002008305_PROKKA_02147:0.00684997,(GCF_003691675_PROKKA_01855:5e-09,GCF_023573625_PROKKA_02085:0.00564876)n3:0.0270628)n2:0.0930062)n1:0.0275999)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001682_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001682_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..937a6a48123a4b6ac921a398e87f048951697d7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001682_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00546:0.0337574,(GCF_005280335_PROKKA_00621:0.0802647,(GCF_003691675_PROKKA_01856:0.00464594,(GCF_002008305_PROKKA_02148:0.00831192,GCF_023573625_PROKKA_02086:0.00825141)n3:0.001951)n2:0.0770375)n1:0.0337574)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001683_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001683_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81f928f3531ddbdf1c0e13b3eaa2218ca80e3d37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001683_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00537:0.214259,(GCF_005280335_PROKKA_00613:0.087706,(GCF_023573625_PROKKA_02092:6e-09,(GCF_002008305_PROKKA_02149:5e-09,GCF_003691675_PROKKA_01862:0.00250464)n3:0.011901)n2:0.0887066)n1:0.214259)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001685_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001685_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9fcdd432f940300f0ea74caf3522ed09bb4a9673
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001685_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00535:0.168803,(GCF_005280335_PROKKA_00611:0.054318,(GCF_023573625_PROKKA_02094:0.00547991,(GCF_002008305_PROKKA_02151:0.00478453,GCF_003691675_PROKKA_01864:5e-09)n3:0.00892659)n2:0.0912727)n1:0.168803)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001686_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001686_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9c0edf6bf5d1d720e4173013e5c3adcace9466b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001686_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00534:0.0381437,(GCF_005280335_PROKKA_00610:0.138389,(GCF_023573625_PROKKA_02095:0.0124709,(GCF_002008305_PROKKA_02152:0.0222174,GCF_003691675_PROKKA_01865:0.00245219)n3:0.00233229)n2:0.184287)n1:0.0381437)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001687_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001687_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4dd47766c41955bc11351e9c466322166ac05d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001687_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00533:0.0687515,(GCF_005280335_PROKKA_00609:0.0469244,(GCF_003691675_PROKKA_01867:0.00355878,(GCF_002008305_PROKKA_02154:0.00884152,GCF_023573625_PROKKA_02097:0.00265265)n3:0.0017778)n2:0.0366228)n1:0.0687515)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001688_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001688_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..420630db12b7ae07ba9bc43606981b86a4b3af87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001688_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00523:0.0568203,(GCF_005280335_PROKKA_00601:0.121365,(GCF_003691675_PROKKA_01870:5e-09,(GCF_002008305_PROKKA_02157:0.00211257,GCF_023573625_PROKKA_02100:5e-09)n3:0.00422847)n2:0.132663)n1:0.0568203)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001689_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001689_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..83a53ee7cfb9aa7c7894b720a73da127f4ceb954
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001689_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00522:0.166023,(GCF_005280335_PROKKA_00600:0.194682,(GCF_002008305_PROKKA_02158:0.0118828,(GCF_003691675_PROKKA_01871:0.0176106,GCF_023573625_PROKKA_02101:0.0126416)n3:0.0161886)n2:0.100734)n1:0.166023)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001690_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001690_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0527beb2994a3d4d9a7dc7a65b983be8e2ab5ba0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001690_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00521:0.14051,(GCF_005280335_PROKKA_00599:0.211138,(GCF_023573625_PROKKA_02103:0.0179321,(GCF_002008305_PROKKA_02159:5e-09,GCF_003691675_PROKKA_01872:0.00441927)n3:0.00943068)n2:0.149047)n1:0.14051)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001692_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001692_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b88166e295846a91e84be7bea64e9805f91eaa3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001692_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00517:0.136005,(GCF_005280335_PROKKA_00594:0.0701851,(GCF_002008305_PROKKA_02163:0.0104894,(GCF_003691675_PROKKA_01877:0,GCF_023573625_PROKKA_02108:0)n3:5e-09)n2:0.0754787)n1:0.136005)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001696_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001696_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8874cbb9bf34a1c1da6cf7f51a857e667bd736e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001696_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00508:0.136506,(GCF_005280335_PROKKA_00582:0.0985065,(GCF_003691675_PROKKA_01884:0.0032146,(GCF_023573625_PROKKA_02115:0.00963693,GCF_002008305_PROKKA_02170:0.00325592)n3:0.00323387)n2:0.0682227)n1:0.136506)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001697_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001697_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7fc8e0e58091acd315dee24e3e2248493e08889
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001697_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00506:0.175874,(GCF_005280335_PROKKA_00579:0.0367688,((GCF_002008305_PROKKA_02173:0,GCF_003691675_PROKKA_01887:0)n3:0.00821808,GCF_023573625_PROKKA_02118:5e-09)n2:0.0370406)n1:0.175874)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001698_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001698_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..575d735677837bca868e2c569a3bd1c288a2ef16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001698_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00504:0.0613411,(GCF_005280335_PROKKA_00577:0.197607,(GCF_003691675_PROKKA_01889:0.0026856,(GCF_002008305_PROKKA_02175:0.00806404,GCF_023573625_PROKKA_02120:5e-09)n3:5e-09)n2:0.121589)n1:0.0613411)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001699_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001699_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5431cfd8bb310b46462a9f47c053032322ba85a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001699_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00503:0.0971902,(GCF_005280335_PROKKA_00576:0.336952,(GCF_002008305_PROKKA_02176:0.00814434,(GCF_003691675_PROKKA_01890:0.00285316,GCF_023573625_PROKKA_02121:5e-09)n3:0.000540501)n2:0.15948)n1:0.0971902)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001700_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001700_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ffe39755f565fda903e778d459af5d1174989d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001700_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00502:0.0909285,(GCF_005280335_PROKKA_00575:0.27041,(GCF_002008305_PROKKA_02177:0.0130392,(GCF_003691675_PROKKA_01891:0.00679946,GCF_023573625_PROKKA_02122:0.0159158)n3:0.021478)n2:0.155009)n1:0.0909285)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001701_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001701_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2525651bb2d3fa466096df83dedea43dc02a17f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001701_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00501:0.0377858,(GCF_005280335_PROKKA_00574:0.250565,(GCF_002008305_PROKKA_02178:5e-09,(GCF_023573625_PROKKA_02123:0.0101069,GCF_003691675_PROKKA_01892:5e-09)n3:0.00335421)n2:0.12248)n1:0.0377858)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001702_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001702_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06a4f17d37d301f517553cf4feaa35bf386dc367
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001702_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00500:0.138397,(GCF_005280335_PROKKA_00573:0.041315,(GCF_023573625_PROKKA_02124:5e-09,(GCF_002008305_PROKKA_02179:5e-09,GCF_003691675_PROKKA_01893:0.00578222)n3:0.0087089)n2:0.0393025)n1:0.138397)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001703_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001703_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a587b0956b9ebfc59ba449a720aab3880e5089d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001703_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00499:0.217705,(GCF_005280335_PROKKA_00572:0.0991483,(GCF_023573625_PROKKA_02125:0.0194883,(GCF_002008305_PROKKA_02180:5e-09,GCF_003691675_PROKKA_01894:0.0132502)n3:0.0118453)n2:0.0932218)n1:0.217705)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001706_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001706_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da5fdace2086e125557aa4410b800ce79c50772a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001706_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00492:0.304894,(GCF_005280335_PROKKA_00567:0.256101,(GCF_023573625_PROKKA_02128:0.00263786,(GCF_003691675_PROKKA_01897:0.0182602,GCF_002008305_PROKKA_02183:0.0187002)n3:0.00636125)n2:0.327282)n1:0.304894)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001707_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001707_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28c6eee26216688b25df68ae86da46ab4f005598
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001707_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00490:0.267517,(GCF_005280335_PROKKA_00565:0.175431,((GCF_002008305_PROKKA_02185:0,GCF_003691675_PROKKA_01899:0)n3:0.006435,GCF_023573625_PROKKA_02130:5e-09)n2:0.219122)n1:0.267517)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001708_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001708_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28c957a97062e3a451983044bf6dcef804346196
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001708_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00489:0.133851,(GCF_005280335_PROKKA_00563:0.096094,(GCF_002008305_PROKKA_02186:6e-09,(GCF_003691675_PROKKA_01900:0.00341476,GCF_023573625_PROKKA_02131:0.00343995)n3:0.0140809)n2:0.0719268)n1:0.133851)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001711_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001711_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..303d9f391d5644278fafd5cadb2ef2bd7b5b99e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001711_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00482:0.399686,(GCF_005280335_PROKKA_00546:0.214186,(GCF_003691675_PROKKA_01907:5e-09,(GCF_002008305_PROKKA_02194:0.0266783,GCF_023573625_PROKKA_02138:6e-09)n3:0.00528832)n2:0.0804259)n1:0.399686)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001713_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001713_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f61541fca918fd690f7f0e431498d91145739ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001713_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00479:0.38788,((GCF_002008305_PROKKA_02196:0,GCF_023573625_PROKKA_02140:0)n2:0.00201738,(GCF_003691675_PROKKA_01909:0.019216,GCF_005280335_PROKKA_00548:0.0308315)n3:0.00926621)n1:0.38788)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001716_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001716_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98360a8e6319fbf9ca82a6d466c8ac2af9218aa4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001716_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01787:0.611508,((GCF_002008305_PROKKA_02200:0,GCF_003691675_PROKKA_01913:0,GCF_023573625_PROKKA_02144:0)n2:0.212896,GCF_005280335_PROKKA_00542:0.0635682)n1:0.611508)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001717_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001717_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65cfde5dc7c149c97b464b0b6c1bc6c8ebce3e3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001717_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01297:0.172833,((GCF_002008305_PROKKA_02201:0,GCF_003691675_PROKKA_01914:0,GCF_023573625_PROKKA_02145:0)n2:0.362128,GCF_005280335_PROKKA_00496:0.278268)n1:0.172833)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001720_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001720_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b575b826f2ef4d27c9ef8ee23480688dc5a02124
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001720_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00468:0.144715,(GCF_005280335_PROKKA_00537:0.0450336,(GCF_002008305_PROKKA_02208:0.00287391,(GCF_003691675_PROKKA_01921:0,GCF_023573625_PROKKA_02152:0)n3:0.0181684)n2:0.0524191)n1:0.144715)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001721_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001721_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f04eedc61a35b6335bf1c3dd9bee561cc7232e29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001721_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00467:0.161077,(GCF_005280335_PROKKA_00525:0.109406,(GCF_023573625_PROKKA_02155:5e-09,(GCF_002008305_PROKKA_02216:0.00739117,GCF_003691675_PROKKA_01929:0.00735351)n3:0.0260629)n2:0.146807)n1:0.161077)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001722_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001722_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca414ec04e457de45b8642189dc2012774290ef5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001722_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00465:0.220046,(GCF_005280335_PROKKA_00527:0.343558,(GCF_023573625_PROKKA_02158:0.00439019,(GCF_003691675_PROKKA_01932:0.0268966,GCF_002008305_PROKKA_02219:5e-09)n3:0.00447401)n2:0.321392)n1:0.220046)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001723_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001723_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..103f6235c36d92c83d5cf5e6e95fce50b98c2caa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001723_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00462:0.0643187,(GCF_005280335_PROKKA_00515:0.128501,(GCF_002008305_PROKKA_02220:0.0107709,(GCF_003691675_PROKKA_01933:0.0109001,GCF_023573625_PROKKA_02159:0.0107269)n3:0.011698)n2:0.316338)n1:0.0643187)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001726_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001726_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d50341f444fcdacd4d34f24179e1e64512e3da30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001726_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00715:0.104045,((GCF_002008305_PROKKA_02241:0.00170306,GCF_003691675_PROKKA_01943:0.00170358)n2:5e-09,(GCF_023573625_PROKKA_02213:0.325721,GCF_023573625_PROKKA_02173:0.00153761)n3:0.000170846)n1:0.398827)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001727_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001727_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ac7b635b3a52dc5c0736cf5eabd6f9fb4195631
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001727_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02088:0.309736,(GCF_005280335_PROKKA_00502:1.06312,(GCF_003691675_PROKKA_01946:5e-09,(GCF_002008305_PROKKA_02244:0.00365792,GCF_023573625_PROKKA_02176:6e-09)n3:0.00364258)n2:0.073891)n1:0.309736)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001728_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001728_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fca5a80ca749002361be03720a2708c0ea420a38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001728_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00511:0.346534,((GCF_002008305_PROKKA_02245:0,GCF_003691675_PROKKA_01947:0,GCF_023573625_PROKKA_02177:0)n2:0.0766568,GCF_005280335_PROKKA_00500:0.0971933)n1:0.346534)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001731_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001731_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..202c5d3a48752420c760d8a79e33a0e516d899c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001731_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00431:0.00224231,(GCF_005280335_PROKKA_00476:0.0204818,(GCF_002008305_PROKKA_02255:0.00405698,(GCF_003691675_PROKKA_01955:0,GCF_023573625_PROKKA_02186:0)n3:5e-09)n2:0.00778458)n1:0.00224231)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001738_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001738_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c819f705991ac9507f8f878c4b32b5ab52cafdb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001738_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00404:0.104153,(GCF_005280335_PROKKA_00451:0.0273051,(GCF_003691675_PROKKA_01977:5e-09,(GCF_002008305_PROKKA_02286:0.00553803,GCF_023573625_PROKKA_02225:0.00554589)n3:5e-09)n2:0.00692559)n1:0.104153)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001739_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001739_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee8db4eca11b2390f7ec61fa13212ed48021d0f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001739_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00403:0.082108,(GCF_005280335_PROKKA_00450:0.0316553,(GCF_003691675_PROKKA_01978:0.0132545,(GCF_002008305_PROKKA_02287:0.00268402,GCF_023573625_PROKKA_02226:0.00791898)n3:0.00552156)n2:0.0238265)n1:0.082108)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001741_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001741_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a6ff143c61e27d2eee514fd0517fa3bb019109d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001741_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_02290:0,GCF_003691675_PROKKA_01982:0,GCF_005280335_PROKKA_00448:0,GCF_023573625_PROKKA_02230:0)n1:0.00621232,GCF_020097155_PROKKA_00400:0.00621232)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001742_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001742_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..73b53f1be581621b93b07074e2adbfe8ce048b1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001742_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00399:0.0651907,(GCF_005280335_PROKKA_00447:0.00556226,(GCF_002008305_PROKKA_02291:0.00529677,(GCF_003691675_PROKKA_01983:5e-09,GCF_023573625_PROKKA_02231:0.0053136)n3:5e-09)n2:0.0103979)n1:0.0651907)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001743_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001743_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23a36c92d440a27e91e9a8d0422826cc6b652c57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001743_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00398:0.0252408,((GCF_002008305_PROKKA_02292:0,GCF_003691675_PROKKA_01984:0,GCF_023573625_PROKKA_02232:0)n2:0.0199097,GCF_005280335_PROKKA_00446:0.00913888)n1:0.0252408)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001745_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001745_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24c3cea99cea695d0ed02bda0dbd6b16c297933f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001745_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00395:0.227492,(GCF_005280335_PROKKA_00442:0.182842,(GCF_003691675_PROKKA_01987:0.0207726,(GCF_002008305_PROKKA_02294:0.0085208,GCF_023573625_PROKKA_02235:0.00844828)n3:0.0142451)n2:0.192175)n1:0.227492)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001751_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001751_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ddc704b7a96b1875408125a8e5ca8eecde78efd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001751_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00385:0.0650791,((GCF_002008305_PROKKA_02304:0,GCF_003691675_PROKKA_01997:0,GCF_023573625_PROKKA_02245:0)n2:0.0601134,GCF_005280335_PROKKA_00433:0.0177236)n1:0.0650791)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001753_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001753_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b9c58fe7527e1ae55e8dd1fbc537da811da52d9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001753_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00382:0.130709,(GCF_005280335_PROKKA_00429:0.0412573,(GCF_003691675_PROKKA_02000:5e-09,(GCF_002008305_PROKKA_02307:0.0084784,GCF_023573625_PROKKA_02248:6e-09)n3:0.00422773)n2:0.0348261)n1:0.130709)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001755_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001755_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..107d99607210fffad2517fee05ce30714e55462e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001755_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00380:0.0710097,((GCF_003691675_PROKKA_02002:0.00208593,GCF_023573625_PROKKA_02250:0.00493228)n2:0.0269187,(GCF_002008305_PROKKA_02309:5e-09,GCF_005280335_PROKKA_00427:0.0186421)n3:0.0358532)n1:0.0710097)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001756_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001756_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88135a3e5bd5c5d2aa00243799552796aa54152f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001756_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00379:0.0887172,(GCF_023573625_PROKKA_02251:5e-09,(GCF_005280335_PROKKA_00426:0.035922,(GCF_002008305_PROKKA_02310:0,GCF_003691675_PROKKA_02003:0)n3:5e-09)n2:0.00875027)n1:0.0887172)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001758_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001758_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4053523973d7a82420939b1889048c152b54cdf1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001758_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00377:0.0107115,((GCF_002008305_PROKKA_02312:0,GCF_003691675_PROKKA_02005:0,GCF_023573625_PROKKA_02253:0)n2:0.0220324,GCF_005280335_PROKKA_00424:0.0217087)n1:0.0107115)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001760_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001760_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db4e9ab849a91eb02d85cef62402af0f55e33684
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001760_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_PROKKA_00303:0.0275822,GCF_005280335_PROKKA_02372:0.0443089)n1:0.425328,(GCF_003691675_PROKKA_02232:0.625712,(GCF_005280335_PROKKA_02196:0.636495,GCF_005280335_PROKKA_02198:0.812303)n3:0.212798)n2:0.425328)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001762_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001762_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e1f03f64ea265bd8dae81d3f926bbbebaabee8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001762_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00540:0.210927,((GCF_003691675_PROKKA_01858:0.0083631,GCF_023573625_PROKKA_02088:0.00361057)n2:0.129259,(GCF_005280335_PROKKA_02658:0.305772,GCF_005280335_PROKKA_00616:0.0977326)n3:0.0108592)n1:0.167231)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001764_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001764_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c316786c043067a2e9d53670011ed73994f721a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001764_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00135:0.289579,((GCF_003691675_PROKKA_02133:0,GCF_023573625_PROKKA_00125:0)n2:0.0184605,(GCF_005280335_PROKKA_00090:0.59509,GCF_005280335_PROKKA_00267:0.0202326)n3:0.00224807)n1:0.903729)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001765_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001765_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e962f426d944b7a73e8ab3b68cadee25dcac660a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001765_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00136:0.278176,((GCF_003691675_PROKKA_02134:0,GCF_023573625_PROKKA_00126:0)n2:5e-09,(GCF_005280335_PROKKA_00089:0.68478,GCF_005280335_PROKKA_00266:0.0368255)n3:0.00409172)n1:0.78235)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001769_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001769_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97a2b6d2b3917a6f5a40d4fb6e96e342cdbf57eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001769_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00886:0.0608174,(GCF_005280335_PROKKA_00946:0.0968596,(GCF_005280335_PROKKA_00518:1.15525,(GCF_005280335_PROKKA_00811:0.643041,GCF_005280335_PROKKA_02387:1.25691)n3:0.3272)n2:0.76126)n1:0.0608174)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001773_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001773_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6806eba89060a49095e529c0562b2ef541f34783
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001773_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00352:0.089077,(GCF_003691675_PROKKA_02064:0.0022917,(GCF_002008305_PROKKA_00051:0.0171494,GCF_023573625_PROKKA_00046:0.00420071)n2:0.00846763)n1:0.089077)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001774_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001774_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5621edcf2e91f3750a78646fde99847ac03f30d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001774_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00351:0.0540747,(GCF_002008305_PROKKA_00052:0.0126845,(GCF_003691675_PROKKA_02065:5e-09,GCF_023573625_PROKKA_00047:0.00629795)n2:5e-09)n1:0.0540747)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001780_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001780_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d342e22dccbe5457d328026927032d080f7eb94
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001780_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00199:0.111706,(GCF_005280335_PROKKA_00264:0.133958,(GCF_002008305_PROKKA_00120:0.00256935,GCF_023573625_PROKKA_00128:0.00506484)n2:0.0677056)n1:0.111706)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001781_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001781_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f753196a646cf64754b543b76c9ae3645f04e3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001781_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00253:0.149176,(GCF_002008305_PROKKA_00132:5e-09,(GCF_003691675_PROKKA_02146:0,GCF_023573625_PROKKA_00140:0)n2:0.0113935)n1:0.149176)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001782_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001782_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dbb42b87f6a555d07a8a2c7ef0d1287a54802357
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001782_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00239:0.129363,(GCF_002008305_PROKKA_00145:0.020941,(GCF_003691675_PROKKA_02159:0.0165105,GCF_023573625_PROKKA_00153:0.0146854)n2:0.00994882)n1:0.129363)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001784_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001784_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6667e6ce998229d7c6a773e17c600e4bf3848abd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001784_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01469:0.728535,(GCF_023573625_PROKKA_00168:0.00654107,(GCF_003691675_PROKKA_02169:0.00137928,GCF_002008305_PROKKA_00155:0.219475)n2:0.0520782)n1:0.728535)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001790_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001790_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3baf5da346c23dc71f858acf87cc050713ab2975
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001790_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00161:0.0808036,(GCF_023573625_PROKKA_00220:0.011759,(GCF_002008305_PROKKA_00219:0.00479442,GCF_003691675_PROKKA_02213:0.00315209)n2:0.00958576)n1:0.0808036)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001791_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001791_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb664c5f99103804281d50a7374c301fa9e30ee7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001791_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00111:0.00906375,((GCF_002008305_PROKKA_00227:0,GCF_003691675_PROKKA_02240:0)n2:5e-09,GCF_023573625_PROKKA_00228:0.00451439)n1:0.00906375)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001793_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001793_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68e110458c0e4ec3a19fee2f907a09229d5b93f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001793_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00091:0.0990267,(GCF_003691675_PROKKA_02259:0.00610083,(GCF_002008305_PROKKA_00247:0.0107977,GCF_023573625_PROKKA_00247:0.00713198)n2:0.00728319)n1:0.0990267)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001795_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001795_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b2f6114be3dd277393155803be7157c760d6389
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001795_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00116:0.00801616,(GCF_002008305_PROKKA_00253:0.00795651,(GCF_003691675_PROKKA_02265:0,GCF_023573625_PROKKA_00253:0)n2:5e-09)n1:0.00801616)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001798_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001798_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5350e7462ab3ca68c14e57e99588595986effee0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001798_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00079:0.224631,(GCF_002008305_PROKKA_00276:6e-09,(GCF_003691675_PROKKA_02291:5e-09,GCF_023573625_PROKKA_00275:0.0103513)n2:0.0420036)n1:0.224631)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001799_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001799_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e40b475dd35125e00883b0e1a4f2945e60ebd3b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001799_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00048:0.192476,(GCF_023573625_PROKKA_00291:0.0121139,(GCF_002008305_PROKKA_00285:0.0301681,GCF_003691675_PROKKA_02307:0.00402206)n2:0.0104575)n1:0.192476)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001800_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001800_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8850c8d93585b5bd16e9e9cf8cf97508b9dec131
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001800_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00068:0.0738909,(GCF_002008305_PROKKA_00286:0.0306073,(GCF_003691675_PROKKA_02308:0.00552459,GCF_023573625_PROKKA_00292:0.0182388)n2:0.012383)n1:0.0738909)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001802_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001802_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a86b204e86afb9f522490e6491652d3baba99b3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001802_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00008:0.0568323,((GCF_002008305_PROKKA_00327:0,GCF_003691675_PROKKA_00043:0)n2:0.00340429,GCF_023573625_PROKKA_00334:0.00815401)n1:0.0568323)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001803_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001803_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..726151b4298c15ebe822fde06afe0b3804aae18e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001803_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00007:0.0515656,((GCF_002008305_PROKKA_00328:0,GCF_003691675_PROKKA_00044:0)n2:0.00531151,GCF_023573625_PROKKA_00335:0.0102036)n1:0.0515656)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001804_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001804_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a6bd9344c11a338c1bbb83cef5b30157ec87c08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001804_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00006:0.0268881,(GCF_002008305_PROKKA_00329:5e-09,(GCF_003691675_PROKKA_00045:0,GCF_023573625_PROKKA_00336:0)n2:0.00370812)n1:0.0268881)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001807_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001807_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0cca4b7f4d3205824ac07f877464e3777c42285
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001807_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02441:0.0014769,(GCF_003691675_PROKKA_00111:0.0285594,(GCF_002008305_PROKKA_00387:0.00484531,GCF_023573625_PROKKA_00393:0.0245676)n2:0.00987179)n1:0.0014769)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001808_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001808_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3bea21da5abedc1ec00fc25a154f28a6bbc36f5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001808_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02566:0.175046,((GCF_002008305_PROKKA_00390:0,GCF_003691675_PROKKA_00114:0)n2:5e-09,GCF_023573625_PROKKA_00396:0.0067864)n1:0.175046)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001812_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001812_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..61a20d78e826e2693746dab470ee0a536e638ee5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001812_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_00476:0,GCF_003691675_PROKKA_00194:0,GCF_023573625_PROKKA_00476:0)n1:0.113002,GCF_020097155_PROKKA_02355:0.113002)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001815_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001815_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eba1ed43fdf4ebfe8f05451c99afc3c84190427e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001815_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02413:0.0831457,(GCF_002008305_PROKKA_00536:6e-09,(GCF_003691675_PROKKA_00260:0,GCF_023573625_PROKKA_00539:0)n2:5e-09)n1:0.0831457)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001816_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001816_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..abff2ec0ea7ca6b33908ff7e0215a18a13921515
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001816_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02259:0.138812,(GCF_002008305_PROKKA_00569:0.0145181,(GCF_003691675_PROKKA_00293:0.0439482,GCF_023573625_PROKKA_00571:0.027696)n2:0.0262696)n1:0.138812)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001818_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001818_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6392d847c794234782de6962771e3e34d7959301
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001818_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02356:0.00193103,((GCF_002008305_PROKKA_00577:0,GCF_003691675_PROKKA_00309:0)n2:5e-09,GCF_023573625_PROKKA_00578:0.00193056)n1:0.00193103)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001819_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001819_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18c5c67331055197f4098079f752af4cfa33e1bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001819_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02355:0.00419503,((GCF_002008305_PROKKA_00578:0,GCF_003691675_PROKKA_00310:0)n2:5e-09,GCF_023573625_PROKKA_00579:0.00278207)n1:0.00419503)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001821_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001821_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4bc5b76a6eb0b17dcc33b53ce21dff79ef44d5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001821_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00752:0.249061,(GCF_023573625_PROKKA_00593:0,(GCF_002008305_PROKKA_00624:0.00959566,GCF_002008305_PROKKA_00638:0)n2:0)n1:0.0123636)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001824_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001824_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef948ee722c0e95a56b9f4020735ea4a42f35311
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001824_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02200:0.001717,(GCF_023573625_PROKKA_00602:5e-09,(GCF_002008305_PROKKA_00629:0.00342244,GCF_005280335_PROKKA_00401:0.0104257)n2:5e-09)n1:0.001717)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001825_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001825_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef7b10b357de834d4b117d7900505d1b70a0b3fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001825_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02197:0,(GCF_005280335_PROKKA_00404:0,(GCF_002008305_PROKKA_00632:0,GCF_023573625_PROKKA_00599:0)n2:0.00862125)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001826_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001826_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e13c0d3ceeb64b8764b45b74f461bfdb693104a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001826_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02194:0.00273811,(GCF_002008305_PROKKA_00635:0.00822332,(GCF_023573625_PROKKA_00596:0.00273369,GCF_005280335_PROKKA_00407:5e-09)n2:5e-09)n1:0.00273811)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001827_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001827_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a51e103587878fe1e1158e9ba76b7c11b8e21620
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001827_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02186:0.0107889,(GCF_002008305_PROKKA_00639:0.0180496,(GCF_003691675_PROKKA_00376:0.0071396,GCF_023573625_PROKKA_00608:0.00356013)n2:0.00349096)n1:0.0107889)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001829_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001829_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..965697521d73e724d218a5dc1d7722fe3a82e08b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001829_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02317:0.139748,(GCF_023573625_PROKKA_00616:5e-09,(GCF_002008305_PROKKA_00646:0.00487873,GCF_003691675_PROKKA_00383:5e-09)n2:0.00487328)n1:0.139748)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001832_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001832_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f352bc4c74aedbba4c6146e6d24e98da832f0420
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001832_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02296:0.0604663,((GCF_002008305_PROKKA_00666:0,GCF_003691675_PROKKA_00403:0)n2:0.00558345,GCF_023573625_PROKKA_00636:6e-09)n1:0.0604663)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001834_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001834_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..11f49c2932effa0e73da71f746fa25ce48d11d4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001834_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02146:0.181693,(GCF_003691675_PROKKA_00415:0.0100633,(GCF_002008305_PROKKA_00678:5e-09,GCF_023573625_PROKKA_00648:0.00998377)n2:5e-09)n1:0.181693)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001836_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001836_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..955745410efde3bd4746f8b18f62020b69cac8c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001836_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02191:0.19984,(GCF_002008305_PROKKA_00739:0.0170802,(GCF_003691675_PROKKA_00470:0.0280107,GCF_023573625_PROKKA_00703:0.049493)n2:0.0247515)n1:0.19984)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001838_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001838_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..276d2e9d62d6f81e758b42e89d6954fab90646f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001838_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02089:0.223001,(GCF_002008305_PROKKA_00846:0.0146619,(GCF_003691675_PROKKA_00568:5e-09,GCF_023573625_PROKKA_00805:5e-09)n2:0.0208704)n1:0.223001)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001840_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001840_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a02f771c038347276366c2503ecd7863b3024e66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001840_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01991:0.0263775,(GCF_002008305_PROKKA_00946:0.00546107,(GCF_003691675_PROKKA_01109:0.913524,GCF_003691675_PROKKA_00665:0.00691299)n2:0.00076811)n1:0.102431)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001843_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001843_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..85ffeab452203c450c7aa2139d5e455663d863b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001843_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01879:0.0148451,((GCF_002008305_PROKKA_01010:0,GCF_003691675_PROKKA_00724:0)n2:0.0325554,GCF_023573625_PROKKA_00953:0.015914)n1:0.0148451)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001844_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001844_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db767680df7c53c2c0a64d400b4876eed4642bab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001844_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01875:0.0155142,((GCF_002008305_PROKKA_01013:0,GCF_023573625_PROKKA_00956:0)n2:5e-09,GCF_003691675_PROKKA_00727:5e-09)n1:0.0155142)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001846_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001846_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..85a5b75479011eeba7c38f3f4295cfbb62532e88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001846_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01712:0.105009,(GCF_002008305_PROKKA_01064:5e-09,(GCF_023573625_PROKKA_01011:0.00460909,GCF_003691675_PROKKA_00783:0.00460132)n2:0.00458123)n1:0.105009)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001847_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001847_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..840e0f7f44a86c4dc8d85ffb4e8e07f748e97e07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001847_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02229:0.0260795,(GCF_003691675_PROKKA_00786:5e-09,(GCF_002008305_PROKKA_01067:0.0102006,GCF_023573625_PROKKA_01014:5e-09)n2:0.0102305)n1:0.0260795)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001848_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001848_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b12527209cf793d750665edf71cff6287baf11cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001848_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01076:0,GCF_003691675_PROKKA_00795:0,GCF_023573625_PROKKA_01025:0)n1:0.20598,GCF_005280335_PROKKA_02322:0.20598)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001849_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001849_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..061b5f0711ac91d5204c46b0f8c67f074d1190b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001849_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01077:0,GCF_003691675_PROKKA_00796:0,GCF_023573625_PROKKA_01026:0)n1:0.20574,GCF_005280335_PROKKA_02323:0.20574)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001851_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001851_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bea82b401ca806a2b50f291eb88818bb866ad7c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001851_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01781:0.0442941,(GCF_003691675_PROKKA_00831:5e-09,(GCF_002008305_PROKKA_01112:5e-09,GCF_023573625_PROKKA_01062:0.00239669)n2:0.0120832)n1:0.0442941)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001852_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001852_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4dc07e376579a7839a07d569474ece956993d2f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001852_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01641:0.238171,(GCF_002008305_PROKKA_01145:0.0179503,(GCF_003691675_PROKKA_00864:0,GCF_023573625_PROKKA_01095:0)n2:0.0451574)n1:0.238171)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001853_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001853_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6ab7a6c20371ded2e497c56e73ab74dc597b06f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001853_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01155:0,GCF_003691675_PROKKA_00874:0,GCF_023573625_PROKKA_01105:0)n1:0.261638,GCF_005280335_PROKKA_01734:0.261638)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001855_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001855_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..afe565f19142cb1d58959dd75210d13a3e30fe55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001855_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01573:0.105462,(GCF_003691675_PROKKA_00931:0.00772437,(GCF_002008305_PROKKA_01212:0.0110905,GCF_023573625_PROKKA_01169:0.00365839)n2:0.00329945)n1:0.105462)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001856_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001856_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9dc162e459516b8ba71e5551ac928c7c9e533694
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001856_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01665:0.0640689,(GCF_002008305_PROKKA_01223:5e-09,(GCF_003691675_PROKKA_00942:0.00945486,GCF_023573625_PROKKA_01181:0.00468666)n2:0.00949371)n1:0.0640689)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001862_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001862_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77bb92b198a8b51b05804fd8facfa8f9223bbe9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001862_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01893:0.266579,((GCF_002008305_PROKKA_01382:0,GCF_023573625_PROKKA_01337:0)n2:0.00860321,GCF_003691675_PROKKA_01102:0.0144755)n1:0.266579)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001863_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001863_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5d8d1a9f744834b686a43b4a3203e418429cca8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001863_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01402:0.104928,(GCF_002008305_PROKKA_01405:5e-09,(GCF_003691675_PROKKA_01135:0,GCF_023573625_PROKKA_01355:0)n2:0.00383681)n1:0.104928)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001865_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001865_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f469b09420b79be7d1d94b3cdf4ab4fc4e6bb0a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001865_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01396:0.308018,(GCF_023573625_PROKKA_01360:0.137591,(GCF_003691675_PROKKA_01140:0.00227414,GCF_002008305_PROKKA_01410:0.018195)n2:0.00763499)n1:0.308018)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001866_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001866_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0fa1e20df6ad6d0734833b96099c821ad1439f7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001866_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01395:0.215731,(GCF_003691675_PROKKA_01141:5e-09,(GCF_002008305_PROKKA_01411:0.00423398,GCF_023573625_PROKKA_01361:5e-09)n2:0.0200578)n1:0.215731)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001872_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001872_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9b645fafa3d770e6021ae3fb2a948b9c6b79fa9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001872_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01477:0,GCF_003691675_PROKKA_01209:0,GCF_023573625_PROKKA_01427:0)n1:0.0105616,GCF_020097155_PROKKA_01325:0.0105616)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001873_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001873_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f26e78efbc2ed00829183e9bb9559c52be4d2457
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001873_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_PROKKA_01506:0.00568268,(GCF_020097155_PROKKA_00640:0.28543,(GCF_020097155_PROKKA_01746:0,GCF_020097155_PROKKA_02236:0)n2:0.0452359)n1:0.00568268)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001874_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001874_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f69464a916a9826dc3a7455c394f8e5f9d6bc63b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001874_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01411:0.0393985,((GCF_002008305_PROKKA_01514:0,GCF_003691675_PROKKA_01223:0)n2:0.00292785,GCF_023573625_PROKKA_01441:0.0058193)n1:0.0393985)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001876_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001876_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..640c9b063f5ffc183dbb63f767d86cd4498026b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001876_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01586:0,GCF_003691675_PROKKA_01297:0,GCF_023573625_PROKKA_01513:0)n1:0.0072449,GCF_005280335_PROKKA_01336:0.0072449)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001879_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001879_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f540c7f669802f2c08b528ef5252468063c5ca5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001879_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01189:0.00542795,(GCF_005280335_PROKKA_01285:0.0161948,(GCF_002008305_PROKKA_01614:0.0107166,GCF_003691675_PROKKA_01324:0.00535844)n2:0.00524755)n1:0.00542795)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001885_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001885_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd044bc94ebdaaf7371e7f621d25c30746729c8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001885_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01111:0.102984,(GCF_023573625_PROKKA_01695:0.00145736,(GCF_002008305_PROKKA_01766:0.00840655,GCF_003691675_PROKKA_01473:0.00166648)n2:0.00356404)n1:0.102984)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001887_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001887_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c138a03e3efeaf5c36495ae105812088f760b671
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001887_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01004:0.092199,(GCF_003691675_PROKKA_01502:0.0255573,(GCF_002008305_PROKKA_01805:0.0249552,GCF_023573625_PROKKA_01726:5e-09)n2:0.0107777)n1:0.092199)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001888_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001888_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f4fbe0a28df1182b49c35ab475f0c3e8f12b57a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001888_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01032:0.129565,(GCF_002008305_PROKKA_01836:0.0153444,(GCF_003691675_PROKKA_01533:0,GCF_023573625_PROKKA_01757:0)n2:0.0147124)n1:0.129565)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001890_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001890_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..975fc2052e47bf167fe4cec68f2898fc528c589f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001890_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00920:0.183998,(GCF_005280335_PROKKA_00982:0.0747636,(GCF_002008305_PROKKA_01877:5e-09,GCF_003691675_PROKKA_01573:0.00941512)n2:0.164276)n1:0.183998)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001892_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001892_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6f086b90ecb8d62dbaec1727a2fb6d7fcb21217b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001892_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00980:0.152867,((GCF_002008305_PROKKA_01879:0,GCF_003691675_PROKKA_01575:0)n2:0.011656,GCF_023573625_PROKKA_01799:0.0123571)n1:0.152867)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001895_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001895_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c24f0984429c081261e33ebeffc6384e7a847d59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001895_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00963:0.0542452,((GCF_002008305_PROKKA_01895:0,GCF_023573625_PROKKA_01815:0)n2:0.0126,GCF_003691675_PROKKA_01591:0.00821494)n1:0.0542452)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001896_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001896_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d73f2a15c6345a3d65c7cbedaaf3e10f6c5f6e88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001896_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00961:0.133966,(GCF_002008305_PROKKA_01898:0.0134004,(GCF_023573625_PROKKA_01818:0.015715,GCF_003691675_PROKKA_01594:0.00514071)n2:0.00746675)n1:0.133966)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001904_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001904_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57efc8bb9806491135d7223b99e3ab38e5139628
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001904_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00848:0.00268334,((GCF_002008305_PROKKA_01946:0,GCF_023573625_PROKKA_01865:0)n2:5e-09,GCF_005280335_PROKKA_00916:0.42454)n1:0.00268334)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001906_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001906_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dea0497de0122b94032a56906ca0b6b209797ba8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001906_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00881:0.0999535,(GCF_002008305_PROKKA_01977:5e-09,(GCF_003691675_PROKKA_01670:0.0235363,GCF_023573625_PROKKA_01902:5e-09)n2:0.0491364)n1:0.0999535)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001912_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001912_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa10ffa13201f1dff3a253d7ffe3523d6a1f64b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001912_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00104:0.0994383,(GCF_002008305_PROKKA_02037:1.26127,(GCF_005280335_PROKKA_00142:0.195113,GCF_005280335_PROKKA_00807:0.602147)n2:0.0669052)n1:0.391367)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001913_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001913_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80627859be3c3da5fc816705f2c799c3145a81f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001913_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00772:0.100677,(GCF_002008305_PROKKA_02044:0.0236283,(GCF_003691675_PROKKA_01750:0.0205293,GCF_023573625_PROKKA_01978:0.0076349)n2:0.00562601)n1:0.100677)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001921_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001921_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ddb00afc7b70396fd25b4eca21c775903f62311e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001921_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00682:0.0984581,(GCF_002008305_PROKKA_02097:0.023971,(GCF_003691675_PROKKA_01804:5e-09,GCF_023573625_PROKKA_02037:0.0023584)n2:0.0199149)n1:0.0984581)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001922_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001922_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7eb607cdef11cc378ec5a926c0bf7d74f600b5fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001922_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00679:0.232468,((GCF_002008305_PROKKA_02100:0,GCF_003691675_PROKKA_01807:0)n2:0.00579873,GCF_023573625_PROKKA_02040:0.00174272)n1:0.232468)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001924_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001924_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b6909f1d2c99a7e184b3565ecb81b16056f139b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001924_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00670:0.0273348,(GCF_023573625_PROKKA_02048:0.00552179,(GCF_002008305_PROKKA_02108:5e-09,GCF_003691675_PROKKA_01815:0.00519105)n2:0.00507844)n1:0.0273348)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001925_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001925_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fdadcb563c56a60698dc78f441fc3c7aa8c993ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001925_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00664:0.119057,(GCF_003691675_PROKKA_01824:0.0156844,(GCF_002008305_PROKKA_02116:0.0211433,GCF_023573625_PROKKA_02054:0.0102908)n2:0.0281542)n1:0.119057)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001926_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001926_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..344ae0e807e4308c0a80989f03adf034664942f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001926_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00573:0.0107836,(GCF_002008305_PROKKA_02124:5e-09,(GCF_003691675_PROKKA_01832:0.00529864,GCF_023573625_PROKKA_02062:5e-09)n2:0.00532696)n1:0.0107836)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001927_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001927_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f141a6a26b0c98db9388ec8f8e79aeb3c6834db5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001927_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00637:0.00751945,(GCF_002008305_PROKKA_02135:0.00894928,(GCF_003691675_PROKKA_01843:0,GCF_023573625_PROKKA_02073:0)n2:0.0119897)n1:0.00751945)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001931_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001931_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b8efa5f3c49e1452a9d68300de4853c7f295fb5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001931_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00580:0.236952,(GCF_002008305_PROKKA_02172:5e-09,(GCF_023573625_PROKKA_02117:0.0283588,GCF_003691675_PROKKA_01886:6e-09)n2:0.00349361)n1:0.236952)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001934_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001934_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8b67e3705ef28afba4e820d98d33dcacb935271
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001934_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00550:0.0272,(GCF_003691675_PROKKA_01905:5e-09,(GCF_002008305_PROKKA_02192:0.0176703,GCF_023573625_PROKKA_02136:0.0361472)n2:0.0180269)n1:0.0272)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001935_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001935_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93b2d4d4df9df3fac0742a72a267991494989fab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001935_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00553:0.151734,(GCF_003691675_PROKKA_01906:0.0505042,(GCF_002008305_PROKKA_02193:0.0103072,GCF_023573625_PROKKA_02137:0.00596562)n2:0.00754766)n1:0.151734)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001936_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001936_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4390d211b170a4417e2ef58f91b00c56c3554fd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001936_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_02203:0,GCF_003691675_PROKKA_01916:0,GCF_023573625_PROKKA_02147:0)n1:0.105077,GCF_005280335_PROKKA_00540:0.105077)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001938_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001938_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64c1c9b6b6e91bbed49782a031965bec1e34695e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001938_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_02209:0,GCF_003691675_PROKKA_01922:0)n1:0.0234336,(GCF_005280335_PROKKA_00535:0.0646695,GCF_005280335_PROKKA_02645:1.70216)n2:0.0234336)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001940_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001940_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49eeb9cf5f23a69289f3d922233a7fe57bf08c67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001940_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00530:0.0790801,(GCF_003691675_PROKKA_01927:0.0126826,(GCF_002008305_PROKKA_02214:0.0127049,GCF_023573625_PROKKA_02153:0.0127361)n2:5e-09)n1:0.0790801)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001941_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001941_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1edd9bc1eda53fcd63af739e4f89c6f1464e43c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001941_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00473:0.279119,(GCF_023573625_PROKKA_02157:5e-09,(GCF_002008305_PROKKA_02218:0.00242136,GCF_003691675_PROKKA_01931:0.00240608)n2:0.0169663)n1:0.279119)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001943_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001943_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28f2a929de36be84536e328e06a6af3de4d966bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001943_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00461:0.0660439,(GCF_002008305_PROKKA_02222:5e-09,(GCF_003691675_PROKKA_01938:0.0114796,GCF_023573625_PROKKA_02161:0.00228352)n2:0.00228664)n1:0.0660439)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001944_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001944_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c077379a0db4bcfd0dcc14f4101e66d046d0a9d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001944_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01229:0.193694,(GCF_002008305_PROKKA_02224:0.00982965,(GCF_003691675_PROKKA_01939:0.00855702,GCF_023573625_PROKKA_02162:0.00434455)n2:0.00309558)n1:0.193694)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001945_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001945_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4bd46a7181289ae25c886554c009a773c56f570c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001945_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00700:0.293305,((GCF_002008305_PROKKA_02259:0,GCF_023573625_PROKKA_02190:0)n2:0.177182,GCF_005280335_PROKKA_00463:0.0368016)n1:0.293305)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001947_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001947_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d67626457c34d0e911ae065b05de26ac927ac522
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001947_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00410:0.219342,(GCF_003691675_PROKKA_01964:0.0289175,(GCF_002008305_PROKKA_02272:0.0789512,GCF_005280335_PROKKA_00460:0.0319186)n2:0.0380774)n1:0.219342)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001949_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001949_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22166c00b36906bd35e9b53011e7a16d5258a4a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001949_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00808:0.461891,(GCF_002008305_PROKKA_02283:0.00308963,(GCF_003691675_PROKKA_01974:0.0102634,GCF_023573625_PROKKA_02222:0.00511059)n2:0.00229719)n1:0.461891)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001950_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001950_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da466b36bf87924f72f2d5eb4dd732c5d5bed508
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001950_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00453:0.0164657,(GCF_023573625_PROKKA_02223:5e-09,(GCF_002008305_PROKKA_02284:0.00246988,GCF_003691675_PROKKA_01975:5e-09)n2:0.00494658)n1:0.0164657)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001952_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001952_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0ed6ab7f0c32fbad8a33fdedaa5da1c44e11b78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001952_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_02300:0,GCF_003691675_PROKKA_01993:0,GCF_023573625_PROKKA_02241:0)n1:0.101546,GCF_020097155_PROKKA_00389:0.101546)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001955_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001955_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1bc9b53a3f1fc85bc855967466cbd6f8f9df0da2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001955_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02300:0.0448856,(GCF_023573625_PROKKA_00534:0.0323021,(GCF_003691675_PROKKA_00255:0.0338375,GCF_005280335_PROKKA_02418:0.879987)n2:0.038117)n1:0.0448856)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001956_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001956_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1c1c14062c641a6c43a5d76cd5858d61055998b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001956_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02298:0.217015,(GCF_005280335_PROKKA_02416:0.181118,(GCF_003691675_PROKKA_00257:0.00415953,GCF_023573625_PROKKA_00536:0.00974654)n2:0.156571)n1:0.217015)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001957_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001957_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee22e367bee6dbbfc08da36a22c47839793c1ebf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001957_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01825:0.00318969,((GCF_003691675_PROKKA_00323:0,GCF_005280335_PROKKA_02273:0)n2:5e-09,GCF_023573625_PROKKA_00592:0.00451553)n1:0.00318969)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001962_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001962_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..622af54230e6de78c644dbbfbaaca120f07865bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001962_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00840:0.115379,(GCF_003691675_PROKKA_01647:0.10084,(GCF_005280335_PROKKA_00901:0.0118975,GCF_023573625_PROKKA_01878:0.0506438)n2:6e-09)n1:0.115379)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001965_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001965_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..714131553c0c37b2ff0cb10453f1fe383d2c0fe3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001965_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00788:0.0749963,((GCF_003691675_PROKKA_01700:0,GCF_023573625_PROKKA_01928:0)n2:0.0206326,GCF_005280335_PROKKA_00851:0.0213432)n1:0.0749963)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001967_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001967_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68c907e6b3c145027915783e3757164e82eb29c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001967_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00786:0.0206252,((GCF_003691675_PROKKA_01702:0,GCF_023573625_PROKKA_01930:0)n2:0.0575727,GCF_005280335_PROKKA_00849:0.083245)n1:0.0206252)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001969_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001969_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8542f5091ed0d4110d8742cbd9d81c5608d0de9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001969_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00779:0.0390988,(GCF_005280335_PROKKA_00846:0.134102,(GCF_003691675_PROKKA_01706:5e-09,GCF_023573625_PROKKA_01934:0.00682564)n2:0.0479524)n1:0.0390988)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001970_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001970_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb9141e0d40185783bae41123ffab37d8266e885
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001970_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00778:0.0960212,((GCF_003691675_PROKKA_01707:0,GCF_023573625_PROKKA_01935:0)n2:0.0938914,GCF_005280335_PROKKA_00845:0.197823)n1:0.0960212)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001971_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001971_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7af03961f78381d21ab964c47c1631bf556340d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001971_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00777:0.0520201,(GCF_005280335_PROKKA_00844:0.160031,(GCF_003691675_PROKKA_01708:0.00592355,GCF_023573625_PROKKA_01936:0.00504453)n2:0.156863)n1:0.0520201)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001973_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001973_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2867241e15a5e4b969a2fdc2669bcb2cf5d73f1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001973_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00541:2.5e-09,(GCF_005280335_PROKKA_00617:0.0424415,(GCF_003691675_PROKKA_01857:0.0101197,GCF_023573625_PROKKA_02087:0.0219531)n2:0.144794)n1:2.5e-09)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001975_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001975_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b8bd9be52f983919894a3471f06ff42895910f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001975_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00436:0.0100616,(GCF_005280335_PROKKA_01324:0.977023,(GCF_003691675_PROKKA_01950:0.00419944,GCF_023573625_PROKKA_02180:5e-09)n2:0.0272194)n1:0.0100616)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001976_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001976_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65c508a7c4b86751d5c34c619e695046a7c52ece
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001976_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00196:0.151936,(GCF_020097155_PROKKA_00148:0.00595341,GCF_020097155_PROKKA_00597:1.13083)n2:0.125647)n1:0.061966,GCF_023573625_PROKKA_00199:0.0251452)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001981_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001981_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e9115acf63a56c66ffb3daa84d8b6ee27cceae4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001981_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02337:0,(GCF_005280335_PROKKA_02342:0,GCF_005280335_PROKKA_02640:0,GCF_005280335_PROKKA_02651:0)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001983_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001983_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48033733b6fa5b5901632dea663d20103726babf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001983_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00423:0.250096,(GCF_020097155_PROKKA_00644:0.847738,(GCF_020097155_PROKKA_01784:0.363418,GCF_020097155_PROKKA_01822:0.250331)n2:0.777738)n1:0.250096)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001984_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001984_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3522970506d6543105dfaccb76b6c527b032636a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001984_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00698:0.00269781,(GCF_020097155_PROKKA_00722:0.023332,(GCF_020097155_PROKKA_00661:0.155872,GCF_020097155_PROKKA_01398:1.37606)n2:0.117665)n1:0.00269781)n0;
\ No newline at end of file