diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000000_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000000_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9967d666e85d014dea335922d3ac80e34cd08b98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000000_tree.txt
@@ -0,0 +1 @@
+(((GCF_023573625_PROKKA_02102:5e-09,GCF_023573625_PROKKA_02106:0.00288249):0.0206525,(GCF_003691675_PROKKA_00352:0.042443,(GCF_005280335_PROKKA_01505:0.25879,GCF_005280335_PROKKA_02339:0.304882):0.287255):0.0287259):0.0103334,((GCF_005280335_PROKKA_00227:0.0028477,(GCF_005280335_PROKKA_01737:0,GCF_005280335_PROKKA_02555:0):0.00300792):0.043213,((GCF_003691675_PROKKA_00137:5e-09,GCF_003691675_PROKKA_01971:0.0353709):0.00702144,(((GCF_003691675_PROKKA_00041:0.0194533,((((GCF_005280335_PROKKA_01499:0,GCF_005280335_PROKKA_02472:0):5e-09,GCF_005280335_PROKKA_02613:0.00287677):5e-09,GCF_005280335_PROKKA_00779:0.0758185):0.00356263,(((GCF_005280335_PROKKA_01768:0,GCF_005280335_PROKKA_02336:0):5e-09,GCF_005280335_PROKKA_02637:0.00289763):5e-09,GCF_005280335_PROKKA_00146:5e-09):0.0419983):0.0311409):0.0442562,(GCF_003691675_PROKKA_01118:0.00999489,(GCF_005280335_PROKKA_02632:0.0613057,(GCF_005280335_PROKKA_00044:5e-09,(GCF_005280335_PROKKA_00556:0.00288709,GCF_005280335_PROKKA_00692:5e-09):6e-09):0.0411965):0.016226):0.0374734):0.0251797,(GCF_003691675_PROKKA_00012:0.00638885,(((GCF_003691675_PROKKA_00312:0.011895,(GCF_002008305_PROKKA_01952:5e-09,GCF_002008305_PROKKA_01337:0.0432482):0.0130261):0.00430081,((GCF_002008305_PROKKA_02278:5e-09,(GCF_002008305_PROKKA_02111:5e-09,GCF_003691675_PROKKA_01818:5e-09):0.00292862):0.0270247,((GCF_003691675_PROKKA_02077:0.0168131,(GCF_002008305_PROKKA_00064:0.00555023,(GCF_002008305_PROKKA_02068:0.00889823,GCF_003691675_PROKKA_01821:0.0119179):0.0277276):0.0154651):0.00348074,(GCF_023573625_PROKKA_00274:0,GCF_023573625_PROKKA_01546:0):0.0164863):0.00929313):0.0190404):5e-09,(GCF_003691675_PROKKA_01236:0.00942898,(GCF_023573625_PROKKA_00879:5e-09,((GCF_023573625_PROKKA_01570:0.00291278,(GCF_023573625_PROKKA_00800:6e-09,GCF_023573625_PROKKA_01175:0.00288019):0.0057635):0.00250032,(GCF_003691675_PROKKA_01160:0.00385663,(GCF_003691675_PROKKA_01968:0.00515122,(GCF_023573625_PROKKA_01997:0.00693576,GCF_023573625_PROKKA_00518:0.0138941):0.00300346):0.00298165):0.00434738):0.000801834):0.0169932):0.00287359):0.0232115):0.0122406):0.0171617):0.022268):0.0103334);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000001_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000001_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7496c539de83284584ebc0882643e60034868440
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000001_tree.txt
@@ -0,0 +1 @@
+((((GCF_002008305_PROKKA_01202:0,GCF_002008305_PROKKA_02030:0):5e-09,(GCF_023573625_PROKKA_02197:0,GCF_023573625_PROKKA_02214:0):0.00229901):0.037448,(GCF_005280335_PROKKA_00896:0.129812,GCF_005280335_PROKKA_00691:5e-09):0.0222397):0.00854238,((GCF_002008305_PROKKA_00603:0.002284,GCF_005280335_PROKKA_02671:0.00463582):0.037088,(((GCF_003691675_PROKKA_01126:0.0284997,(GCF_023573625_PROKKA_01344:0.00226378,(GCF_003691675_PROKKA_01127:6e-09,(GCF_002008305_PROKKA_01394:0.00226318,GCF_023573625_PROKKA_01996:5e-09):5e-09):5e-09):0.00715389):0.421963,(((GCF_002008305_PROKKA_02266:5e-09,(GCF_002008305_PROKKA_02231:0.00295219,(GCF_002008305_PROKKA_02065:0.00346372,GCF_002008305_PROKKA_02229:0.00575251):0.0037022):5e-09):0.00942841,((GCF_002008305_PROKKA_00174:0,GCF_002008305_PROKKA_00589:0,GCF_002008305_PROKKA_00713:0,GCF_002008305_PROKKA_01399:0):5e-09,GCF_002008305_PROKKA_02226:0.00702547):0.00231512):0.0223796,(GCF_002008305_PROKKA_00623:0.0113847,(GCF_002008305_PROKKA_02064:0.0669297,GCF_002008305_PROKKA_02232:0.0564102):0.00503313):0.0024637):0.0834388):0.127961,(GCF_005280335_PROKKA_00721:0.00210909,(GCF_002008305_PROKKA_01504:0.144714,((GCF_002008305_PROKKA_01505:0.111612,(GCF_002008305_PROKKA_00602:0,GCF_002008305_PROKKA_01070:0,GCF_002008305_PROKKA_02271:0):5e-09):0.00460946,GCF_005280335_PROKKA_02500:5e-09):5e-09):0.00249882):0.0103711):0.0265433):0.00854238);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000003_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000003_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..114c5cdc791ae759b14dc445f6df6631b4dfb74d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000003_tree.txt
@@ -0,0 +1 @@
+(((GCF_023573625_PROKKA_00114:6e-09,(GCF_003691675_PROKKA_01116:5e-09,GCF_023573625_PROKKA_01884:0.00642897):0.00642558):0.0064542,((((GCF_005280335_PROKKA_01281:0,GCF_005280335_PROKKA_01312:0):0.00752593,((GCF_005280335_PROKKA_02347:6e-09,GCF_005280335_PROKKA_02631:0.0150545):0.0150917,((GCF_002008305_PROKKA_02280:0.135022,GCF_020097155_PROKKA_00317:0.0497284):0.0472623,GCF_005280335_PROKKA_01304:5e-09):0.00757128):5e-09):0.00758893,GCF_020097155_PROKKA_00625:0.00745579):5e-09,(GCF_002008305_PROKKA_01068:0.0149832,(GCF_003691675_PROKKA_01658:0.00646513,(((GCF_003691675_PROKKA_00319:0,GCF_003691675_PROKKA_02267:0):0.00740272,GCF_003691675_PROKKA_00788:5e-09):0.00738558,GCF_005280335_PROKKA_01317:0.0074632):6e-09):0.0129635):0.00655117):0.00648215):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):5e-09,(GCF_020097155_PROKKA_01796:0,GCF_020097155_PROKKA_01836:0,GCF_020097155_PROKKA_02207:0):0.00738984):5e-09):5e-09):2.5e-09);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000007_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000007_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a63c844c9b9ed89e15be3a2fbbaf079ee249699
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000007_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01213:0,(GCF_002008305_PROKKA_00158:0,GCF_002008305_PROKKA_01293:0,GCF_002008305_PROKKA_02076:0,GCF_003691675_PROKKA_01016:0,GCF_003691675_PROKKA_01103:0,GCF_003691675_PROKKA_01115:0,GCF_003691675_PROKKA_02022:0,GCF_023573625_PROKKA_00589:0,GCF_023573625_PROKKA_00591:0,GCF_023573625_PROKKA_01251:0,GCF_023573625_PROKKA_01338:0,GCF_023573625_PROKKA_01886:0,GCF_023573625_PROKKA_02204:0,(GCF_003691675_PROKKA_01111:0.00916342,(GCF_002008305_PROKKA_01033:0.00914985,GCF_002008305_PROKKA_01383:5e-09):5e-09):5e-09):0);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000008_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000008_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ac373224883d222767d7ba3095a3341e860ad7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000008_tree.txt
@@ -0,0 +1 @@
+(((GCF_002008305_PROKKA_00711:0,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):5e-09,(GCF_002008305_PROKKA_01398:0.0719037,(GCF_002008305_PROKKA_01502:0.00443704,GCF_002008305_PROKKA_02225:0.46793):0.00244087):0.0621436):2.5e-09,(GCF_002008305_PROKKA_02227:0.026191,(GCF_023573625_PROKKA_01016:0,GCF_023573625_PROKKA_01158:0):0.00373267):2.5e-09);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000010_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000010_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02e077879d948467eaa48d376f725bfa540274cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000010_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00630:0,GCF_020097155_PROKKA_00638:0,GCF_020097155_PROKKA_00839:0):0.163425,((GCF_005280335_PROKKA_01092:0.0286223,(GCF_005280335_PROKKA_00508:5e-09,(GCF_005280335_PROKKA_00108:5e-09,(GCF_005280335_PROKKA_00509:0,GCF_005280335_PROKKA_01091:0):0.0174212):5e-09):0.0139274):0.231105,(GCF_002008305_PROKKA_00845:0.12347,(GCF_002008305_PROKKA_00454:0.133764,(GCF_003691675_PROKKA_01124:5e-09,(GCF_002008305_PROKKA_01392:0.0071479,GCF_023573625_PROKKA_01343:5e-09):0.00715271):0.288002):0.169868):0.855007):0.163425);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000012_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000012_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ddf916fde3923d01bc7d99aaafd8e8722e06ce0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000012_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02223:0,(GCF_002008305_PROKKA_02063:0,(GCF_003691675_PROKKA_00297:0.255798,((GCF_005280335_PROKKA_00722:0.139128,(GCF_003691675_PROKKA_00338:0,GCF_003691675_PROKKA_00345:0,GCF_003691675_PROKKA_00794:0):5e-09):0.00624757,(GCF_002008305_PROKKA_01075:5e-09,(GCF_002008305_PROKKA_00159:0.0218981,(GCF_002008305_PROKKA_00156:0.0266784,(GCF_005280335_PROKKA_00720:0,GCF_023573625_PROKKA_01024:0):0.0148181):0.00599024):5e-09):0.00932758):0.240536):0.445773):0);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000013_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000013_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7461f544607aa0434e2b66156523ef46f17f18af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000013_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01887:0.0140417,(GCF_023573625_PROKKA_00898:0.0157493,(GCF_003691675_PROKKA_00341:0.124098,(GCF_023573625_PROKKA_01544:0.406222,(GCF_005280335_PROKKA_00706:0.38075,(GCF_003691675_PROKKA_01765:0.0218988,((GCF_005280335_PROKKA_02276:0.00125225,GCF_005280335_PROKKA_02636:0.0115439)0.83:0.012746,(GCF_005280335_PROKKA_02496:0.211792,(GCF_005280335_PROKKA_02495:0.00541976,GCF_005280335_PROKKA_02615:5e-09)0.423:5e-09)0.325:0.00349261)0.914:0.0204545)0.943:0.16121)0.791:0.0906104)0.887:0.0616112)0.999:0.13763)1:0.0140417);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000014_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000014_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1aa7ea77e165ab5a851d96a2524c7a60a2123b5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000014_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02220:0.00402046,(GCF_002008305_PROKKA_02060:5e-09,(GCF_003691675_PROKKA_00298:0.230585,(GCF_023573625_PROKKA_01023:5e-09,(GCF_005280335_PROKKA_00723:0.00200906,((GCF_002008305_PROKKA_00160:0,GCF_002008305_PROKKA_01074:0,GCF_003691675_PROKKA_00346:0):5e-09,(GCF_003691675_PROKKA_00337:5e-09,GCF_003691675_PROKKA_00793:0.00201048):0.0020099):0.00200908):0.00201403):0.241378):0.201634):0.00402046);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000015_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000015_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fe6b3fef0efc66f3476a170dbad87291df8b258
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.46:0.0035327)0.911:0.00840392)0.278:0.0137265)1:0.239249,(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)0.769:0.00178836)0.759:0.00257201)0.815:0.0229549)1:0.239249);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000016_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000016_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e56434e7eedbdad47900b654773d935bc41546c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000016_tree.txt
@@ -0,0 +1 @@
+((((GCF_002008305_PROKKA_01771:0,GCF_003691675_PROKKA_01478:0):0.00640386,GCF_023573625_PROKKA_01700:0.00630266):0.00346542,(GCF_005280335_PROKKA_01106:0.0334911,GCF_020097155_PROKKA_01032:0.109175):0.0194111):0.0112761,((GCF_003691675_PROKKA_00706:0.00583165,GCF_023573625_PROKKA_00935:0.00254211):0.00401193,(GCF_005280335_PROKKA_01897:0.0411368,(GCF_002008305_PROKKA_00992:0.0145508,GCF_020097155_PROKKA_01844:0.0149575):0.00218125):0.00277314):0.0112761);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000017_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000017_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c459eef1e2c99ea7b0483e4d52cacebb9436db3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000017_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00880:0.0423769,(GCF_002008305_PROKKA_01915:0.00450215,(GCF_003691675_PROKKA_01611:0.00167757,GCF_023573625_PROKKA_01835:5e-09)0.915:0.0090813)0.995:0.0981629)1:0.286273,(GCF_020097155_PROKKA_02288:0.0842702,(GCF_005280335_PROKKA_02407:0.0434259,(GCF_023573625_PROKKA_00545:0.00395954,(GCF_002008305_PROKKA_00542:0.00312239,GCF_003691675_PROKKA_00267:0.0125146)0.763:0.00233325)0.983:0.0296226)0.782:0.0459401)1:0.286273);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000020_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000020_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a0a316dca51922acf7cff55f4a9b5113e371280
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000020_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02299:0.133083,((GCF_005280335_PROKKA_01211:0.992211,(GCF_003691675_PROKKA_00245:0.0141942,(GCF_002008305_PROKKA_00524:5e-09,GCF_023573625_PROKKA_00524:0.00253447)0.706:0.0104374)1:0.463805)0.98:0.19563,(GCF_005280335_PROKKA_02417:0.0971786,(GCF_003691675_PROKKA_00256:0.00353325,GCF_023573625_PROKKA_00535:0.0173079)0.998:0.0794717)0.96:0.109912)1:0.133083);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000024_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000024_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e85fd05169eab5e4bad12aadb25746795fb696e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000024_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_02437:0.576216,(GCF_005280335_PROKKA_01839:0.551945,GCF_023573625_PROKKA_00587:1.08451)0.959:0.228638)1:0.448381,(GCF_005280335_PROKKA_00439:0.233083,(GCF_020097155_PROKKA_00392:0.179118,(GCF_002008305_PROKKA_02297:0.00900788,(GCF_003691675_PROKKA_01990:0.00833318,GCF_023573625_PROKKA_02238:0.00278536)0.808:0.00318286)1:0.185176)0.922:0.12125)1:0.448381);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000025_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000025_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7243bd4d1492f5526de7ef13b92276158ac50f65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000025_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00670:0,GCF_023573625_PROKKA_02014:0):0.16136,(GCF_020097155_PROKKA_00617:0.327506,((GCF_002008305_PROKKA_00099:0,GCF_003691675_PROKKA_02112:0,GCF_023573625_PROKKA_00094:0):5e-09,GCF_005280335_PROKKA_00292:0.0247036):0.571753):0.16136);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000026_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000026_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..020511db5003112db7b6d94f75bc25bfdb986c07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000026_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00186:0.106609,(GCF_020097155_PROKKA_00187:0.223121,GCF_020097155_PROKKA_02180:0.567515):0.153244):0.0404099,(GCF_005280335_PROKKA_00251:0.0130743,((GCF_002008305_PROKKA_00134:0,GCF_003691675_PROKKA_02148:0):5e-09,GCF_023573625_PROKKA_00142:0.00199743):0.025709):0.0404099);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000027_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000027_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..653aad71323731065f73069a3c6d53e9b42a89dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000027_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00724:0,(GCF_002008305_PROKKA_00161:0,GCF_002008305_PROKKA_01073:0,GCF_003691675_PROKKA_00336:0,GCF_003691675_PROKKA_00347:0,(GCF_003691675_PROKKA_00792:0,GCF_023573625_PROKKA_01022:0):0.0217507):0);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000028_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000028_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4e9f1dbb3f3f695fbdcd5d1a5821391b4287368
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000028_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00725:0.00160657,(GCF_003691675_PROKKA_00791:0.00321476,((GCF_002008305_PROKKA_01072:0,GCF_003691675_PROKKA_00335:0,GCF_003691675_PROKKA_00348:0,GCF_023573625_PROKKA_01021:0):5e-09,GCF_002008305_PROKKA_00162:5e-09):5e-09):0.00160657);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000031_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000031_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fdbec4d6a08d6c440f58c09934d9ffe90880e61f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000031_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_00172:1.1355,GCF_020097155_PROKKA_02230:1.40715):0.208375,(GCF_020097155_PROKKA_01399:5e-09,(GCF_005280335_PROKKA_01488:0.0190202,(GCF_002008305_PROKKA_01408:0.00287771,(GCF_003691675_PROKKA_01138:0,GCF_023573625_PROKKA_01358:0):5e-09):0.0203531):0.0619171):0.208375);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000033_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000033_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18299608750aeff30b205689ba96675046128ccb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000033_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00590:0.963637,GCF_020097155_PROKKA_00524:1.11025)0.971:0.172153,(GCF_020097155_PROKKA_00077:0.322084,(GCF_005280335_PROKKA_00109:0.168366,(GCF_003691675_PROKKA_02273:0.00620004,(GCF_002008305_PROKKA_00260:5e-09,GCF_023573625_PROKKA_00258:0.00452916)0.831:0.00753046)1:0.22856)0.999:0.370411)0.971:0.172153);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000035_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000035_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4af54d3bc4c6db983ffb0206ac29181115b6aa5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0101513):0.0101082,(GCF_002008305_PROKKA_00627:0.0101356,(GCF_003691675_PROKKA_00372:0,GCF_023573625_PROKKA_00604:0):5e-09):5e-09):0.0259167);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000036_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000036_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea3d9150b15d278f0858b003ca6fb100762ba9f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.273357):0.332923,(GCF_005280335_PROKKA_00403:5e-09,(GCF_020097155_PROKKA_02198:0.0127561,(GCF_002008305_PROKKA_00631:0,GCF_023573625_PROKKA_00600:0):0.00776946):0.00959987):0.332923);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000040_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000040_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ab947b754d44785494d224ffe422f498eac807f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000040_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02256:0.642535,(GCF_005280335_PROKKA_00822:1.33938,(GCF_003691675_PROKKA_00729:5e-09,(GCF_005280335_PROKKA_01873:0.0054313,(GCF_023573625_PROKKA_00959:0.00223951,(GCF_023573625_PROKKA_00958:5e-09,GCF_002008305_PROKKA_01015:5e-09)0.947:0.00361236)0.734:5e-09)0.563:0.00361637)0.934:0.386898)1:0.642535);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000041_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000041_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78e3deb79c653ee60e2c67c4fc489ae6cc3bb65f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000041_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00314:0.937969,GCF_020097155_PROKKA_01606:0.464668)0.922:0.0814579,(GCF_005280335_PROKKA_01707:0.254725,(GCF_005280335_PROKKA_01708:0.366497,(GCF_003691675_PROKKA_00900:0.00837367,(GCF_002008305_PROKKA_01181:0.0052912,GCF_023573625_PROKKA_01131:0.00523531)0.766:0.00492912)0.76:0.0531759)0.769:0.0789723)0.922:0.0814579);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000042_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000042_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bdab0bc777a7e5270b34f7d01912120fd6759017
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000042_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00712:0.113821,(((GCF_002008305_PROKKA_01288:0,GCF_003691675_PROKKA_01007:0):0.00580768,GCF_023573625_PROKKA_01246:0.00924807):0.117612,(GCF_005280335_PROKKA_00620:0.29439,(GCF_002008305_PROKKA_01627:0.011325,GCF_023573625_PROKKA_01556:0.0103459):0.253559):0.176295):0.113821);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000043_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000043_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2178fc8f9ab93447ef87ab501d2fb6a3526df96e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000043_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00412:0.00857074,(GCF_020097155_PROKKA_00648:0,GCF_020097155_PROKKA_02216:0):0.0171769):2.5e-09,(GCF_020097155_PROKKA_00325:0.0171188,(GCF_023573625_PROKKA_01347:0.00853601,(GCF_002008305_PROKKA_01397:5e-09,GCF_003691675_PROKKA_01130:0.00851276):5e-09):0.00859983):2.5e-09);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000044_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000044_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..973ef34ba7f859a0cfa48038a47ab9820c62dbf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000044_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01401:0.111216,GCF_020097155_PROKKA_00326:0.0842186):0.00136351,((GCF_005280335_PROKKA_00413:0.0251613,(GCF_003691675_PROKKA_01131:5e-09,GCF_023573625_PROKKA_01351:0.0533726):0.00716629):0.00346679,(GCF_020097155_PROKKA_00649:0,GCF_020097155_PROKKA_02217:0):5e-09):0.00136351);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000045_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000045_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d0114522876b74bce35a644083f751e953576d38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.752:0.128768)0.996:0.427507)0.991:0.078349,(GCF_023573625_PROKKA_01517:0.00179652,(GCF_002008305_PROKKA_01590:0.010479,GCF_003691675_PROKKA_01302:5e-09)0.869:0.00660547)0.991:0.078349);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000048_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000048_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..485f74399bde22d0b9d272b05455ff89361a9b34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000048_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01001:0.083454,((GCF_005280335_PROKKA_00398:0.156203,GCF_005280335_PROKKA_02643:0.809193):0.146632,((GCF_002008305_PROKKA_01808:0,GCF_003691675_PROKKA_01505:0):0.0207031,(GCF_005280335_PROKKA_01066:0.00926969,GCF_023573625_PROKKA_01729:5e-09):0.0178622):0.108492):0.083454);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000049_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000049_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c5799305299f95ebcfcc7824941cd4c15c50f39
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000049_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00774:0.0178715,((GCF_023573625_PROKKA_00173:0.527292,GCF_023573625_PROKKA_00174:0.595234)0.852:0.277659,(GCF_005280335_PROKKA_00837:0.0460029,(GCF_023573625_PROKKA_01943:0.0033264,(GCF_003691675_PROKKA_01715:0.00786137,GCF_002008305_PROKKA_02005:0.0125602)0.729:0.0028999)1:0.0533522)0.939:0.0585172)1:0.0178715);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000050_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000050_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..153cba5063a9d2f7c8d400558eaee394d5b5519a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000050_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_01308:0.0105914,GCF_020097155_PROKKA_02237:0.0127592)0.981:0.12808,(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)0.599:0.0094745)0.829:0.0143074)0.785:0.0908522)0.981:0.12808);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000051_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000051_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26be52949fa58c6196710b90725e3df4dc390000
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000051_tree.txt
@@ -0,0 +1 @@
+(((GCF_003691675_PROKKA_01802:0.000133362,GCF_020097155_PROKKA_00600:0.0666336)0.596:0.017847,((GCF_020097155_PROKKA_02101:0.508887,GCF_023573625_PROKKA_02031:0.613187)0.994:0.624215,GCF_020097155_PROKKA_00599:0.111869)0.449:0.0263643)0.747:0.00668587,(GCF_002008305_PROKKA_02094:0.0409894,GCF_005280335_PROKKA_00684:0.0387512)0.747:0.00668587);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000052_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000052_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a5ae6e75287aabfc6f42a7787b2a7f2d6fd31a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000052_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00520:0.027572,((GCF_005280335_PROKKA_00589:0.530802,GCF_005280335_PROKKA_02580:1.52373):0.28795,(GCF_005280335_PROKKA_00598:0.044012,((GCF_002008305_PROKKA_02160:0,GCF_003691675_PROKKA_01873:0):0.00810445,GCF_023573625_PROKKA_02104:5e-09):0.021444):0.0586633):0.027572);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000054_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000054_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef76d6743769e60b8578a284f36db147b9b823a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000054_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00434:0.00303817,(GCF_023573625_PROKKA_02184:0.00403191,(GCF_005280335_PROKKA_00488:0.0161824,((GCF_002008305_PROKKA_02275:0.28969,GCF_005280335_PROKKA_00493:0.173257)0.933:0.157487,(GCF_002008305_PROKKA_02253:0.00712782,GCF_003691675_PROKKA_01952:0.00300307)0.756:0.0018574)0.866:0.00610443)0.735:0.00199749)1:0.00303817);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000056_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000056_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..721367fc62fee4dd3d0267542c4002a51454f63e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000056_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00353:0.221286,(GCF_005280335_PROKKA_00370:0.0256665,(GCF_005280335_PROKKA_00371:0.017816,(GCF_002008305_PROKKA_00025:0.0157216,(GCF_023573625_PROKKA_00025:0.00957219,GCF_003691675_PROKKA_02043:0.00638713)0.822:0.00717563)0.535:0.000664308)0.567:0.0198962)1:0.221286);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000057_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000057_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a92846f8cb4e977180f3cbf8d3b6ff20ba2bfbd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000057_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00427:0.509673,(GCF_005280335_PROKKA_00464:0.960635,(GCF_002008305_PROKKA_00568:1.40758,(GCF_002008305_PROKKA_00037:0.850779,(GCF_002008305_PROKKA_02274:0.190842,GCF_023573625_PROKKA_02208:0.250534)1:0.772146)0.872:0.220298)0.966:0.386398)1:0.509673);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000058_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000058_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3878154ec7b9401196d8f21ba407c47fcfc44fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000058_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01503:0.163223,(GCF_005280335_PROKKA_01608:0.131404,(GCF_005280335_PROKKA_00354:0.109288,(GCF_003691675_PROKKA_02062:6e-09,(GCF_023573625_PROKKA_00044:0.0140957,GCF_002008305_PROKKA_00049:5e-09)0.832:0.00561735)0.997:0.12813)1:0.365245)1:0.163223);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000061_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000061_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de7f372a9fccf44994ce7a76e1c4cc19f628d106
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000061_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00266:0.0507778,GCF_020097155_PROKKA_00684:0.781922)0.769:0.0146412,(GCF_005280335_PROKKA_00326:0.0759528,(GCF_023573625_PROKKA_00062:0.00531867,(GCF_002008305_PROKKA_00068:6e-09,GCF_003691675_PROKKA_02081:0.0106655)0.688:0.0065055)0.933:0.0343515)0.769:0.0146412);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000063_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000063_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2940afb7774577e9baf2cf92345e719a38d804b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.577:0.00623731,(GCF_023573625_PROKKA_00100:0.00411274,(GCF_002008305_PROKKA_00105:0.00205499,GCF_003691675_PROKKA_02118:5e-09)0.833:5e-09)0.95:0.01531)1:0.0464833);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000064_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000064_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64e0b6e6007d2dfef75503cf86e39e5d976ca32d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000064_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00137:0.231945,(GCF_005280335_PROKKA_00088:0.61229,(GCF_002008305_PROKKA_00119:5e-09,((GCF_003691675_PROKKA_02135:0,GCF_023573625_PROKKA_00127:0):5e-09,GCF_005280335_PROKKA_00265:0.0576621):0.00940129):0.450584):0.231945);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000065_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000065_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ba99281f4ea19d0e09dcb7d9ec60dbea2c1f825
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000065_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01975:0.234658,(GCF_002008305_PROKKA_00175:1.70614,(GCF_005280335_PROKKA_02080:0.112439,(GCF_002008305_PROKKA_00854:5e-09,(GCF_003691675_PROKKA_00576:0,GCF_023573625_PROKKA_00813:0):0.0191092):0.0968617):0.162919):0.234658);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000069_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000069_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..167d009ce4e2b032958505e1141c1e36ffb42f61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000069_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00117:0.103974,(GCF_005280335_PROKKA_00086:1.0168,(GCF_005280335_PROKKA_00159:0.0990047,(GCF_023573625_PROKKA_00222:0.000901637,(GCF_002008305_PROKKA_00221:0.00658315,GCF_003691675_PROKKA_02234:0.00564873)0.879:0.00571932)1:0.0879877)0.958:0.0931407)1:0.103974);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000072_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000072_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6988c0474ab37213891288bf79e1ed1adeb172c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000072_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00088:0.0781417,GCF_020097155_PROKKA_02472:0.394103)1:0.0485506,(GCF_005280335_PROKKA_00120:0.0301196,(GCF_002008305_PROKKA_00250:0.00617101,(GCF_003691675_PROKKA_02262:0.00491775,GCF_023573625_PROKKA_00250:0.00185262)0.787:0.00782996)0.993:0.0346302)1:0.0485506);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000074_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000074_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..855068c012fcc3204abe7a42e4d63bf8f085f17d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000074_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02346:0.129278,(GCF_003691675_PROKKA_00203:0.0521876,(GCF_002008305_PROKKA_00279:0.00519361,(GCF_005280335_PROKKA_00074:0.00533227,(GCF_003691675_PROKKA_02294:6e-09,GCF_023573625_PROKKA_00278:0.00799105)0:6e-09)0.73:0.00545202)1:1.43336)1:0.129278);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000076_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000076_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0d5edb21a4720a36a6f0182b14cb9e453193b88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000076_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00046:0.0505111,(GCF_002008305_PROKKA_01958:1.50018,(GCF_005280335_PROKKA_00067:0.0350465,(GCF_002008305_PROKKA_00287:0.00870315,(GCF_003691675_PROKKA_02309:0.00352282,GCF_023573625_PROKKA_00293:0.00242894)0.939:0.00324163)1:0.0389738)0.741:0.0651844)1:0.0505111);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000082_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000082_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..19062a9df2b5d9e33bee1664efe115b76777c8d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000082_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_02569:0.0292659,GCF_020097155_PROKKA_01756:0.0962103)0.446:0.00286866,((GCF_023573625_PROKKA_00392:0.00663066,(GCF_002008305_PROKKA_00386:5e-09,GCF_003691675_PROKKA_00110:0.00346887)0.875:0.00379943)0.848:0.00361157,GCF_020097155_PROKKA_02444:0.0341839)0.446:0.00286866);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000084_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000084_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e5d02263d85d5a8bc896aaead0edfff1925ad2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000084_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02410:0.415657,(GCF_005280335_PROKKA_02542:0.663339,(GCF_005280335_PROKKA_02541:0.230212,(GCF_003691675_PROKKA_00139:0.0561719,(GCF_002008305_PROKKA_00418:5e-09,GCF_023573625_PROKKA_00421:0.00173399)0.951:0.0325798)0.792:0.0723654)0.999:0.356889)1:0.415657);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000087_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000087_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5ed63a00ccf2b91ca45a09cc47ef7d26941a3c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000087_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02342:0.0253247,(GCF_023573625_PROKKA_01553:1.31449,(GCF_005280335_PROKKA_02458:0.00388434,((GCF_002008305_PROKKA_00489:0,GCF_003691675_PROKKA_00210:0):0.00199757,GCF_023573625_PROKKA_00488:5e-09):0.00212173):0.0753449):0.0253247);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000088_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000088_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b8d70d883803d20886550763b7adf7ba56ec3d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000088_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02336:0.0514642,(GCF_005280335_PROKKA_01221:1.41679,(GCF_003691675_PROKKA_00216:5e-09,(GCF_002008305_PROKKA_00495:0.00917144,(GCF_005280335_PROKKA_02452:0.0303728,GCF_023573625_PROKKA_00494:0.0202532)0.574:0.00494818)0.851:0.0112162)0.949:0.185651)1:0.0514642);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000089_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000089_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48020c7539e5804b5751389406ca0df8feb7408d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000089_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02325:0.0113135,(GCF_005280335_PROKKA_01218:1.78079,(GCF_003691675_PROKKA_00229:0.0305873,(GCF_005280335_PROKKA_02441:0.0504917,(GCF_002008305_PROKKA_00509:0.00992303,GCF_023573625_PROKKA_00508:0.0188854)0.947:0.0156897)0.509:0.00653855)0.83:0.0361289)1:0.0113135);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000090_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000090_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71bad7c1c9132233f0a68fd3951ee7515dcf7e4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000090_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02311:0.00444868,(GCF_005280335_PROKKA_02428:0.00892789,((GCF_005280335_PROKKA_01219:1.79404,GCF_023573625_PROKKA_00521:5e-09)1:0.0301173,(GCF_003691675_PROKKA_00243:0.00592033,GCF_002008305_PROKKA_00521:0.0118539)0:5e-09)0.774:0.00296109)1:0.00444868);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000091_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000091_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57cccf584f6ce70e9e1938ee2cd132cc11a96980
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000091_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02283:0.208509,(GCF_005280335_PROKKA_02400:0.146037,(GCF_005280335_PROKKA_02399:0.0757527,(GCF_002008305_PROKKA_00547:0.00378451,(GCF_023573625_PROKKA_00550:0.00711717,GCF_003691675_PROKKA_00272:0.0106191)0.763:0.00328331)0.955:0.0788898)0.913:0.125163)1:0.208509);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000092_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000092_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..19ff7f367016c34cad6baa3514b77db9871769da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000092_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02275:0.121882,((GCF_002008305_PROKKA_00554:0,GCF_003691675_PROKKA_00279:0,GCF_023573625_PROKKA_00557:0):0.181141,(GCF_005280335_PROKKA_00640:1.60505,GCF_005280335_PROKKA_02391:0.0188826):0.124957):0.121882);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000094_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000094_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3142b38fc7f61b03322b4b482b299a00e6ae4fbb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000094_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02202:0.00424779,(GCF_005280335_PROKKA_00399:5e-09,(GCF_023573625_PROKKA_02004:0.185889,(GCF_005280335_PROKKA_02642:0.836624,(GCF_002008305_PROKKA_00610:0.0252467,GCF_003691675_PROKKA_01770:0.00912117)0.88:0.0739602)0.805:0.0564079)0.994:0.113143)1:0.00424779);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000098_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000098_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f89dce23846e4297a554968a1d69a9684c0c4994
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.911:0.0136526,(GCF_003691675_PROKKA_00371:0.00338791,GCF_023573625_PROKKA_00605:0.00682011)0.957:5e-09)0.834:0.00865701)1:0.0183117);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000100_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000100_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cdfe497373729f07fdda356aa5ed0a1026c3aa0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000100_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_PROKKA_02319:0.0574924,GCF_020097155_PROKKA_02178:0.101592)0.999:0.099134,GCF_002008305_PROKKA_00644:0.0103235)0.564:0.00387647,((GCF_020097155_PROKKA_00584:1.10257,GCF_023573625_PROKKA_00614:0.00342599)0.821:0.0107788,GCF_003691675_PROKKA_00381:0.0072037)0.564:0.00387647);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000104_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000104_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b673900550c05a0226cd8d944eda625bb0b315c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000104_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00342:1.42967,GCF_020097155_PROKKA_02098:0.305461)0.999:0.15462,(GCF_005280335_PROKKA_02222:0.175407,(GCF_003691675_PROKKA_00462:0.0158796,(GCF_002008305_PROKKA_00731:0.00187336,GCF_023573625_PROKKA_00695:0.00282214)0.91:0.0131673)1:0.157637)0.999:0.15462);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000105_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000105_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a39be8e7b9bbbcfe3f43cd73f7d6d43b12954df2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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_002008305_PROKKA_00748:0.0143762,(GCF_003691675_PROKKA_00478:5e-09,GCF_002008305_PROKKA_00747:0.0379611)0.95:0.0633809)0.867:0.0248406)0.97:0.341552)1:0.4101);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000106_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000106_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9543b4559177a54861f4294b92f405a13aaf9a91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000106_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00528:1.67612,GCF_020097155_PROKKA_02063:0.0856185)0.841:0.0526844,(GCF_005280335_PROKKA_02168:0.19968,(GCF_023573625_PROKKA_00726:5e-09,(GCF_002008305_PROKKA_00762:0.00731715,GCF_003691675_PROKKA_00492:0.00360066)0.937:0.014716)1:0.208996)0.841:0.0526844);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000107_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000107_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44444628411249e519e68963451969b0f226eb92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000107_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02057:0.0493715,(GCF_005280335_PROKKA_02161:0.0300277,((GCF_003691675_PROKKA_00499:0.00380606,GCF_023573625_PROKKA_00733:0.00206797)0.757:0.00365605,(GCF_002008305_PROKKA_00769:0.0115989,GCF_005280335_PROKKA_00806:0.918393)0.582:0.0016907)0.999:0.0466502)1:0.0493715);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000108_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000108_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6094b6bdb4f5b44dd00aeebe0818a0831867d4dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000108_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01711:0.0406012,(GCF_002008305_PROKKA_00838:0.715086,(GCF_005280335_PROKKA_01822:0.0750625,(GCF_002008305_PROKKA_01065:0.00849817,(GCF_003691675_PROKKA_00784:0,GCF_023573625_PROKKA_01012:0):5e-09):0.0519126):0.102233):0.0406012);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000109_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000109_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9fac0226450da5d819532ffa75b6267d1afd4d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000109_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01946:0.181728,((GCF_005280335_PROKKA_02052:0.00463609,GCF_023573625_PROKKA_00842:0.00703262):0.281195,((GCF_002008305_PROKKA_00886:0,GCF_003691675_PROKKA_00608:0):0.298792,GCF_005280335_PROKKA_02050:1.39198):0.194171):0.181728);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000110_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000110_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a65ec57d487916c7a78a02b91d72df0f2fd9f263
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000110_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00709:1.31066,GCF_020097155_PROKKA_01871:0.143327)0.741:0.0282719,(GCF_005280335_PROKKA_01922:0.0857048,(GCF_003691675_PROKKA_00678:0.0013114,(GCF_002008305_PROKKA_00965:0.00848095,GCF_023573625_PROKKA_00911:0.00419578)0.759:0.00707947)0.965:0.0583519)0.741:0.0282719);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000111_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000111_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1f4727bfa02eb4614ed821eab90dfea8d3870c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000111_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01843:0.0759705,(GCF_005280335_PROKKA_01817:1.20204,(GCF_023573625_PROKKA_00936:0.00464997,(GCF_002008305_PROKKA_00993:0.0139345,(GCF_005280335_PROKKA_01896:0.0478119,GCF_003691675_PROKKA_00707:5e-09)0.036:0.0139007)0.883:0.0141468)0.848:0.0937577)1:0.0759705);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000112_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000112_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e2292294b6a9db799df01e5ec49239df3da9cf9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000112_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01764:0.459075,((GCF_002008305_PROKKA_01012:0,GCF_003691675_PROKKA_00726:0):0.011003,(GCF_005280335_PROKKA_01877:0.0383644,(GCF_005280335_PROKKA_01876:0.0427981,GCF_023573625_PROKKA_00955:0.0190787):0.0151453):0.0131261):0.459075);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000113_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000113_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7097cdf92072138ddeae047aa9b310e0e0b0cee0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0591364,(GCF_005280335_PROKKA_00185:1.03623,GCF_005280335_PROKKA_01852:0.802572):0.942112):1.8335e-05);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000114_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000114_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..348046376d38b26ec28dba91dbf3831698da4df1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000114_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01743:0.0116777,((GCF_002008305_PROKKA_01029:0,GCF_003691675_PROKKA_00744:0,GCF_023573625_PROKKA_00973:0):0.00291619,(GCF_005280335_PROKKA_00187:0.47771,GCF_005280335_PROKKA_01854:0.500427):0.607899):0.0116777);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000115_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000115_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0bd715fa9a2775a02b15ad8248d2d1f2f50ccbff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000115_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01742:0.00886725,((GCF_002008305_PROKKA_01030:0,GCF_003691675_PROKKA_00745:0,GCF_023573625_PROKKA_00974:0):5e-09,(GCF_005280335_PROKKA_00186:0.500752,GCF_005280335_PROKKA_01853:0.482677):0.815193):0.00886725);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000116_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000116_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ed0b5f7362b750d8627d3d39676d3cff7ce9957
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000116_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01735:0.343353,((GCF_005280335_PROKKA_00331:0.000496434,GCF_005280335_PROKKA_00544:0.0120449)0.978:0.205386,(GCF_003691675_PROKKA_00755:0.0184529,(GCF_002008305_PROKKA_01042:5e-09,GCF_023573625_PROKKA_00983:0.00608895)0.744:0.00661242)0.969:0.163577)1:0.343353);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000117_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000117_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96ca35e5bf19db86aebac53993beb950efe15b92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000117_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01683:0.156685,((GCF_005280335_PROKKA_01792:0.317347,GCF_005280335_PROKKA_01793:0.804854)0.98:0.139555,(GCF_002008305_PROKKA_01102:5e-09,(GCF_003691675_PROKKA_00821:0.0132238,GCF_023573625_PROKKA_01051:5e-09)0.846:0.00879136)1:0.380575)1:0.156685);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000118_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000118_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd2735b6fa9b89cef9d8a7c4ff8ec93be8e8ab37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000118_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01679:0.0649956,(GCF_005280335_PROKKA_01788:0.314388,((GCF_002008305_PROKKA_01106:0,GCF_003691675_PROKKA_00825:0,GCF_023573625_PROKKA_01055:0):0.0610359,GCF_005280335_PROKKA_01787:0.0359858):0.107992):0.0649956);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000123_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000123_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b108b0e22847467fb2d20d3a7730baa2b91dcb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000123_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01510:0.0199705,(GCF_023573625_PROKKA_01882:1.52538,((GCF_002008305_PROKKA_01272:0,GCF_003691675_PROKKA_00991:0,GCF_023573625_PROKKA_01230:0):0.0448732,GCF_005280335_PROKKA_01615:0.0327305):0.0464907):0.0199705);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000128_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000128_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe0bbf82ae466cebdfa87b83db2478c9c71bea82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000128_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_01366:0.115207,GCF_020097155_PROKKA_02442:0.909664):0.0331519,(GCF_005280335_PROKKA_01458:0.061134,(GCF_002008305_PROKKA_01440:0.000739679,(GCF_003691675_PROKKA_01172:0,GCF_023573625_PROKKA_01390:0):0.000766677):0.0768897):0.0331519);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000130_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000130_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb13ce18c4611c2660f1291a05374733d7a1ab2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000130_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00286:1.71958,GCF_020097155_PROKKA_01277:0.16554)0.64:0.0129787,(GCF_005280335_PROKKA_01386:0.079855,(GCF_003691675_PROKKA_01249:0.0190697,(GCF_002008305_PROKKA_01539:0.00762368,GCF_023573625_PROKKA_01466:0.00370659)0.027:0.00878536)0.975:0.0501834)0.64:0.0129787);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000131_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000131_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dba03c6af3c9bbbedd5db999173ac2f9047a0874
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000131_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_01267:0.00863428,GCF_020097155_PROKKA_01296:1.47263)0.871:0.0571502,(GCF_005280335_PROKKA_01376:0.0343491,(GCF_023573625_PROKKA_01476:5e-09,(GCF_003691675_PROKKA_01259:0.00437517,GCF_002008305_PROKKA_01549:5e-09)0.777:0.00435445)0.982:0.0481655)0.871:0.0571502);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000133_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000133_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07f7c22ab31b697f3dd6be02d1b0aba1874d0105
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000133_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01248:0.060227,(GCF_005280335_PROKKA_02577:0.292769,(GCF_005280335_PROKKA_01355:0.0701402,(GCF_023573625_PROKKA_01496:0.00765813,(GCF_002008305_PROKKA_01569:5e-09,GCF_003691675_PROKKA_01279:0.00414549)0.101:0.00708532)1:0.112051)0.991:0.0797216)1:0.060227);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000134_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000134_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..405fd23bcaee6d9348b0c6e3ff5b61d675dc8b7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000134_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01581:0.00505921,(GCF_005280335_PROKKA_01342:0.0136529,GCF_020097155_PROKKA_01767:1.58933)0.789:0.0223173)0.768:0.000634585,(GCF_020097155_PROKKA_01235:0.00716569,(GCF_003691675_PROKKA_01291:0.00247269,GCF_023573625_PROKKA_01508:5e-09)0.779:0.00137153)0.768:0.000634585);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000135_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000135_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..af47c501688e32c88081036d5529358139aff421
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000135_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01234:0.00361291,(GCF_023573625_PROKKA_01509:0.00897469,(GCF_002008305_PROKKA_01582:5e-09,((GCF_003691675_PROKKA_01293:0.00615029,GCF_005280335_PROKKA_01340:0.00923984)0.217:0.00614751,GCF_003691675_PROKKA_01292:0.00334118)0.013:5e-09)0.848:0.00358763)1:0.00361291);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000136_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000136_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62bd10f7154458aaa1e0fef5f43e389123fbd503
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000136_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00458:0.0796873,(GCF_002008305_PROKKA_02249:0.0799541,((GCF_002008305_PROKKA_01584:0,GCF_005280335_PROKKA_01338:0,GCF_023573625_PROKKA_01511:0):0.00405034,GCF_003691675_PROKKA_01295:6e-09):1.3278):0.0796873);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000138_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000138_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7326097ed671bbf228050cc21e08d94771fccc74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000138_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_01201:5e-09,(GCF_020097155_PROKKA_00271:1.76351,GCF_020097155_PROKKA_01824:1.68265):0.0174657):0.00915209,(GCF_002008305_PROKKA_01601:0.00730083,(GCF_003691675_PROKKA_01313:0,GCF_023573625_PROKKA_01528:0):0.00729401):0.00915209);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000139_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000139_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a791bfb79f3d7dd98b90099e185c2e43536ee998
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.808:0.0265374,(GCF_023573625_PROKKA_01531:0.00540258,(GCF_002008305_PROKKA_01604:0.0017942,GCF_003691675_PROKKA_01316:5e-09)0.792:0.00179762)0.929:0.0110508)1:0.013121);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000141_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000141_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e9b73a78a4c7cd784a8abc5503a56d668bdff2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000141_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_01168:0.00462484,(GCF_002008305_PROKKA_01636:0.0208938,GCF_023573625_PROKKA_01565:0.0206399)0.987:0.0417626)0.951:0.0144835,(GCF_005280335_PROKKA_01259:0.0375414,(GCF_020097155_PROKKA_01210:0.777983,GCF_003691675_PROKKA_01341:5e-09)0.733:0.0120832)0.951:0.0144835);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000142_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000142_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12959feabf60a263c1a26674f793821c10f0edd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000142_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01126:0.0878436,(GCF_005280335_PROKKA_01209:0.218086,(GCF_005280335_PROKKA_01197:0.115888,(GCF_003691675_PROKKA_01385:0.00272092,(GCF_002008305_PROKKA_01681:0.00848626,GCF_023573625_PROKKA_01610:0.00281284)0.753:0.00290541)1:0.103973)0.988:0.110621)1:0.0878436);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000143_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000143_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..720eb3209d87f32819b6d3ee01a8f1441f408dfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000143_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00038:0.928312,GCF_020097155_PROKKA_01121:0.245858):0.0714919,(GCF_005280335_PROKKA_01191:0.154711,(GCF_002008305_PROKKA_01687:0.00496388,(GCF_003691675_PROKKA_01391:0,GCF_023573625_PROKKA_01616:0):0.0133813):0.0420013):0.0714919);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000144_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000144_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c58c2412fa06ab2b108f3e0b8e70d347330c7e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000144_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_01022:0.163286,GCF_020097155_PROKKA_01806:1.46328)0.568:0.00820567,(GCF_005280335_PROKKA_01098:0.0916714,(GCF_023573625_PROKKA_01708:0.0135036,(GCF_002008305_PROKKA_01779:0.0138398,GCF_003691675_PROKKA_01486:0.014148)0.843:0.0116171)1:0.0901985)0.568:0.00820567);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000145_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000145_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4cdd9346ad0e60c5b20ebd7c6502c6de9b3ecc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000145_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00729:0.241491,((GCF_002008305_PROKKA_01790:0,GCF_005280335_PROKKA_01086:0):1.03319,(GCF_023573625_PROKKA_01985:0.0118496,(GCF_003691675_PROKKA_01757:0.0147093,GCF_002008305_PROKKA_02051:5e-09):0.00285663):0.151109):0.241491);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000147_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000147_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aee63912c20a5424fca313d45d4cb44c415ce74f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000147_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01000:0.0619796,(GCF_005280335_PROKKA_02644:0.967376,(GCF_005280335_PROKKA_01065:0.0501368,((GCF_002008305_PROKKA_01809:0,GCF_003691675_PROKKA_01506:0):0.00737441,GCF_023573625_PROKKA_01730:0.0156063):0.0714646):0.0529771):0.0619796);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000148_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000148_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f74e4a32c082eb1b7916a2366e10d584c657c063
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000148_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_01038:0.149934,(GCF_005280335_PROKKA_00744:0.533326,GCF_005280335_PROKKA_02335:1.56671)0.342:0.106927)0.987:0.0589014,(GCF_023573625_PROKKA_01751:0.0162092,(GCF_002008305_PROKKA_01830:0.00739438,GCF_003691675_PROKKA_01527:0.0124955)0.743:0.00374241)0.987:0.0589014);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000149_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000149_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e240b13d9f924e2cc52113b6a968861a0716bc7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000149_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00965:0.0353257,(GCF_005280335_PROKKA_01331:1.8297,(GCF_005280335_PROKKA_01024:0.0644875,((GCF_002008305_PROKKA_01844:0,GCF_003691675_PROKKA_01541:0):0.00154969,GCF_023573625_PROKKA_01765:0.0031322):0.148159):0.00472119):0.0353257);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000150_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000150_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee93312a6b748dc41671eb99af0c02837c133296
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000150_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00958:0.0580179,(GCF_005280335_PROKKA_01058:1.56045,(GCF_005280335_PROKKA_01016:0.113085,(GCF_002008305_PROKKA_01852:0.00350694,(GCF_003691675_PROKKA_01548:0.0255414,GCF_023573625_PROKKA_01772:0.0036326)0.857:0.00733116)0.971:0.0595456)0.897:0.123397)1:0.0580179);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000151_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000151_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..209088159c58c9060f0e90cadf17d5411af2f94d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000151_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00874:0.228715,(GCF_005280335_PROKKA_00939:0.0553323,(GCF_023573625_PROKKA_01841:0.0134394,(GCF_003691675_PROKKA_01617:0.0111856,(GCF_005280335_PROKKA_00786:1.78314,GCF_002008305_PROKKA_01921:5e-09)0.773:0.00197961)0.858:0.00942511)0.977:0.0527282)1:0.228715);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000153_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000153_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96f9f18b332e3617f2f0ccef7c349745f16ea330
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000153_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00817:0.0308704,((GCF_002008305_PROKKA_01975:6e-09,GCF_005280335_PROKKA_00882:0.11307)0.842:0.00857515,(GCF_003691675_PROKKA_01669:5e-09,(GCF_002008305_PROKKA_01976:0.0085242,GCF_023573625_PROKKA_01901:0.00407248)0.965:0.00821689)0.583:5e-09)1:0.0308704);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000155_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000155_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4eaf18a0ae30c4ccc2e43dbe3cd319f1b953f66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000155_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_PROKKA_01911:6e-09,(GCF_005280335_PROKKA_00872:0.124314,GCF_020097155_PROKKA_00818:0.170248)0.997:0.121846)0:2.5e-09,(GCF_020097155_PROKKA_00808:0.0144486,(GCF_003691675_PROKKA_01679:0.0047924,GCF_002008305_PROKKA_01985:0.019219)0.236:0.00475592)0:2.5e-09);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000157_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000157_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b829b87e462dd40107f1d8a62b7c2068e6054ded
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000157_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00762:0.00710752,(GCF_003691675_PROKKA_00095:1.255,(GCF_005280335_PROKKA_00803:0.0678242,(GCF_023573625_PROKKA_01955:0.0101962,(GCF_003691675_PROKKA_01727:0.0238696,GCF_002008305_PROKKA_02018:0.0101454)0.099:5e-09)0.828:0.00999737)0.121:0.018937)1:0.00710752);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000162_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000162_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c18be4cbf1a164f4e67296f00f20c0a48864044
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.427:0.0699416)0.786:0.0609639,(GCF_003691675_PROKKA_01800:0.0650793,(GCF_005280335_PROKKA_00685:0.0318044,GCF_020097155_PROKKA_00601:0.0321214)1:0.294598)0.786:0.0609639);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000163_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000163_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..175adf8c636a871b7cf20b551f17f44247b83fd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000163_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00595:0.0719317,(GCF_005280335_PROKKA_01500:1.41162,(GCF_005280335_PROKKA_00681:0.0412738,((GCF_002008305_PROKKA_02098:0,GCF_003691675_PROKKA_01805:0):0.00345045,GCF_023573625_PROKKA_02038:5e-09):0.0257444):0.061948):0.0719317);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000165_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000165_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92096cf0da55e2b0837d7bf8d4a3b9399a54e03b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000165_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00518:0.364133,(GCF_005280335_PROKKA_00595:0.110131,((GCF_002008305_PROKKA_02162:5e-09,GCF_003691675_PROKKA_01875:0.0154399)0.789:0.012428,(GCF_023573625_PROKKA_02107:6e-09,GCF_003691675_PROKKA_01876:0.0216387)0.922:0.0693043)0.96:0.208592)1:0.364133);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000168_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000168_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e77b48b2c4323f35d785cc89c291087234c5c386
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000168_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00435:0.00424512,((GCF_003691675_PROKKA_01951:0.00564189,GCF_023573625_PROKKA_02183:6e-09)0.776:0.00565926,(GCF_005280335_PROKKA_00489:0.0495112,(GCF_002008305_PROKKA_02252:0.00563832,GCF_002008305_PROKKA_02276:0.0170355)0.77:0.00286199)0.757:0.00279431)1:0.00424512);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000170_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000170_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2b14b4327c777e6cf059d2a3035d3d36e10c05d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000170_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00386:0.0377915,(GCF_005280335_PROKKA_00739:0.590509,(GCF_005280335_PROKKA_00434:0.044086,(GCF_003691675_PROKKA_01996:0.00307433,(GCF_023573625_PROKKA_02244:0.00575636,GCF_002008305_PROKKA_02303:0.00301314)0.31:0.00285659)0.977:0.0374611)0.824:0.0515312)1:0.0377915);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000171_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000171_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1cb34b5ae76eee33d1a18abbb5c85ba1cfaf6cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000171_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00384:0.0553472,(GCF_005280335_PROKKA_01948:1.89173,(GCF_005280335_PROKKA_00432:0.163476,((GCF_002008305_PROKKA_02305:0,GCF_003691675_PROKKA_01998:0):0.00305769,GCF_023573625_PROKKA_02246:5e-09):0.00840558):0.174569):0.0553472);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000173_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000173_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..296188e9eeb9ffa5e685ad3bd2296d39a72eecaf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000173_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00092:0.600483,GCF_020097155_PROKKA_00133:0.967764)0.801:0.124049,(GCF_005280335_PROKKA_00093:0.553211,(GCF_005280335_PROKKA_00195:0.156468,(GCF_020097155_PROKKA_00146:6e-09,GCF_023573625_PROKKA_00201:0.0154097)0.978:0.135211)0.952:0.427716)0.801:0.124049);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000176_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000176_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5b5e2eba8cdb798177a1fc21e2f5a155f76a9ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000176_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00374:0.0478978,(GCF_005280335_PROKKA_00421:0.0404644,(GCF_023573625_PROKKA_00003:5e-09,(GCF_002008305_PROKKA_00003:5e-09,GCF_003691675_PROKKA_02008:0.00744217)0.948:0.00987668)1:0.0611955)1:0.0478978);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000177_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000177_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0cf8fcf04f2024517dd29432072776324b367c86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000177_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00373:0.0846994,(GCF_005280335_PROKKA_00420:0.0477243,((GCF_002008305_PROKKA_00004:0,GCF_003691675_PROKKA_02009:0):0.00539401,GCF_023573625_PROKKA_00004:6e-09):0.0223467):0.0846994);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000178_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000178_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..692ca9a44f76e1160346546f098b60491b72b5a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000178_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00371:0.045835,(GCF_005280335_PROKKA_00419:0.0245618,(GCF_002008305_PROKKA_00005:0.00275032,(GCF_003691675_PROKKA_02010:0,GCF_023573625_PROKKA_00005:0):5e-09):0.0326011):0.045835);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000181_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000181_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15c5bd2d633150c23afb478b79cf7b575872f3a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000181_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00367:0.345627,(GCF_005280335_PROKKA_00415:0.0633596,(GCF_002008305_PROKKA_00009:0.0183272,(GCF_003691675_PROKKA_02014:0,GCF_023573625_PROKKA_00009:0):6e-09):0.0979362):0.345627);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000185_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000185_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..029ab9a26cd8848d1ffa6a3e6336229884600a81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000185_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00362:0.166928,(GCF_005280335_PROKKA_00381:0.220099,(GCF_003691675_PROKKA_02034:0.0189359,(GCF_002008305_PROKKA_00016:0.0064883,GCF_023573625_PROKKA_00016:0.00963284)0.597:0.000965236)0.965:0.0786738)1:0.166928);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000186_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000186_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b15c2dc58b4ae377e4f1b1f9f8d32739b09e0a40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000186_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00361:0.115399,(GCF_005280335_PROKKA_00380:0.063982,(GCF_023573625_PROKKA_00017:5e-09,(GCF_002008305_PROKKA_00017:0.0102753,GCF_003691675_PROKKA_02035:0.010357)0:5e-09)0.868:0.0510506)1:0.115399);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000187_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000187_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..846cfee78128b8e20f13608724a41aae65fc7fab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.675:6e-09)0.963:0.0418007)1:0.0511346);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000191_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000191_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b49a3eb382580b40e3c4c333001e002f004aed17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.884:0.00453288)0.163:0.0063618)1:0.0861282);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000192_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000192_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eecba67ef9f3e04fb9f4639caffe5919f1857e3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000192_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00355:0.188857,(GCF_023573625_PROKKA_00023:0.0118673,(GCF_005280335_PROKKA_00373:0.024749,(GCF_002008305_PROKKA_00023:0.0179641,GCF_003691675_PROKKA_02041:0.00934061)0.961:0.0101378)0.836:0.00791402)1:0.188857);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000193_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000193_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..761c8e03da2e95f1fd5d4a443ca70bb7ecc4e065
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.792:0.00523565)0.254:0.00523569)1:0.119758);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000199_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000199_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14bd80765b29c25ba84f6f519190b4eb4c66fe1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000199_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00301:0.125032,(GCF_005280335_PROKKA_00360:0.109715,(GCF_003691675_PROKKA_02053:0.00347483,(GCF_002008305_PROKKA_00040:0.00648055,GCF_023573625_PROKKA_00035:0.00983506)0.815:0.00629262)0.988:0.0960354)1:0.125032);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000202_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000202_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..062d6ca0f3a8c67a420283bd18b874d3ee87688e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000202_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00298:0.0705577,(GCF_005280335_PROKKA_00356:0.0503349,(GCF_002008305_PROKKA_00044:0.020819,(GCF_003691675_PROKKA_02057:0.00513158,GCF_023573625_PROKKA_00039:0.00257321)0.774:0.00399779)0.98:0.0397243)1:0.0705577);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000204_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000204_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e1f5ab2c888113f446356e6d13b4c5e97a8d7ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000204_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00294:0.207845,(GCF_005280335_PROKKA_00349:0.145257,((GCF_002008305_PROKKA_00046:0,GCF_003691675_PROKKA_02059:0):5e-09,GCF_023573625_PROKKA_00041:0.0116531):0.0773094):0.207845);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000206_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000206_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15e37bce0a82038928f541b388b61f43b88112c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000206_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01218:0.738686,(GCF_005280335_PROKKA_00353:0.0853524,(GCF_003691675_PROKKA_02063:0.0182035,(GCF_002008305_PROKKA_00050:0.0208483,GCF_023573625_PROKKA_00045:0.0078744)0.311:0.00526997)0.881:0.124639)1:0.738686);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000207_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000207_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c5fc8590c3e4e7cdcf54cd4705080b834671be6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000207_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00282:0.00797867,(GCF_003691675_PROKKA_02067:0.00422946,(GCF_002008305_PROKKA_00054:0.00222573,(GCF_005280335_PROKKA_00344:0.114345,GCF_023573625_PROKKA_00049:0.00820349)0.789:0.00362995)0.687:0.00401289)1:0.00797867);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000209_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000209_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b927765b622e051079f6be8dec8e16eddad5b49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000209_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00279:0.152119,(GCF_005280335_PROKKA_00339:0.165671,((GCF_002008305_PROKKA_00056:0,GCF_023573625_PROKKA_00051:0):5e-09,GCF_003691675_PROKKA_02069:0.0071414):0.163467):0.152119);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000214_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000214_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfc523dfea10f145887532a42b02566f690a24c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.745:0.00318142)1:0.255438)1:0.0378614);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000215_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000215_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64ae2611ed1ae5c17e5809007bc21a0a75469ba9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000215_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00272:0.0578698,(GCF_005280335_PROKKA_00330:0.045598,(GCF_003691675_PROKKA_02078:0.00478667,(GCF_002008305_PROKKA_00065:0.0115713,GCF_023573625_PROKKA_00059:0.00476725)0.405:0.00233335)0.98:0.0295389)1:0.0578698);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000216_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000216_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd652880852a3437227f07db03d1aef2cfa1d525
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.75:0.00368295)0.987:0.0565247)1:0.0417756);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000217_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000217_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..af4c5d78c9dc4ca64993d4a7c721b152cac1f0be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00467595,GCF_023573625_PROKKA_00061:5e-09):0.0415797):0.0697169);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000220_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000220_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62684c1d64906ba53344a1d125992c12351799fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.435:0.00857201)0.999:0.152309)1:0.0983498);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000222_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000222_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..42a4bfa0d2d43b3606f0bf7649e1379d836f837c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000222_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00260:0.0669619,(GCF_005280335_PROKKA_00319:0.0185857,(GCF_003691675_PROKKA_02087:0.00142896,(GCF_023573625_PROKKA_00068:0.00429699,GCF_002008305_PROKKA_00074:6e-09)0.763:5e-09)0.994:0.0285172)1:0.0669619);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000228_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000228_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..909777da1ce2e0a2d7a23e2ca0b5227af5e4ec33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000228_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00253:0.243386,(GCF_005280335_PROKKA_00312:0.167943,(GCF_003691675_PROKKA_02094:0.00102156,(GCF_002008305_PROKKA_00081:5e-09,GCF_023573625_PROKKA_00075:0.00184669)0.907:0.00641181)1:0.157102)1:0.243386);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000229_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000229_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d4133d47852060b746c48d488c0ac763e779ae8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000229_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00252:0.0540051,(GCF_005280335_PROKKA_00311:0.102886,(GCF_002008305_PROKKA_00082:0.0061764,(GCF_003691675_PROKKA_02095:0,GCF_023573625_PROKKA_00076:0):0.00307331):0.0993154):0.0540051);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000231_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000231_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d8aa1bc00c3defecf77d62aa0e839c09ec1bee2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000231_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00250:0.259677,((GCF_003691675_PROKKA_02099:0.00238123,GCF_023573625_PROKKA_00081:5e-09)0.905:0.0168689,(GCF_005280335_PROKKA_00305:0.0361702,GCF_002008305_PROKKA_00086:0.0081876)0.637:0.00500821)1:0.259677);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000238_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000238_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3dfb299ef9d32e01981600041ffae1ace58832cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000238_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00243:0.120567,(GCF_005280335_PROKKA_00298:0.0573284,(GCF_003691675_PROKKA_02106:0.00892396,(GCF_002008305_PROKKA_00093:0.00146786,GCF_023573625_PROKKA_00088:5e-09)0.95:0.0103531)0.992:0.0375026)1:0.120567);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000239_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000239_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e4173d63e0f5d5b2a6c9dcd5ed3f2e495471bcb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000239_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00242:0.305661,(GCF_005280335_PROKKA_00297:0.154895,(GCF_003691675_PROKKA_02107:0.0297839,(GCF_002008305_PROKKA_00094:5e-09,GCF_023573625_PROKKA_00089:0.00587755)0.88:5e-09)0.999:0.320202)1:0.305661);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000240_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000240_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5721dc74fa4ca08a3dc544e25f60016d73da5f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000240_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00241:0.0644812,(GCF_005280335_PROKKA_00296:0.151284,(GCF_023573625_PROKKA_00090:0.000856846,(GCF_003691675_PROKKA_02108:5e-09,GCF_002008305_PROKKA_00095:0.012404)0.285:0.00532291)1:0.107215)1:0.0644812);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000241_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000241_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0224966cc33b7ac507885fba1d27a0766b63f491
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.863:0.00965796)0.997:0.077794)1:0.056131);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000246_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000246_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..120b1e979eeceafcfe26ddb5fc397353a7a6b652
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000246_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00234:0.0824927,(GCF_005280335_PROKKA_00288:0.0475527,(GCF_023573625_PROKKA_00097:0.0111383,(GCF_002008305_PROKKA_00102:0.00553736,GCF_003691675_PROKKA_02115:5e-09)0.29:5e-09)0.961:0.0572682)1:0.0824927);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000248_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000248_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dda71b987645f320bd4f1473e5e994504e5dc733
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000248_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00232:0.280609,(GCF_005280335_PROKKA_00286:0.155976,(GCF_023573625_PROKKA_00099:5e-09,(GCF_003691675_PROKKA_02117:0.00691936,GCF_002008305_PROKKA_00104:0.0138719)0.909:0.0175703)0.998:0.172312)1:0.280609);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000249_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000249_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb1b95904c4dde977e4fdcc63e74ee5223da98fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000249_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00225:0.102354,(GCF_005280335_PROKKA_00284:0.0828517,(GCF_003691675_PROKKA_02119:5e-09,(GCF_002008305_PROKKA_00106:0.0075657,GCF_023573625_PROKKA_00101:5e-09)0.24:0.0100639)1:0.0933733)1:0.102354);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000254_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000254_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75e61227460756d76c12d55a511c0c3f5082b5bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000254_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00220:0.278215,(GCF_005280335_PROKKA_00279:0.103004,(GCF_023573625_PROKKA_00106:0.00299943,(GCF_002008305_PROKKA_00111:5e-09,GCF_003691675_PROKKA_02124:0.0030064)0.752:5e-09)0.998:0.124264)1:0.278215);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000255_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000255_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a63eb11d64a8a6215cbd2b83d92cceec613b7fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000255_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00219:0.206952,((GCF_002008305_PROKKA_00112:0,GCF_003691675_PROKKA_02125:0,GCF_023573625_PROKKA_00107:0):0.0773217,GCF_005280335_PROKKA_00278:0.0653813):0.206952);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000260_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000260_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..730d82818635971ad39092796fb057058cd28c34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.999:0.0582516)0.53:0.0268986)1:0.0548041);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000262_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000262_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..606217538e4447ba0a631c087e4fad56f0dc629d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.971:0.0992326)0.81:0.0685022)1:0.454165);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000263_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000263_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..661d0e991308b63ba67fd748161b298e2cf3302d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000263_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00194:0.0233356,(GCF_005280335_PROKKA_00260:0.115012,(GCF_002008305_PROKKA_00125:0.0232797,(GCF_003691675_PROKKA_02139:0.00647329,GCF_023573625_PROKKA_00133:0.00318668)0.878:0.0269719)1:0.484681)1:0.0233356);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000265_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000265_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23f88609e51570c7aa0b5094665c47ff3f8338d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000265_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00192:0.0710278,(GCF_005280335_PROKKA_00258:0.0302543,(GCF_023573625_PROKKA_00135:5e-09,(GCF_003691675_PROKKA_02141:0.0154779,GCF_002008305_PROKKA_00127:5e-09)0.879:0.00771103)0.868:0.023736)1:0.0710278);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000268_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000268_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..87eba9164a4f826d4fdb562d3a8214ab80e8003f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000268_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00185:0.0945764,(GCF_005280335_PROKKA_00250:0.0040315,((GCF_002008305_PROKKA_00135:0,GCF_003691675_PROKKA_02149:0):0.00499701,GCF_023573625_PROKKA_00143:5e-09):0.00265151):0.0945764);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000271_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000271_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e88100802138257e7b146c0fbf7769088c59dd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000271_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00180:0.0615904,(GCF_005280335_PROKKA_00246:0.145803,(GCF_002008305_PROKKA_00138:6e-09,(GCF_003691675_PROKKA_02152:0.0032899,GCF_023573625_PROKKA_00146:0.00654695)0.285:0.00980789)1:0.108092)1:0.0615904);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000272_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000272_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae8c74f8bf5e629ef9ecf795b16d131e405c7a1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000272_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00179:0.19114,(GCF_005280335_PROKKA_00245:0.0163525,(GCF_003691675_PROKKA_02153:0.0163959,(GCF_002008305_PROKKA_00139:0,GCF_023573625_PROKKA_00147:0):0.00657517):5e-09):0.19114);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000273_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000273_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34fc6458007e2dfc84d837aad6d56c9891065f68
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0175469,GCF_003691675_PROKKA_02154:0.00771428):0.0304354):0.0302064);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000277_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000277_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c493c483e45bee84fbd4d8598fa526289d09896b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000277_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00174:0.0829506,(GCF_005280335_PROKKA_00240:0.0244711,(GCF_002008305_PROKKA_00144:5e-09,(GCF_003691675_PROKKA_02158:0.00338741,GCF_023573625_PROKKA_00152:0.00340491)0.721:0.00685021)0.99:0.0656193)1:0.0829506);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000285_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000285_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff55dd0d0fff313f88d9f100c9fe5637781819cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000285_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00420:0.0960411,(GCF_005280335_PROKKA_00470:0.0848986,(GCF_023573625_PROKKA_00167:0.0183591,(GCF_002008305_PROKKA_00154:0.0162741,GCF_003691675_PROKKA_02168:0.0151109)0.861:0.0193951)1:0.201625)1:0.0960411);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000288_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000288_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..72d38a1c6c16968631a0e12e68ad6c74c5445b30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000288_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00168:0.0119336,(GCF_005280335_PROKKA_00222:0.0190949,(GCF_023573625_PROKKA_00176:0.00234565,(GCF_002008305_PROKKA_00179:5e-09,GCF_003691675_PROKKA_02175:0.00234356)0.762:0.00233953)0.939:0.00937941)1:0.0119336);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000290_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000290_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a34ffb86f83997a355f24c9cf764337c0e3441f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000290_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00165:0.190677,((GCF_003691675_PROKKA_02177:0,GCF_023573625_PROKKA_00178:0):5e-09,(GCF_002008305_PROKKA_00181:0.00780542,GCF_005280335_PROKKA_00220:0.0233204):0.00376088):0.190677);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000291_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000291_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ee2fa8ead0a7a3f61181cafe533effa4eb8087e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000291_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00164:0.335998,(GCF_005280335_PROKKA_00219:0.0138662,(GCF_002008305_PROKKA_00182:0.0265513,(GCF_003691675_PROKKA_02178:0,GCF_023573625_PROKKA_00179:0):0.0269957):0.0444455):0.335998);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000293_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000293_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cfb1eacf8ff3e49ec400e8469c08c9791618854f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000293_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00162:0.019239,(GCF_023573625_PROKKA_00181:0.00779563,(GCF_002008305_PROKKA_00184:0.0019556,(GCF_005280335_PROKKA_00217:0.0236363,GCF_003691675_PROKKA_02180:0.00358809)0.667:0.00345364)0.937:0.0103556)1:0.019239);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000296_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000296_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bfd35f717b083f888182d9f42bcd4504f3d9c800
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00179029,GCF_003691675_PROKKA_02183:0.00180222):5e-09):0.00454226);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000304_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000304_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb2b6df837255081f19337f559eb3db4d7280598
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000304_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00143:0.00500522,(GCF_005280335_PROKKA_00188:0.253022,(GCF_023573625_PROKKA_00205:0.0023934,(GCF_002008305_PROKKA_00203:5e-09,GCF_003691675_PROKKA_02198:0.00235831)0.881:0.00470162)0.149:0.00910449)1:0.00500522);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000307_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000307_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ffacbc094ffa7c4e19a8fd13ae7769f2f216b9f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000307_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00128:0.357422,(GCF_005280335_PROKKA_00182:0.117529,(GCF_023573625_PROKKA_00209:5e-09,(GCF_002008305_PROKKA_00209:0.0313413,GCF_003691675_PROKKA_02202:5e-09)0.494:0.00767506)0.963:0.099287)1:0.357422);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000308_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000308_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b12fc8fde54ca6ff4f17aa45439163d62028d80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000308_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00127:0.29651,(GCF_005280335_PROKKA_00181:0.184703,((GCF_002008305_PROKKA_00210:0,GCF_003691675_PROKKA_02203:0):0.0156627,GCF_023573625_PROKKA_00210:5e-09):0.0661857):0.29651);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000311_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000311_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ba66b4cfc9cb5fff63bb10772916ef2a1b501ec3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_003691675_PROKKA_02206:0.0110794):0.0092283):0.0244466);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000315_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000315_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f95a617f440a736add8a48b2162de5bbf663b03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000315_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00118:0.0516792,(GCF_005280335_PROKKA_00160:0.236542,(GCF_002008305_PROKKA_00220:0.0286656,(GCF_003691675_PROKKA_02233:0.00831888,GCF_023573625_PROKKA_00221:5e-09)0.915:0.0181064)1:0.181466)1:0.0516792);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000317_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000317_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e382f919291373832ceb95ff7cd6839fb11d6a2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.488:0.00624948)0.996:0.185076)1:0.235028);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000318_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000318_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..83296a6a934ded79d69351753548768142ee33fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000318_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00113:0.0212979,((GCF_002008305_PROKKA_00225:0,GCF_003691675_PROKKA_02238:0,GCF_023573625_PROKKA_00226:0):0.0101709,GCF_005280335_PROKKA_00155:5e-09):0.0212979);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000319_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000319_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49f5339913c2f5a220dc0996942253ebdb9de7c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000319_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00112:0.142305,(GCF_005280335_PROKKA_00154:0.1794,(GCF_003691675_PROKKA_02239:0.0104514,(GCF_002008305_PROKKA_00226:0.0109475,GCF_023573625_PROKKA_00227:0.0110726)0.538:0.00684316)1:0.143732)1:0.142305);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000322_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000322_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..043d023f41f4a9ed71cd3d759b9456a452b2ca03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00347542,GCF_023573625_PROKKA_00232:0.0034832):0.0357755):0.0649343);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000324_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000324_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f38224c974c075c8a8fdea850a92fd64d055c745
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.743:0.00430671)0.993:0.0891917)1:0.162257);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000325_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000325_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3796edd941b83cc60ae4afe4a641204c2d39cd8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000325_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00102:0.296157,(GCF_005280335_PROKKA_00137:0.24252,(GCF_003691675_PROKKA_02247:0.00287066,(GCF_002008305_PROKKA_00234:0.00804742,GCF_023573625_PROKKA_00235:0.0106253)0.841:0.0210584)0.977:0.152619)1:0.296157);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000327_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000327_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2dc341279e9f3fd78ec2077297978034631edff8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.826:0.00911151)0.936:0.0664826)1:0.384004);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000334_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000334_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e2335ab80e87e747868bbe7b2864e87a0e8ad60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000334_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00090:0.0503244,(GCF_005280335_PROKKA_00122:0.0500657,(GCF_003691675_PROKKA_02260:5e-09,(GCF_002008305_PROKKA_00248:0.0111089,GCF_023573625_PROKKA_00248:6e-09)0.873:0.00369305)0.9:0.0242071)1:0.0503244);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000335_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000335_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a884cde1324ee9e3429457ac6d0325b54bbc0f06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09):0.0770112):0.0994527);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000338_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000338_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52fde18e1d042a948d36d477f440fb8b7d497424
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000338_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00081:0.0876231,(GCF_005280335_PROKKA_00113:0.044996,(GCF_002008305_PROKKA_00256:5e-09,(GCF_003691675_PROKKA_02270:0.00253067,GCF_023573625_PROKKA_00255:0.00507344)0.498:0.00253744)0.991:0.0438918)1:0.0876231);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000339_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000339_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..399b0f2d93548922153ec048202eb210a0b10441
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000339_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00080:0.233065,(GCF_005280335_PROKKA_00112:0.0846592,(GCF_003691675_PROKKA_02271:0.00444185,(GCF_002008305_PROKKA_00257:0.00708633,GCF_023573625_PROKKA_00256:0.00355554)0.781:0.00627517)0.993:0.113913)1:0.233065);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000340_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000340_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e8432ac8113736e04d1e8f4fac948e8303d1416
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000340_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00076:0.0971563,(GCF_005280335_PROKKA_00106:0.0338842,((GCF_002008305_PROKKA_00261:0,GCF_023573625_PROKKA_00259:0):6e-09,GCF_003691675_PROKKA_02274:0.00616035):0.0444494):0.0971563);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000341_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000341_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b9463df42433cbc05416bcd69c2370c6dc3fafd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.886:0.0213307)0.983:0.174658)1:0.342472);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000342_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000342_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..743523659d35df84afa69cfbfb533351a2d932ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000342_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00071:0.0862732,(GCF_005280335_PROKKA_00100:0.0751504,(GCF_023573625_PROKKA_00261:0.00346563,(GCF_002008305_PROKKA_00263:6e-09,GCF_003691675_PROKKA_02276:0.00346974)0:5e-09)0.976:0.0494805)1:0.0862732);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000344_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000344_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..058aefda21849b83ffea911831c23fcfa964567e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000344_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00069:0.0580013,((GCF_002008305_PROKKA_00265:0,GCF_003691675_PROKKA_02278:0,GCF_023573625_PROKKA_00263:0):0.00947403,GCF_005280335_PROKKA_00098:0.0781022):0.0580013);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000345_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000345_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5759c73bbfa6cc1f2c18aaf982c24316b9c9df80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.75:0.004734)0.997:0.077188)1:0.0537833);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000350_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000350_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5dad66d4c1f9f77984f387b98c1eb5cfea118dc8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000350_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00063:0.140575,(GCF_005280335_PROKKA_00080:0.41379,(GCF_023573625_PROKKA_00273:0.00769185,(GCF_002008305_PROKKA_00275:0.00384032,GCF_003691675_PROKKA_02290:0.00387337)0.402:5e-09)1:0.252276)1:0.140575);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000352_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000352_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..782f89b31d63cad389dcdbf137264fab1fad88d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000352_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00060:0.0559183,((GCF_002008305_PROKKA_00278:0,GCF_003691675_PROKKA_02293:0,GCF_023573625_PROKKA_00277:0):5e-09,GCF_005280335_PROKKA_00075:0.00571009):0.0559183);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000354_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000354_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86623c8c309e2d51dc84545bb3503506bcd979af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000354_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00058:0.28101,(GCF_005280335_PROKKA_00072:0.193116,(GCF_023573625_PROKKA_00280:0.0057023,(GCF_002008305_PROKKA_00281:0.00724657,GCF_003691675_PROKKA_02296:0.00600691)0.975:0.0157113)1:0.129618)1:0.28101);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000355_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000355_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94b1a86f7524d6ebad87d548b572ca895b2a21cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)1:0.0500678)0.958:0.0354758)1:0.0846097);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000357_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000357_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..231b3c56fc7b8a879f420eeb1bcbb16289d59d08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00652336):0.0200393):0.120967);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000358_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000358_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9a6afd139142f2d3beb9b2f6bb488edceb578fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0117195):0.113053):0.248446);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000359_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000359_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..545981fa49d1f147e7c5a3c37fc91a5e317be416
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.759:0.0102029)0.994:0.0858688)1:0.0524966);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000360_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000360_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0eeb28c0f42e3e3ecca8f6b79a0afd74ba0c0ac6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000360_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00041:0.0524701,(GCF_005280335_PROKKA_00062:0.0312241,(GCF_002008305_PROKKA_00292:0.00197776,(GCF_003691675_PROKKA_02315:0,GCF_023573625_PROKKA_00299:0):0.0026542):0.0436041):0.0524701);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000365_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000365_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2f1c6185a5e6c6e71078418d4d7cc2a56c457a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000365_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00033:0.0731573,(GCF_005280335_PROKKA_00055:0.0423063,(GCF_002008305_PROKKA_00299:0.00137662,(GCF_003691675_PROKKA_00007:0.00413042,GCF_023573625_PROKKA_00306:0.00551784)0.763:0.00136414)0.996:0.0270947)1:0.0731573);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000368_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000368_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..42cf93b026d17e4a4864757eddedd799de1909cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000368_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00030:0.294637,(GCF_005280335_PROKKA_00051:0.185377,(GCF_023573625_PROKKA_00310:5e-09,(GCF_002008305_PROKKA_00303:0.0238753,GCF_003691675_PROKKA_00011:0.0272789)0.6:0.0126493)0.998:0.200847)1:0.294637);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000369_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000369_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97f8ce8ddabb5683192c4b600e019d47dad5ba94
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00582216):0.0553794):0.0547392);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000370_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000370_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f57c5715808e0a729b386340e4db312fa6e0547
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000370_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00027:0.219292,(GCF_005280335_PROKKA_00031:0.0588647,(GCF_003691675_PROKKA_00021:0.0056101,(GCF_002008305_PROKKA_00306:0.0155805,GCF_023573625_PROKKA_00313:5e-09)0.611:0.000552585)0.954:0.0295391)1:0.219292);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000371_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000371_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bc439ebc135899a37229757108ccc8c7cbd7415
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000371_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00026:0.106138,(GCF_005280335_PROKKA_00030:0.129961,(GCF_002008305_PROKKA_00307:0.00990882,(GCF_003691675_PROKKA_00022:5e-09,GCF_023573625_PROKKA_00314:0.00106136)0.966:0.0117113)1:0.109484)1:0.106138);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000372_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000372_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb59e0153424833e1df51a4d8b14cdc49749a679
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000372_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00025:0.100956,(GCF_005280335_PROKKA_00029:0.175924,(GCF_002008305_PROKKA_00308:5e-09,(GCF_023573625_PROKKA_00315:0.00382702,GCF_003691675_PROKKA_00023:5e-09)0.897:0.00254642)1:0.183118)1:0.100956);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000374_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000374_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74b16ba04eb185abf9a2f31c80ecfedc132c1dd3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000374_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00020:0.166436,(GCF_005280335_PROKKA_00024:0.183836,(GCF_003691675_PROKKA_00028:5e-09,(GCF_002008305_PROKKA_00313:0.0242438,GCF_023573625_PROKKA_00320:0.00803087)0.775:0.00795709)0.925:0.0646742)1:0.166436);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000375_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000375_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..abd669e4c38a7a2ff612914aaf8aec7b71c2dc33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00542315):0.0253253):0.0769854);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000377_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000377_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f9ce166f1240ba445ee7b5b3403765187f0cc373
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.02193):0.123467):0.319252);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000379_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000379_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..85e5d128735c26e2533d710dd55cea25862a3521
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000379_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00014:0.113567,(GCF_005280335_PROKKA_00018:0.0659021,(GCF_002008305_PROKKA_00319:0.00519975,(GCF_003691675_PROKKA_00034:0.00428273,GCF_023573625_PROKKA_00326:5e-09)0.919:0.0163843)0.868:0.0354733)1:0.113567);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000380_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000380_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b72ffb2561367c2ecf11b6af29ddb0be580b516c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_023573625_PROKKA_00327:0.00235154):0.0256753):0.0897262);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000381_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000381_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e1732c9af438d41e9216117189273a7a02db471
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000381_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00012:0.042008,((GCF_002008305_PROKKA_00321:0,GCF_003691675_PROKKA_00036:0,GCF_023573625_PROKKA_00328:0):0.0337201,GCF_005280335_PROKKA_00016:0.0070954):0.042008);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000382_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000382_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..747212ebd5cbdb7fb264a6e7ae0c70c7343a3a7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0894851,GCF_005280335_PROKKA_00015:0.140622):0.281983);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000383_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000383_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad1b7d4193b40b684fbe3aa24e63ae22704d3df9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00615218,GCF_023573625_PROKKA_00330:5e-09):0.0212699):0.0187213);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000384_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000384_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df971f881367a7821e1213581d4271d7d930d859
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000384_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00009:0.114608,(GCF_005280335_PROKKA_00013:0.0821439,(GCF_023573625_PROKKA_00331:0.0204808,(GCF_002008305_PROKKA_00324:0.00664419,GCF_003691675_PROKKA_00039:0.00758931)0.792:0.00627005)0.999:0.0835629)1:0.114608);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000386_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000386_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2514b1b3b81771b3a729e324fa540dddd478c6d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_023573625_PROKKA_00333:0.00603977):0.0388034):0.0385114);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000389_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000389_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e737ec62d2d43da574d5b2a36c6cefff8ea7013f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.758:0.0244372)0.928:0.305267)1:0.674034);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000390_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000390_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..35ce3d0a934c595008ebea948fd62691c047d599
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000390_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02488:0.0697254,(GCF_005280335_PROKKA_02676:0.232839,(GCF_002008305_PROKKA_00337:0.0453573,(GCF_003691675_PROKKA_00053:0.0155637,GCF_023573625_PROKKA_00344:0.0259108)0.854:0.0229196)0.996:0.162581)1:0.0697254);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000392_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000392_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b65d85a224ffb3a9ac98bbe0a4b70d121d18a09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000392_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02485:0.296848,(GCF_005280335_PROKKA_02673:0.194301,(GCF_002008305_PROKKA_00339:0.00991876,(GCF_003691675_PROKKA_00055:0.0191531,GCF_023573625_PROKKA_00346:0.00716922)0.783:0.0175012)0.999:0.161804)1:0.296848);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000393_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000393_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c8fdaa1f3901cf4805bfd725a80abd7a5bbdaa74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000393_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02484:0.229279,(GCF_005280335_PROKKA_02629:0.17391,(GCF_023573625_PROKKA_00347:0.0140632,(GCF_002008305_PROKKA_00340:0.00829435,GCF_003691675_PROKKA_00056:0.0190637)0.861:0.0225155)0.983:0.119989)1:0.229279);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000395_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000395_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..406acb7c5b935294d27ba4d456c970b8def38400
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.566:0.00582207)0.995:0.110348)1:0.153362);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000398_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000398_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c8e6f042b1a6c3a162e8762e215e6c93622e61e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.474:0.0023102)0.974:0.0381849)1:0.0748785);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000399_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000399_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d93e3ea2c057322ba3560838a1e29be8342feee3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000399_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02474:0.242081,(GCF_005280335_PROKKA_02622:0.127403,(GCF_002008305_PROKKA_00347:0.0294318,(GCF_003691675_PROKKA_00063:5e-09,GCF_023573625_PROKKA_00354:0.00333867)0.976:0.044092)0.977:0.0839706)1:0.242081);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000400_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000400_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..924d851f24dec0e6c5e7ed0f4cbc698aa5ff7e16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.291:0.00262184)0.999:0.106985)1:0.160577);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000404_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000404_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..041d8a1abf07dee2bef0ef77aa7120ad29b7d0e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000404_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02466:0.211639,(GCF_005280335_PROKKA_02607:0.143132,(GCF_002008305_PROKKA_00354:0.0146008,(GCF_003691675_PROKKA_00070:0.0137027,GCF_023573625_PROKKA_00361:0.0028571)0.815:0.0133358)0.999:0.135542)1:0.211639);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000405_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000405_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a30879c4ca26cd727e748802a382913d29405b01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.756:0.00296811)0.999:0.103189)1:0.178866);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000413_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000413_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..72554ae1560b2aab29c0909570107f9612cb5ee8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000413_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02455:0.0840796,((GCF_002008305_PROKKA_00365:0,GCF_003691675_PROKKA_00081:0,GCF_023573625_PROKKA_00372:0):5e-09,GCF_005280335_PROKKA_02596:0.0317213):0.0840796);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000418_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000418_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a7fd1dfd977d34156426a35577fcc159494ef4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000418_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01177:0.259676,(GCF_005280335_PROKKA_01002:0.367142,((GCF_002008305_PROKKA_00373:0,GCF_023573625_PROKKA_00380:0):0.0286009,GCF_005280335_PROKKA_02589:6e-09):0.511713):0.259676);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000423_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000423_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6525919b74f5abf863000e772483ba6a60609a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000423_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02446:0.00467653,(GCF_005280335_PROKKA_02574:0.0612034,(GCF_003691675_PROKKA_00105:0.00935175,(GCF_002008305_PROKKA_00381:0.00931974,GCF_023573625_PROKKA_00387:5e-09)0.807:5e-09)0.339:0.00932159)1:0.00467653);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000427_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000427_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57c02ab523e45a45bfe1e4c89d653ced56a18fc3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000427_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01755:0.0197977,(GCF_005280335_PROKKA_02570:0.018371,((GCF_002008305_PROKKA_00385:0,GCF_003691675_PROKKA_00109:0):0.00830318,GCF_023573625_PROKKA_00391:0.00353788):0.00860184):0.0197977);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000430_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000430_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb38e0ffb9bad29d4f7249ec107e3e906d6faab4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.537:5e-09)1:0.0913416)1:0.076323);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000431_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000431_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b28788f60d212a73790b737a0cd6bb8315a7d3ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000431_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02435:0.0967513,((GCF_002008305_PROKKA_00392:0,GCF_003691675_PROKKA_00116:0,GCF_023573625_PROKKA_00398:0):0.0323864,GCF_005280335_PROKKA_02564:0.0411685):0.0967513);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000433_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000433_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d634f4b9897991edf4d25bcec71f79d46c3ae4f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000433_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02434:0.0183341,((GCF_002008305_PROKKA_00394:0,GCF_003691675_PROKKA_00118:0,GCF_023573625_PROKKA_00400:0):0.0452645,GCF_005280335_PROKKA_02562:0.0270461):0.0183341);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000434_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000434_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2db4d6af2c507a9cef941166bf633ce66862995
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000434_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02432:0.0601928,(GCF_005280335_PROKKA_02561:0.0725942,(GCF_023573625_PROKKA_00402:5e-09,(GCF_002008305_PROKKA_00396:5e-09,GCF_003691675_PROKKA_00120:0.00248528)0.912:0.00497439)0.969:0.0373937)1:0.0601928);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000436_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000436_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52ec0bf8813aea0b123a711b61c33876008c1012
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000436_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02430:0.293069,(GCF_005280335_PROKKA_02559:0.170549,((GCF_002008305_PROKKA_00398:0,GCF_003691675_PROKKA_00122:0):0.00700669,GCF_023573625_PROKKA_00404:5e-09):0.0293021):0.293069);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000437_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000437_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30d55f1326b76346d2ada502adc83283b05bb649
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000437_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02429:0.0999565,(GCF_005280335_PROKKA_02558:0.0267888,((GCF_002008305_PROKKA_00399:0,GCF_003691675_PROKKA_00123:0):0.0104781,GCF_023573625_PROKKA_00405:5e-09):0.0156839):0.0999565);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000438_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000438_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd25055ed25716393f5da25223dca4d7048f2190
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000438_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02427:0.0888295,(GCF_005280335_PROKKA_02557:0.0373582,(GCF_003691675_PROKKA_00124:5e-09,(GCF_002008305_PROKKA_00400:0.0043177,GCF_023573625_PROKKA_00406:0.0108177)0.949:0.00650184)0.995:0.0431995)1:0.0888295);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000440_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000440_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5aa9de93db6e0f00ced7bd99b8ab7d9d9e8dea71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000440_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02422:0.0589014,(GCF_005280335_PROKKA_02553:0.0256104,(GCF_003691675_PROKKA_00126:0.0122199,(GCF_002008305_PROKKA_00403:0.00295601,GCF_023573625_PROKKA_00409:0.00895604)0.867:0.00477)0.704:0.0155248)1:0.0589014);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000445_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000445_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aea8751110f26a359711198fa6f052c935c2e58f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0024596,GCF_023573625_PROKKA_00414:0.00992389):0.0152176):0.00497999);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000447_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000447_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d9b88aab7dc22f5e6d81c1c3e098f6148bcc110
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00694998):0.0257116):0.0621583);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000450_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000450_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ebe5c808042ff8d9a6a73f56fae99f4c56c461f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000450_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02409:0.00282126,((GCF_002008305_PROKKA_00419:0,GCF_023573625_PROKKA_00422:0):0.0103105,(GCF_003691675_PROKKA_00140:0.010517,GCF_005280335_PROKKA_02540:0.0806126):0.00172125):0.00282126);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000451_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000451_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b84c4bd8d304f633c1bbefaf89b6c186fbba041
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000451_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02408:0.00116422,((GCF_002008305_PROKKA_00420:0,GCF_003691675_PROKKA_00141:0,GCF_023573625_PROKKA_00423:0):5e-09,GCF_005280335_PROKKA_02539:0.0502925):0.00116422);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000453_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000453_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d22f75d2d522905e0796012b23502b8a89ae6c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.772:0.00302932)0.972:0.0362143)1:0.0812052);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000454_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000454_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c95992b5dafb3e91f1c10faecdd5d9c65fcf793
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.268:0.00229004)0.957:0.0288583)1:0.151936);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000455_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000455_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88eca426bf78cff3af537c6467ce9f8a2b8e5911
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000455_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02402:0.139093,(GCF_005280335_PROKKA_02532:0.078461,((GCF_002008305_PROKKA_00425:0,GCF_003691675_PROKKA_00146:0):0.00847362,GCF_023573625_PROKKA_00428:0.0239686):0.0751707):0.139093);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000456_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000456_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad61dfa35938eb39f63533bafb1e6b1639d8ae03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000456_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02401:0.0928477,(GCF_005280335_PROKKA_02531:0.0587433,(GCF_023573625_PROKKA_00429:0.00327267,(GCF_002008305_PROKKA_00426:5e-09,GCF_003691675_PROKKA_00147:0.00328123)0.752:5e-09)0.939:0.0371145)1:0.0928477);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000457_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000457_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b3af0c3a535846bac0da4c8a718d25828dc6438
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000457_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02400:0.00842439,(GCF_005280335_PROKKA_02530:0.0908731,(GCF_002008305_PROKKA_00427:5e-09,(GCF_003691675_PROKKA_00148:0.011028,GCF_023573625_PROKKA_00430:0.00272819)0.444:0.00274852)0.534:0.0114716)1:0.00842439);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000461_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000461_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e92459b542822f9282d5132ad694aa188dcfe650
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000461_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02396:0.33213,(GCF_005280335_PROKKA_02525:0.139133,(GCF_002008305_PROKKA_00432:0.027396,(GCF_003691675_PROKKA_00153:0.0242718,GCF_023573625_PROKKA_00435:0.0172785)0.919:0.0348748)0.999:0.339221)1:0.33213);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000464_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000464_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04f624580c3507277e50cd0e2268777c4210dc9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000464_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02393:0.10774,((GCF_002008305_PROKKA_00435:0,GCF_003691675_PROKKA_00156:0,GCF_023573625_PROKKA_00438:0):0.046199,GCF_005280335_PROKKA_02522:0.0519144):0.10774);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000466_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000466_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a3a9489151998b1ef1ec1f92e320a9d755240542
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.826:0.00467453)0.941:0.0261105)1:0.0852755);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000468_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000468_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..478d04363327004dc24b7dc57f0b1c61295fb947
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.983:0.0260863)0.982:0.0821424)1:0.1043);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000469_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000469_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..33767f110530d808704823c3594bc196a910d0bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000469_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02388:0.0227878,(GCF_005280335_PROKKA_02517:0.126108,(GCF_002008305_PROKKA_00440:0.00740185,(GCF_003691675_PROKKA_00161:0.00192823,GCF_023573625_PROKKA_00443:0.00171352)0.382:0.00370929)0.999:0.0595771)1:0.0227878);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000470_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000470_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4671d680f54021fe20d060e85ba4aeead1296e2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.46:0.00204138)1:0.142398)1:0.0810846);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000471_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000471_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db161a5efb615173a520a525d08ee480eb176c34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.498:0.00227503)1:0.131406)1:0.0610846);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000473_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000473_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c63bd3c8d990be671a672471502788aa10b850f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000473_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02384:0.0525817,(GCF_005280335_PROKKA_02513:0.027118,(GCF_003691675_PROKKA_00165:0.00685451,(GCF_023573625_PROKKA_00447:0.00668959,GCF_002008305_PROKKA_00444:0.00211902)0.05:0.00204191)1:0.0616486)1:0.0525817);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000474_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000474_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93fadc89b74c0768361c09490a951eb7771b4b3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000474_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02383:0.204411,(GCF_005280335_PROKKA_02512:0.149794,(GCF_023573625_PROKKA_00448:5e-09,(GCF_002008305_PROKKA_00445:0.00482842,GCF_003691675_PROKKA_00166:5e-09)0.876:0.00970281)0.915:0.0781073)1:0.204411);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000476_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000476_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee1fe071f7fca44b0aaacbef4b5298042fc936bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.716:0.00592164)0.994:0.115361)1:0.154346);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000478_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000478_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f2c24b6802254218f7fd91a0398379787e2c37c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000478_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02378:0.127309,(GCF_005280335_PROKKA_02506:0.0301627,(GCF_002008305_PROKKA_00450:0.00359771,(GCF_003691675_PROKKA_00171:5e-09,GCF_023573625_PROKKA_00453:0.00547633)0.666:0.0110364)0.865:0.0127847)1:0.127309);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000481_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000481_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..42319a7e8f68f394649ffcff02c16b640a1a0ba1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000481_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02374:0.138713,(GCF_005280335_PROKKA_02490:0.0714857,(GCF_002008305_PROKKA_00457:5e-09,(GCF_003691675_PROKKA_00175:0.00303053,GCF_023573625_PROKKA_00457:0.00306361)0.954:0.0122706)1:0.110364)1:0.138713);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000483_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000483_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f26da0ab7576c3d9ce079600394bcf318f80e50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.557:0.000515945)0.997:0.0804881)1:0.0992653);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000484_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000484_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f2b3e1fb16416963c05337535e8c43fd61b4993
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000484_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02371:0.233982,(GCF_005280335_PROKKA_02487:0.137269,(GCF_002008305_PROKKA_00460:0.00766823,(GCF_003691675_PROKKA_00178:0.00920244,GCF_023573625_PROKKA_00460:0.00454586)0.753:0.0108222)0.966:0.117995)1:0.233982);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000485_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000485_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f04f4678d0dac7d4ba8001164ffe6757901cbef3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000485_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02370:0.0635124,(GCF_005280335_PROKKA_02486:0.021218,((GCF_002008305_PROKKA_00461:0,GCF_003691675_PROKKA_00179:0):0.00594962,GCF_023573625_PROKKA_00461:5e-09):0.0286886):0.0635124);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000487_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000487_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d071e080a810c20cc54affd97b00967bfc60adf5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000487_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02367:0.150967,(GCF_005280335_PROKKA_02483:0.105436,(GCF_003691675_PROKKA_00182:0.00751675,(GCF_002008305_PROKKA_00464:5e-09,GCF_023573625_PROKKA_00464:0.0149888)0.792:0.00742813)0.874:0.0475822)1:0.150967);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000488_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000488_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e5b0827dcf1921eda71d36f4538a8e7aa54a7b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.894:0.00858828)0.986:0.0570658)1:0.11489);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000490_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000490_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c9d91bbbe700a4e1416a8eb2bb46b02ca41e04a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.014914,GCF_003691675_PROKKA_00185:5e-09):0.159044):0.168255);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000491_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000491_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58f033c6c118fefe1b036f4b5e9dadb0acca1bc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.801:0.00205315)0.997:0.0753633)1:0.0884787);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000493_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000493_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3d8ee01816ae8ca78569392b297d82a1415ec03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000493_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02361:0.0299965,((GCF_002008305_PROKKA_00470:0,GCF_003691675_PROKKA_00188:0,GCF_023573625_PROKKA_00470:0):0.0281758,GCF_005280335_PROKKA_02477:0.0252572):0.0299965);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000494_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000494_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41a4955c91958f9568eba0ed0522d88a7b814d5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000494_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02360:0.0414623,(GCF_005280335_PROKKA_02476:0.149161,((GCF_002008305_PROKKA_00471:0,GCF_003691675_PROKKA_00189:0):5e-09,GCF_023573625_PROKKA_00471:0.00431064):0.132641):0.0414623);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000498_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000498_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad9cbd8d8760a964d61256c4b0178bcb7f4abb05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00653933,GCF_003691675_PROKKA_00193:0.00857647):0.0965862):0.199281);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000500_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000500_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbb775eeacfa930cc42b366801f0c57ae44b1017
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000500_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02353:0.105606,(GCF_005280335_PROKKA_02469:0.0489193,((GCF_002008305_PROKKA_00478:0,GCF_023573625_PROKKA_00478:0):5e-09,GCF_003691675_PROKKA_00196:0.0222082):0.0732304):0.105606);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000503_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000503_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77d79c313d6d0760f2da8152511508552bd029e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000503_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02350:0.161241,(GCF_005280335_PROKKA_02466:0.0545644,(GCF_002008305_PROKKA_00481:0.00552588,(GCF_003691675_PROKKA_00199:0.0111294,GCF_023573625_PROKKA_00481:5e-09)0.317:2.174e-06)0.971:0.12641)1:0.161241);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000505_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000505_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60f4849fd75b8877ba1b72a508b9f1c1434188af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000505_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02348:0.0308797,(GCF_005280335_PROKKA_02464:0.0143331,(GCF_003691675_PROKKA_00201:0.00190672,(GCF_002008305_PROKKA_00483:0.00190947,GCF_023573625_PROKKA_00483:5e-09)0.7:5e-09)0.993:0.0231663)1:0.0308797);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000507_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000507_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18d32d6e7a4e632fea40d706369925cba3387c7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000507_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02345:0.154448,(GCF_005280335_PROKKA_02462:0.116818,(GCF_023573625_PROKKA_00485:6e-09,(GCF_003691675_PROKKA_00204:0.00632559,GCF_002008305_PROKKA_00485:0.0063203)0.751:0.00157969)0.991:0.0861797)1:0.154448);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000509_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000509_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b793afac28252d717e95a176808ff17770187e8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.932:0.0131568)0.967:0.0313191)1:0.115917);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000512_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000512_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a6f15e6657ab9af80241cd3ad2f10e2dd7b8e71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000512_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02339:0.053565,(GCF_005280335_PROKKA_02455:0.106073,(GCF_002008305_PROKKA_00492:6e-09,(GCF_003691675_PROKKA_00213:0.0063174,GCF_023573625_PROKKA_00491:5e-09)0.916:0.00637551)0.978:0.0497355)1:0.053565);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000518_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000518_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..782a5ffbd9eeeaa95e7ea1ee28e0269b8a7dd3a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000518_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02331:0.225606,(GCF_005280335_PROKKA_02447:0.223682,(GCF_003691675_PROKKA_00223:0.00855063,(GCF_023573625_PROKKA_00502:0.0344707,GCF_002008305_PROKKA_00503:0.0171137)0.884:0.0179393)1:0.20622)1:0.225606);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000520_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000520_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9db8b288b429c44a318995351ddc853c4ee80834
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.331:0.00755429)0.997:0.074163)1:0.0603962);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000523_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000523_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..362edfaf3ae769cb4fad7153fefa93f44be1a8ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.739:0.00210574)1:0.0437146)1:0.0406196);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000526_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000526_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d928b8d5ac9da26d1538ce4b392e6aa89ab92eb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000526_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02321:0.0733603,(GCF_005280335_PROKKA_02438:0.0692489,(GCF_023573625_PROKKA_00512:0.0753434,(GCF_002008305_PROKKA_00513:0.0824887,GCF_003691675_PROKKA_00233:0.0620532)0.998:0.0832273)0.667:0.0484339)1:0.0733603);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000527_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000527_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a8e89ce14343a7370f5d8f431964e31c8eaa19bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000527_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02317:0.0200072,(GCF_002008305_PROKKA_00516:0.0673187,(GCF_023573625_PROKKA_00515:0.0276126,(GCF_003691675_PROKKA_00236:0.0424248,GCF_005280335_PROKKA_02435:0.0584181)0.389:0.00575124)0.792:0.016341)1:0.0200072);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000528_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000528_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c40a68ccee4960a9364af55990b9667e9a4f24ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.882:0.00837414)0.816:0.00672034)1:0.00589746);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000530_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000530_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1bddf4e191264b3372aef823c97623bb97d5329b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000530_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02307:0.0465676,(GCF_005280335_PROKKA_02424:0.0401259,(GCF_023573625_PROKKA_00527:0.00529222,(GCF_002008305_PROKKA_00527:0.0104786,GCF_003691675_PROKKA_00248:0.00532006)0.751:0.00527215)0.634:0.00221295)1:0.0465676);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000534_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000534_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc4466d8167ade590ba7bb276285001beb0d0f1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000534_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02302:0.35373,(GCF_005280335_PROKKA_02420:0.234583,(GCF_023573625_PROKKA_00532:0.00227956,(GCF_002008305_PROKKA_00532:0.0438063,GCF_003691675_PROKKA_00253:0.0357382)0.771:0.0251848)0.988:0.3425)1:0.35373);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000535_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000535_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70bd8f62e99363276ef3fb95ce59ac4f39d138e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.869:0.0216699)0.998:0.19673)1:0.220971);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000538_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000538_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67d13d6b3c6ab019e25e4886a2ecdf4fb25b26f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000538_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02294:0.111212,(GCF_005280335_PROKKA_02412:0.042319,((GCF_002008305_PROKKA_00537:0,GCF_023573625_PROKKA_00540:0):0.0125497,GCF_003691675_PROKKA_00261:0.0134456):0.0517201):0.111212);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000540_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000540_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df57a4838f3634e20a5f0dd327fc374bf6e73f63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000540_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02292:0.0543127,(GCF_005280335_PROKKA_02410:0.0486958,((GCF_002008305_PROKKA_00539:0,GCF_023573625_PROKKA_00542:0):0.00324387,GCF_003691675_PROKKA_00263:0.00363849):0.0412545):0.0543127);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000541_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000541_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec3c74daac33eef741a6cd1766d6caa6df6bfbd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.929:0.00925963)0.996:0.0692899)1:0.0717797);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000542_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000542_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fc920613aca6abbebe20a16fff492755f8bd971
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000542_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02290:0.0456196,(GCF_005280335_PROKKA_02408:0.0761057,(GCF_003691675_PROKKA_00265:5e-09,(GCF_002008305_PROKKA_00541:0.0085683,GCF_023573625_PROKKA_00544:0.00640418)0.797:0.00212187)1:0.136057)1:0.0456196);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000544_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000544_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e87e68ef2a272e973f1b406549792df96848bdf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.833:0.00394707)0.994:0.0364232)1:0.0557967);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000545_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000545_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbd502930ffe368e1cc9d7ef5fc5cd8ab04fb09f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000545_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02285:0.331871,(GCF_005280335_PROKKA_02402:0.055189,((GCF_002008305_PROKKA_00545:0,GCF_023573625_PROKKA_00548:0):0.0319873,GCF_003691675_PROKKA_00270:5e-09):0.269382):0.331871);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000548_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000548_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27a6bc84c67fb2ce7d65eee517859f1bbcea14ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.83:0.00495922)0.986:0.0479088)1:0.115185);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000549_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000549_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2684dd218bb450cb35f26dcbc8a92fbe34d7a29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0745542,GCF_005280335_PROKKA_02396:0.060993):0.0940854);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000550_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000550_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b9d8cb1c205c1133e4a4947cd534e6e4c742287c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000550_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02278:0.0752442,(GCF_005280335_PROKKA_02393:0.0404507,((GCF_002008305_PROKKA_00552:0,GCF_003691675_PROKKA_00277:0):0.00325023,GCF_023573625_PROKKA_00555:5e-09):0.101668):0.0752442);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000554_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000554_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43711051705531f7250e58e4c6d6ca464c23aff7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000554_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02271:0.0513603,(GCF_005280335_PROKKA_02388:0.0191245,((GCF_002008305_PROKKA_00557:0,GCF_023573625_PROKKA_00560:0):5e-09,GCF_003691675_PROKKA_00282:0.00383245):0.0125229):0.0513603);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000559_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000559_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9238705f3ce4bebc58b99215088bffebe5e9e7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.741:0.00429927)0.985:0.0603857)1:0.154363);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000560_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000560_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be56ea2ac450652c9afa28a65c661745425b9730
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000560_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02264:0.147614,(GCF_005280335_PROKKA_02380:0.0881762,(GCF_003691675_PROKKA_00288:0.0125806,(GCF_002008305_PROKKA_00563:0.0166932,GCF_023573625_PROKKA_00566:0.00326434)0.587:0.000651475)0.997:0.103201)1:0.147614);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000561_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000561_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b86502e32bb97689269f9c02d90abe934f6ec937
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000561_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02263:0.135453,(GCF_005280335_PROKKA_02379:0.0868574,(GCF_003691675_PROKKA_00289:0.00457656,(GCF_002008305_PROKKA_00564:0.00354816,GCF_023573625_PROKKA_00567:0.00540412)0.756:0.00862608)1:0.179635)1:0.135453);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000562_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000562_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf526fba6b8b93a34b8b8695a01e11765165813e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0250804,GCF_003691675_PROKKA_00290:5e-09):0.0462702):0.0654399);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000563_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000563_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27ef59ff70c0502726895e4e879989b3af0b1869
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000563_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02261:0.0413469,(GCF_005280335_PROKKA_02377:0.0225014,(GCF_003691675_PROKKA_00291:0.00878232,(GCF_002008305_PROKKA_00566:0.00445875,GCF_023573625_PROKKA_00569:0.00221395)0.865:0.00563428)0.993:0.0311193)1:0.0413469);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000564_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000564_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c1f72ad6291f4726cdde7fbff1dd9ba2c7af230
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.996:0.0686859)1:0.286982)1:0.0619843);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000565_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000565_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b474c28f046ab3687091c2eb4b70a5277e9e33a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000565_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02253:0.0316841,(GCF_005280335_PROKKA_02373:0.0806931,(GCF_003691675_PROKKA_00296:0.0225903,(GCF_002008305_PROKKA_00572:5e-09,GCF_023573625_PROKKA_00573:0.0147774)0.566:0.0189101)0.998:0.0871691)1:0.0316841);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000568_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000568_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b17d702f6931ec56ec7336ebfecf5584d0f5877
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000568_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02249:0.0926598,(GCF_005280335_PROKKA_02358:0.034336,(GCF_023573625_PROKKA_00576:0.00803684,(GCF_002008305_PROKKA_00575:0.00380013,GCF_003691675_PROKKA_00307:0.00786978)0.751:0.00380011)0.982:0.0372262)1:0.0926598);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000569_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000569_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1dd85341537ab1f747ac63378cc32040e5081fc7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000569_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02248:0.181238,(GCF_002008305_PROKKA_00579:0.0361074,(GCF_005280335_PROKKA_02354:0.123323,(GCF_003691675_PROKKA_00311:0.0130469,GCF_023573625_PROKKA_00580:5e-09)0.864:0.0140485)0.925:0.0422831)1:0.181238);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000570_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000570_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b9592408548d30e97d8c6f88f7cd9d2bff450c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000570_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02247:0.0585769,(GCF_005280335_PROKKA_02353:0.0814544,(GCF_002008305_PROKKA_00580:0.015008,(GCF_003691675_PROKKA_00313:0.0262411,GCF_023573625_PROKKA_00581:0.0243463)0.435:0.00551646)1:0.0952862)1:0.0585769);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000573_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000573_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b2afa7445a61c5afce9d2b436898a54ccbdd11e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.877:0.0576136)0.988:0.0432156,(GCF_002008305_PROKKA_00608:0.0427432,GCF_003691675_PROKKA_01768:0.0275979)0.988:0.0432156);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000574_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000574_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b169717a069898caf1468b1fc657d2c14f184eee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000574_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02343:0.0187785,((GCF_003691675_PROKKA_00328:0.00430392,GCF_023573625_PROKKA_02009:5e-09)1:0.207966,(GCF_002008305_PROKKA_00612:0.0484081,GCF_003691675_PROKKA_01772:0.108672)0.984:0.0898122)1:0.0187785);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000576_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000576_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..872c79f5ef3e040162df02659ba532293504dec2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000576_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_PROKKA_00408:0.096765,GCF_023573625_PROKKA_00595:5e-09)0.283:0.00333113,GCF_002008305_PROKKA_00636:0.00333991)0.582:8.17685e-05,(GCF_020097155_PROKKA_02193:0.0232575,GCF_020097155_PROKKA_02192:0.0046953)0.582:8.17685e-05);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000577_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000577_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5815b18bb1d5c050c5853dbaaa39e8c9ede36dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000577_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02191:0.0121827,((GCF_002008305_PROKKA_00637:0,GCF_023573625_PROKKA_00594:0):0.0155661,(GCF_005280335_PROKKA_01994:0.0340228,GCF_023573625_PROKKA_00894:0.098747):0.172369):0.0121827);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000583_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000583_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92796bc00184914e0436b31d71a9aae8f19bb846
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000583_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02171:0.214012,(GCF_005280335_PROKKA_02314:0.0534236,(GCF_003691675_PROKKA_00386:0.0153736,(GCF_002008305_PROKKA_00649:0.0186052,GCF_023573625_PROKKA_00619:0.00585684)0.823:0.00912447)0.97:0.0577645)1:0.214012);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000589_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000589_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0856b1bc716de1ac1abb7aeaf21edddf7c0e611
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000589_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02163:0.20124,(GCF_005280335_PROKKA_02306:0.0836552,((GCF_002008305_PROKKA_00657:0,GCF_003691675_PROKKA_00394:0):0.0100563,GCF_023573625_PROKKA_00627:0.00470421):0.0416014):0.20124);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000590_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000590_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7f6d6a29f29b78651d87f3ebabc44552a3da13b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.811:0.00256753)0.935:0.0292409)1:0.211371);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000593_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000593_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c73cfdb4acb774329414efa16d8d7e34eb94533
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000593_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02158:0.132325,(GCF_005280335_PROKKA_02302:0.112857,(GCF_003691675_PROKKA_00398:0.00629425,(GCF_023573625_PROKKA_00631:5e-09,GCF_002008305_PROKKA_00661:0.0063034)0:5e-09)0.639:0.00689945)1:0.132325);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000597_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000597_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07dd152db7a4e2ad323b905edbd98417f53c3b13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000597_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02155:0.0483285,(GCF_005280335_PROKKA_02293:0.027057,(GCF_002008305_PROKKA_00669:0.0111118,(GCF_003691675_PROKKA_00406:5e-09,GCF_023573625_PROKKA_00639:0.0036951)0.245:5e-09)0.727:0.0106736)1:0.0483285);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000599_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000599_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92cd182a8061358aea2fc8927ab7afcaa2e0b4eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000599_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02153:0.122462,((GCF_002008305_PROKKA_00671:0,GCF_003691675_PROKKA_00408:0,GCF_023573625_PROKKA_00641:0):0.0977828,GCF_005280335_PROKKA_02291:0.0718224):0.122462);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000600_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000600_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6db32f3f27d43760ed24ed174ecb2655e935719a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09):0.0233795):0.023483);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000601_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000601_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2f4e4928727aa6b0965f71fc84b024c92f13a76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000601_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02151:0.229597,(GCF_005280335_PROKKA_02289:0.0649509,(GCF_023573625_PROKKA_00643:0.00820399,(GCF_002008305_PROKKA_00673:0.00313152,GCF_003691675_PROKKA_00410:5e-09)0.821:0.00766891)0.939:0.0508281)1:0.229597);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000605_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000605_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5c7e82f38b2e16e7c7d75871a962db86574d6e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000605_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02147:0.0943738,((GCF_002008305_PROKKA_00677:0,GCF_003691675_PROKKA_00414:0,GCF_023573625_PROKKA_00647:0):0.0266902,GCF_005280335_PROKKA_02285:0.0365757):0.0943738);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000606_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000606_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5f316dbf51e8f818284bd92445745f9be95b77e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.8:5e-09)0.992:0.0278771)1:0.0299911);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000607_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000607_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b168b54f56cfae29eee6a3bcf7fc29740bdaf663
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_023573625_PROKKA_00650:0.0064166):0.0366625):0.035354);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000610_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000610_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7ef69bc8792694001884d00ca75cddada8cefc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0864833,GCF_005280335_PROKKA_02280:0.118886):0.115374);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000613_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000613_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7da1a6520b1f61852f4c51339079b239b6806814
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000613_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02138:0.119794,(GCF_005280335_PROKKA_02271:0.228513,((GCF_002008305_PROKKA_00686:0,GCF_023573625_PROKKA_00656:0):0.00987914,GCF_003691675_PROKKA_00423:0.00549922):0.206443):0.119794);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000615_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000615_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..241eea0c1105e29bf01bcc11d3b302711afa54d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_003691675_PROKKA_00425:0.00128559):0.0141544):0.0273553);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000617_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000617_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ed5b82b01cfb69b0217c26ea3cde69ca672c4be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000617_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02133:0.0740899,((GCF_002008305_PROKKA_00690:0,GCF_003691675_PROKKA_00427:0,GCF_023573625_PROKKA_00660:0):0.0730418,GCF_005280335_PROKKA_02265:0.0871492):0.0740899);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000618_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000618_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee3f9fee178f48d5b356eb5e685397ea918cfb0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000618_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02132:0.271623,(GCF_005280335_PROKKA_02264:0.0466018,(GCF_023573625_PROKKA_00661:6e-09,(GCF_002008305_PROKKA_00691:0.0357847,GCF_003691675_PROKKA_00428:6e-09)0.845:0.00577268)0.985:0.15424)1:0.271623);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000624_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000624_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7bd4e731caf39b436bac18b74a05978387362bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0138689,GCF_005280335_PROKKA_02255:0.051324):0.10974);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000625_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000625_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e77fca1637068c4916b4585e965ea4ae94fcf7ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000625_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02126:0.111137,((GCF_002008305_PROKKA_00700:0,GCF_003691675_PROKKA_00437:0,GCF_023573625_PROKKA_00670:0):0.0249736,GCF_005280335_PROKKA_02254:0.0637942):0.111137);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000628_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000628_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..126ffbd5b577d6b043e12c2684321b3a719a7796
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_003691675_PROKKA_00440:0.00378648):0.0090729):0.0224907);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000629_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000629_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14b242a7af0752dbc88f57bcf101d0090756bcc9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000629_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02122:0.005334,(GCF_005280335_PROKKA_02250:0.217799,(GCF_002008305_PROKKA_00707:0.0234143,(GCF_003691675_PROKKA_00441:0.0160511,GCF_023573625_PROKKA_00674:0.0113321)0.847:0.0112139)0.805:0.0113625)1:0.005334);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000631_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000631_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f05913ada776166d36e6d2f84d3c29a4f0477d28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000631_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02119:0.0120537,(GCF_005280335_PROKKA_02246:0.0138915,(GCF_002008305_PROKKA_00709:0.00886424,(GCF_003691675_PROKKA_00443:5e-09,GCF_023573625_PROKKA_00676:0.00472122)0.866:0.0150856)1:0.302988)1:0.0120537);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000632_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000632_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f4a4649e1a1a59321e53b80aaa4463bd94aaa8b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0134789):0.385566):0.00540314);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000634_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000634_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58fb39215ccdd08999af6c72d93a719e3d5513b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.77:0.00337349)0.995:0.0344678)1:0.0499969);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000635_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000635_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6472b5caecd71bf4218b17a730a512eb0d4a938d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000635_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02114:0.0753614,(GCF_005280335_PROKKA_02242:0.0142964,(GCF_003691675_PROKKA_00447:0.00402755,(GCF_002008305_PROKKA_00716:0.00409281,GCF_023573625_PROKKA_00680:0.00816729)0.41:5e-09)0.989:0.0533121)1:0.0753614);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000636_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000636_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7429438e0dddac8521546444ac3dc420abc935ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000636_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02113:0.217646,((GCF_002008305_PROKKA_00717:0,GCF_003691675_PROKKA_00448:0,GCF_023573625_PROKKA_00681:0):0.0631345,GCF_005280335_PROKKA_02241:0.0648312):0.217646);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000639_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000639_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69653183af465ea45dfebb03042d671c07714ad9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000639_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02110:0.0816815,(GCF_005280335_PROKKA_02238:0.0184382,((GCF_002008305_PROKKA_00720:0,GCF_003691675_PROKKA_00451:0):5e-09,GCF_023573625_PROKKA_00684:0.00464737):0.0521524):0.0816815);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000640_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000640_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da6ea85fb3386f8a7b040458609bf4c47aaa30f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0148529,GCF_005280335_PROKKA_02237:0.0263008):0.0935358);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000641_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000641_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4f149d54eb91779cce2fad1dcf4fd91521a1ba4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00380803):0.0220394):0.0596623);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000650_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000650_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98c6979df19c66c232432b5e365ffcfd4fc08bb8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000650_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02097:0.0675361,(GCF_005280335_PROKKA_02221:0.0480915,((GCF_002008305_PROKKA_00732:0,GCF_003691675_PROKKA_00463:0):5e-09,GCF_023573625_PROKKA_00696:0.00239867):0.027299):0.0675361);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000651_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000651_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b73a114b2027bb24c2ac1375203feb5d3014f75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.476:0.00349021)1:0.0784953)1:0.110518);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000652_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000652_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aeef96985aa9b552add2234b0f36d3c5435472e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000652_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02095:0.161117,(GCF_005280335_PROKKA_02219:0.0978702,(GCF_023573625_PROKKA_00698:0.00883749,(GCF_002008305_PROKKA_00734:0.00316794,GCF_003691675_PROKKA_00465:5e-09)0.83:0.0106099)0.995:0.106743)1:0.161117);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000659_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000659_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..55631463a94047882ea8739578bf558abdcd3eab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000659_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02085:0.00365668,(GCF_023573625_PROKKA_00707:0.00486978,(GCF_002008305_PROKKA_00742:5e-09,(GCF_003691675_PROKKA_00473:5e-09,GCF_005280335_PROKKA_02187:0.00974879)0.881:0.00243049)0.791:0.00244094)1:0.00365668);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000660_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000660_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93379858ef774675aa88a167d3ad6cf73b28259b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000660_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02084:0.00947756,((GCF_005280335_PROKKA_02186:0.067309,GCF_002008305_PROKKA_00743:0.00753388)0.303:5e-09,(GCF_003691675_PROKKA_00474:0.00747375,GCF_023573625_PROKKA_00708:5e-09)0.775:0.0037014)1:0.00947756);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000661_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000661_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1426e721f016bd8d7e22bf3267b8dabff4a7be84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.787:0.00443383)0.761:0.00446181)1:0.00442549);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000663_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000663_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc5509306021f9f7f95813d121b2fb397112a31e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000663_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02075:0.0457713,(GCF_005280335_PROKKA_02180:0.0327876,(GCF_002008305_PROKKA_00750:0.0052441,(GCF_003691675_PROKKA_00480:0.0106484,GCF_023573625_PROKKA_00714:5e-09)0.726:0.00534749)0.888:0.0166364)1:0.0457713);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000665_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000665_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88074817f5072224970ef3440de50ceb0d7cb495
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.613:0.00610421)1:0.122953)1:0.195378);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000666_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000666_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a84f6d6b5ca3ce7f60a211da922b122a79a3f323
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000666_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02072:0.0694813,(GCF_005280335_PROKKA_02177:0.0426669,((GCF_002008305_PROKKA_00753:0,GCF_023573625_PROKKA_00717:0):5e-09,GCF_003691675_PROKKA_00483:0.00382249):0.0519247):0.0694813);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000668_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000668_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9b5b5ee91caed01c42456d2f9ed876f5ad8797f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09):0.0473509):0.0802517);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000672_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000672_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..108e1974266fd38568fb6d656582622257cc0486
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):6e-09,GCF_023573625_PROKKA_00723:0.00839093):0.0389905):0.0759111);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000673_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000673_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e5a35b1857a90558fadf88234f22192dc8ca9df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000673_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02065:0.148579,(GCF_005280335_PROKKA_02170:0.285907,(GCF_023573625_PROKKA_00724:0.0085772,(GCF_002008305_PROKKA_00760:0.0199509,GCF_003691675_PROKKA_00490:0.0111206)0.206:0.0102185)1:0.185976)1:0.148579);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000675_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000675_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ac12f02a72fcfa8d1bb8e11fb34646ad622bed3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.899:0.0129118)0.93:0.0697473)1:0.124114);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000678_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000678_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6764f0acfabc903726258355e6277eb66477a112
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000678_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02059:0.0712817,(GCF_005280335_PROKKA_02163:0.0500062,(GCF_002008305_PROKKA_00766:0.00373034,(GCF_003691675_PROKKA_00496:0.00410338,GCF_023573625_PROKKA_00730:0.00623037)0.914:0.00411088)1:0.0445196)1:0.0712817);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000679_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000679_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..788f3ef0a5765de5acac8bc0065933d20be48d28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000679_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02058:0.0589417,(GCF_005280335_PROKKA_02162:0.0919243,(GCF_003691675_PROKKA_00497:0.00465891,(GCF_002008305_PROKKA_00767:0.00545588,GCF_023573625_PROKKA_00731:0.00182914)0.744:0.00267841)0.999:0.0652057)1:0.0589417);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000682_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000682_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..952d612c4fe877288b6865e96899722887e67d9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000682_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02053:0.0988243,(GCF_005280335_PROKKA_02158:0.0335439,(GCF_003691675_PROKKA_00503:0.00767533,(GCF_002008305_PROKKA_00772:0.00753943,GCF_023573625_PROKKA_00739:5e-09)0.88:0.00744739)1:0.0876814)1:0.0988243);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000683_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000683_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..38332323883a93b3bd4e2b68c26865c6b4f51533
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.848:0.00337443)0.877:0.0238496)1:0.116883);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000687_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000687_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10f1c960cc06e910aaa1319ebe3d8bc4c01dee50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000687_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02047:0.0699475,((GCF_002008305_PROKKA_00778:0,GCF_003691675_PROKKA_00509:0,GCF_023573625_PROKKA_00745:0):5e-09,GCF_005280335_PROKKA_02152:0.0107787):0.0699475);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000689_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000689_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0644545c1939c9325320bc109ac4857c13a9834
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000689_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02044:0.0830451,(GCF_005280335_PROKKA_02150:0.00513164,(GCF_003691675_PROKKA_00511:5e-09,(GCF_002008305_PROKKA_00780:0.00177644,GCF_023573625_PROKKA_00747:0.0053247)0.357:0.0035442)0.918:0.0128676)1:0.0830451);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000691_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000691_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..239aa75c0fff9f6ad558edff2766de6b37a5c1e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_023573625_PROKKA_00749:0.00218359):0.0241414):0.0801097);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000692_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000692_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10b17535f329ad855ebb04bcaeff312a1854ef17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0290363,GCF_005280335_PROKKA_02147:0.0133714):0.0472908);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000693_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000693_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b2c1ef1dc2ff17b0806fcf08e4b81b9056d6e85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000693_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02040:0.171411,(GCF_005280335_PROKKA_02146:0.0819429,(GCF_023573625_PROKKA_00751:0.0032986,(GCF_002008305_PROKKA_00784:0.0124532,GCF_003691675_PROKKA_00515:0.00291821)0.763:0.00924269)0.995:0.0894315)1:0.171411);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000694_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000694_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..243e56e7677985651aea11cee1ce1fe180057261
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000694_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02039:0.119443,(GCF_005280335_PROKKA_02145:0.0670001,(GCF_003691675_PROKKA_00516:0.0041509,(GCF_023573625_PROKKA_00752:0.00853349,GCF_002008305_PROKKA_00785:0.00284252)0.385:0.00148335)0.997:0.0620941)1:0.119443);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000695_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000695_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0b7d064f696c44e3a9eac080aa9a128f53d0d8b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0027169,GCF_023573625_PROKKA_00753:0.00256207):0.0156241):0.0688439);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000696_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000696_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7d610e824f388dea8ce558198c8ae48b6b45be7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000696_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02036:0.0786905,(GCF_005280335_PROKKA_02143:0.067983,((GCF_002008305_PROKKA_00788:0,GCF_003691675_PROKKA_00519:0):5e-09,GCF_023573625_PROKKA_00755:0.0113211):0.0491301):0.0786905);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000698_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000698_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..746d288d8061c36d5b5e4e3499126bd3b562bfa0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000698_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02034:0.234152,(GCF_005280335_PROKKA_02141:0.0750644,((GCF_002008305_PROKKA_00790:0,GCF_003691675_PROKKA_00521:0):0.0215477,GCF_023573625_PROKKA_00757:5e-09):0.17164):0.234152);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000700_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000700_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6aeb32c310835d47c70184439f83f56b127c815f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0228128,GCF_020097155_PROKKA_02032:0.0228128);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000703_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000703_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7e2f460bb01e60ce329eb5c425e3c7867bf7954
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.824:5e-09)0.987:0.0171517)1:0.0319928);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000711_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000711_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8136af5346380dca11af49fc4709a4b9468a6db3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.745:0.00300109)0.964:0.0476661)1:0.131326);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000715_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000715_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f3e4fa504bbc94c806e0dc861f3689e31e0e6d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000715_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02016:0.041086,(GCF_005280335_PROKKA_02123:0.0587485,(GCF_023573625_PROKKA_00774:0.000854569,(GCF_002008305_PROKKA_00807:0.00652993,GCF_003691675_PROKKA_00538:0.00160458)0.801:0.00565743)0.963:0.0217638)1:0.041086);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000717_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000717_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8995c60b472bea1c76239c28302e91d71ea30b41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000717_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02011:0.1011,((GCF_002008305_PROKKA_00810:0,GCF_003691675_PROKKA_00542:0,GCF_023573625_PROKKA_00779:0):0.000885626,GCF_005280335_PROKKA_02120:0.0209625):0.1011);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000718_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000718_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..297519ef5c4e9e907c97f93c1468bb090b297dd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000718_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02010:0.0900825,((GCF_002008305_PROKKA_00811:0,GCF_003691675_PROKKA_00543:0,GCF_023573625_PROKKA_00780:0):0.0521342,GCF_005280335_PROKKA_02119:0.0822726):0.0900825);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000721_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000721_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..067c773ceef3a6c95c3d71b6cabe80bc71ea95bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.527:0.00762579)0.999:0.101155)1:0.0897134);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000723_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000723_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a773eaf0f922193d4f9e8e86901f04e9c83943a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000723_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02005:0.0837692,(GCF_005280335_PROKKA_02114:0.0962612,(GCF_002008305_PROKKA_00816:0.00543887,(GCF_003691675_PROKKA_00548:5e-09,GCF_023573625_PROKKA_00785:0.00430898)0.632:0.00319278)0.697:0.0247343)1:0.0837692);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000729_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000729_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3660d937d12ba0a4a46cfae04b83b3e23ea5ec9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000729_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01999:0.066895,(GCF_005280335_PROKKA_02108:0.0561372,((GCF_002008305_PROKKA_00822:0,GCF_003691675_PROKKA_00554:0):0.000788166,GCF_023573625_PROKKA_00791:0.0073549):0.0749369):0.066895);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000730_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000730_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54dc3cf7bf74120903a02b5b9029cbd5b611849e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000730_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01998:0.192485,(GCF_005280335_PROKKA_02107:0.123931,((GCF_002008305_PROKKA_00823:0,GCF_003691675_PROKKA_00555:0):0.0116988,GCF_023573625_PROKKA_00792:0.0103317):0.119429):0.192485);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000731_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000731_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6588775e7dabb1bcbe854006580122bcffdc7796
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_023573625_PROKKA_00794:0.00611883):0.0559516):0.0478163);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000734_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000734_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7895dab9051b9ae8df5395827dd27f5c34139ac5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000734_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02024:0.0838874,(GCF_005280335_PROKKA_02131:0.431352,(GCF_002008305_PROKKA_00830:0.010562,(GCF_023573625_PROKKA_00799:0.0397067,GCF_003691675_PROKKA_00562:0.0442832)0.617:0.00111948)1:0.951464)1:0.0838874);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000735_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000735_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e81d5798b2d458564c84f14ca7617e21da4c18db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000735_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01992:0.0663216,(GCF_005280335_PROKKA_02093:0.0228326,(GCF_023573625_PROKKA_00801:5e-09,(GCF_002008305_PROKKA_00831:0.00776555,GCF_003691675_PROKKA_00563:0.00465525)0.613:0.00153297)0.907:0.0110035)1:0.0663216);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000736_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000736_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41b307c969006bf0b42613e2dcd81a2a5ae8dbe5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000736_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01991:0.0421822,((GCF_002008305_PROKKA_00832:0,GCF_003691675_PROKKA_00564:0,GCF_005280335_PROKKA_02092:0):5e-09,GCF_023573625_PROKKA_00802:0.00568246):0.0421822);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000738_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000738_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec45a609a0c3b253497c481e9a0bebd96cf6c76f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09):0.0300741):0.0949316);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000740_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000740_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf6c84d826b34e59d604e01ce926c9654925813e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000740_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01987:0.0741312,(GCF_005280335_PROKKA_02087:0.0210291,(GCF_002008305_PROKKA_00848:0.00330922,(GCF_003691675_PROKKA_00570:0,GCF_023573625_PROKKA_00807:0):0.0021278):0.0625409):0.0741312);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000741_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000741_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..239f570939a5f1b924d9bd86e1a04c9e59ddd52f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000741_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01986:0.0164895,(GCF_005280335_PROKKA_02086:0.0695582,(GCF_002008305_PROKKA_00849:0.00704011,(GCF_003691675_PROKKA_00571:0,GCF_023573625_PROKKA_00808:0):0.00414726):0.0139801):0.0164895);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000744_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000744_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90cd170f1ecd51b9d525d8861258bfb5580e3fe9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000744_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01977:0.0293192,(GCF_005280335_PROKKA_02082:0.0285782,(GCF_002008305_PROKKA_00852:0.00567442,(GCF_003691675_PROKKA_00574:0,GCF_023573625_PROKKA_00811:0):0.0132664):0.0226268):0.0293192);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000747_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000747_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b17c1a5adf87ee935766b2a26da03122762818ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000747_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01969:0.192729,(GCF_005280335_PROKKA_02075:0.0851802,(GCF_002008305_PROKKA_00860:0.0110302,(GCF_003691675_PROKKA_00582:0.00810743,GCF_023573625_PROKKA_00819:0.00791308)0.488:0.007784)1:0.12228)1:0.192729);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000748_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000748_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7d0f701ec7f4f37d4fbdfbd6b117625fad365ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.9:0.00736741)0.982:0.0394899)1:0.0610696);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000751_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000751_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74bc08f53c7ffe1fcae6d28f4d7caa5932874715
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000751_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01965:0.08445,(GCF_005280335_PROKKA_02071:0.0095082,((GCF_002008305_PROKKA_00864:0,GCF_023573625_PROKKA_00823:0):0.00494257,GCF_003691675_PROKKA_00586:0.00492276):0.031125):0.08445);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000754_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000754_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9e3b3331c6438fb7097f2b0f5d8b736c8b6dc9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000754_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01962:0.0913401,(GCF_005280335_PROKKA_02068:0.0432179,(GCF_023573625_PROKKA_00826:0.00271026,(GCF_003691675_PROKKA_00589:0.00542184,GCF_002008305_PROKKA_00867:0.00544549)0.438:5e-09)0.986:0.0404973)1:0.0913401);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000755_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000755_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eae9557279e2b061e91367284812ccbf32efed8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.775:0.00450078)0.979:0.0506588)1:0.0856614);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000758_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000758_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f75ee002d462d393618b06434c925e62e45200c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000758_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01958:0.253464,(GCF_005280335_PROKKA_02064:0.112796,(GCF_023573625_PROKKA_00830:0.00486493,(GCF_003691675_PROKKA_00593:0.00864662,GCF_002008305_PROKKA_00871:0.0184866)0.811:0.00664407)0.954:0.0651487)1:0.253464);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000763_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000763_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..87affdc1256cc8d273981959857bbaa26537eb99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.318:0.00342339)0.991:0.0597035)1:0.0818785);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000764_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000764_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ab8395352039232555548a82fcbb7bacca5a196
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000764_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01952:0.122047,(GCF_005280335_PROKKA_02058:0.0252524,((GCF_002008305_PROKKA_00877:0,GCF_003691675_PROKKA_00599:0):5e-09,GCF_023573625_PROKKA_00836:0.00536534):0.0409161):0.122047);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000765_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000765_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..76b06bd9f90dfcec1d0b957dc08667ce23436b99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0133131,GCF_005280335_PROKKA_02057:0.000695741):0.0303888);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000767_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000767_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe0c09a6a283fbd2748481d57c9495a231704880
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000767_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01949:0.107283,(GCF_005280335_PROKKA_02055:0.0418662,(GCF_003691675_PROKKA_00602:0.0104304,(GCF_023573625_PROKKA_00839:0.00996948,GCF_002008305_PROKKA_00880:0.00331872)0.716:0.0027874)0.984:0.0584348)1:0.107283);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000768_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000768_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dea3fa36f1d1df98dfce589a5565d07609a53c55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000768_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01948:0.281781,(GCF_005280335_PROKKA_02054:0.11747,(GCF_003691675_PROKKA_00603:0.0028365,(GCF_002008305_PROKKA_00881:0.0187567,GCF_023573625_PROKKA_00840:0.0132413)0.773:0.00523308)0.997:0.137558)1:0.281781);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000769_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000769_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..588090797bfc7ae90d51b67a99620c9cb867cbb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.999:0.105849,(GCF_002008305_PROKKA_00882:0.00872689,GCF_003691675_PROKKA_00604:0.00943392)0.911:0.0304066)1:0.179464);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000772_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000772_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc94eda7f4b052ea03cdc21ba8aef3d4fd2f4b41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000772_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01941:0.243167,(GCF_023573625_PROKKA_00847:0.736992,(GCF_005280335_PROKKA_02043:0.253541,(GCF_002008305_PROKKA_00896:5e-09,GCF_003691675_PROKKA_00618:0.0136628)0.965:0.130066)0.997:0.370772)1:0.243167);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000776_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000776_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e39fcd168c9bf654d57bb6cb327ba2e04928bb16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000776_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01937:0.0628152,((GCF_002008305_PROKKA_00903:0,GCF_005280335_PROKKA_02039:0):0.108216,(GCF_003691675_PROKKA_00622:0.0107167,GCF_023573625_PROKKA_00851:0.00143916):0.105836):0.0628152);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000779_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000779_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97e110738bef59f5eb7e0070b25e13a20903c83c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000779_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01934:0.0452379,((GCF_002008305_PROKKA_00906:0,GCF_003691675_PROKKA_00625:0,GCF_023573625_PROKKA_00854:0):0.0122899,GCF_005280335_PROKKA_02036:5e-09):0.0452379);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000780_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000780_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fe11a79ae6724a6baebd36a396139125b696206
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000780_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01933:0.157991,(GCF_005280335_PROKKA_02035:0.0425513,(GCF_002008305_PROKKA_00907:0.00456957,(GCF_003691675_PROKKA_00626:0.0101986,GCF_023573625_PROKKA_00855:0.00510614)0.91:0.0160357)0.959:0.0719424)1:0.157991);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000787_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000787_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52bde1ecafaa5c74a901dbb6d91068a469cf5d5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000787_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01926:0.115006,(GCF_005280335_PROKKA_02028:0.0215518,((GCF_002008305_PROKKA_00914:0,GCF_023573625_PROKKA_00862:0):0.00442798,GCF_003691675_PROKKA_00633:0.0177116):0.112325):0.115006);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000788_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000788_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..378690b09b6015fef22f90ccb4672fbc5b279c2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000788_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01925:0.13014,(GCF_005280335_PROKKA_02027:0.0791113,((GCF_002008305_PROKKA_00915:0,GCF_023573625_PROKKA_00863:0):0.00818962,GCF_003691675_PROKKA_00634:0.00495282):0.0735626):0.13014);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000789_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000789_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7919231ba95513f7fbcde6b097f37f5a5609cc3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.703:0.0101574)0.998:0.101176)1:0.149268);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000790_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000790_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d7608046bfb2bef7c81a77d9b882647a9984b50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000790_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01923:0.187213,(GCF_005280335_PROKKA_02024:0.104277,(GCF_003691675_PROKKA_00636:0.00117953,(GCF_002008305_PROKKA_00917:0.0230226,GCF_023573625_PROKKA_00865:0.0181693)0.893:0.0185452)0.992:0.10841)1:0.187213);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000795_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000795_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2069de92dd00e142ca8b08fcf16ded96a332a7b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000795_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01918:0.0923208,(GCF_005280335_PROKKA_02019:0.0291391,(GCF_002008305_PROKKA_00922:0.00930127,(GCF_003691675_PROKKA_00641:0.00311178,GCF_023573625_PROKKA_00870:5e-09)0.57:5.9844e-05)0.998:0.0643682)1:0.0923208);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000796_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000796_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7831c39188ac577e6c447bf47eb7354334b62dac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000796_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01917:0.132683,(GCF_005280335_PROKKA_02018:0.0664398,(GCF_003691675_PROKKA_00642:0.00387098,(GCF_023573625_PROKKA_00871:0.00996319,GCF_002008305_PROKKA_00923:5e-09)0.631:0.00109012)0.983:0.0488322)1:0.132683);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000797_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000797_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f320200c3b967a8bd0ad71002c44255159b263de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000797_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01916:0.00957233,(GCF_005280335_PROKKA_02017:0.0792766,(GCF_002008305_PROKKA_00924:0.00319876,(GCF_003691675_PROKKA_00643:0.00109559,GCF_023573625_PROKKA_00872:5e-09)0.774:0.00119166)0.802:0.006222)1:0.00957233);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000798_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000798_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90e735fd68e026ca50e21185dbb4d40bae45d280
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000798_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01915:0.123673,(GCF_005280335_PROKKA_02016:0.0751506,((GCF_002008305_PROKKA_00925:0,GCF_023573625_PROKKA_00873:0):5e-09,GCF_003691675_PROKKA_00644:0.00692485):0.0523817):0.123673);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000800_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000800_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e87e40e4f92dc23743edacdb505812b3b726d261
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000800_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01911:0.187965,(GCF_005280335_PROKKA_02012:0.0680959,(GCF_003691675_PROKKA_00647:0.0198803,(GCF_002008305_PROKKA_00928:0.0296518,GCF_023573625_PROKKA_00876:0.00724471)0.885:0.0175047)0.998:0.143472)1:0.187965);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000801_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000801_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..11235feaea6b6b887e847f9bbbcebda741321b07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.868:0.0085981)0.945:0.074233)1:0.127557);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000802_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000802_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b63a31351c5c5c9b0589a26cfe89abf5a3e0679
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000802_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01908:0.23576,(GCF_005280335_PROKKA_02010:0.191531,(GCF_002008305_PROKKA_00930:5e-09,(GCF_023573625_PROKKA_00878:0.0515658,GCF_003691675_PROKKA_00649:0.00771137)0.414:0.0125401)0.922:0.12202)1:0.23576);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000803_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000803_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2eb99289bcd4de7a7ec10f05d5406180af217e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0125591,GCF_005280335_PROKKA_02009:0.0424573):0.172608);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000804_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000804_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c4d8af3b18399fff11e70f5e5ae30f4315e8928
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000804_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01904:0.0384795,((GCF_002008305_PROKKA_00932:0,GCF_003691675_PROKKA_00651:0,GCF_023573625_PROKKA_00881:0):0.0102253,GCF_005280335_PROKKA_02008:0.0032634):0.0384795);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000806_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000806_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0980250fc2289be073911fd4b986cf5350e5b99e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000806_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01902:0.0556633,(GCF_005280335_PROKKA_02005:0.0585471,(GCF_002008305_PROKKA_00934:0.00502593,(GCF_003691675_PROKKA_00653:0,GCF_023573625_PROKKA_00883:0):5e-09):0.0409053):0.0556633);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000808_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000808_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c7e0bd46e5e20739553a661b81fdee50ba080e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000808_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01900:0.146981,(GCF_002008305_PROKKA_00936:0.00486272,(GCF_023573625_PROKKA_00885:5e-09,(GCF_003691675_PROKKA_00655:0.0152712,GCF_005280335_PROKKA_02003:0.0101431)0.773:5e-09)0.762:0.00536115)1:0.146981);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000810_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000810_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5333b2955b3a998041243e5993157fbdf707ed56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000810_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01898:0.333099,(GCF_005280335_PROKKA_02001:0.0429599,(GCF_003691675_PROKKA_00657:0.00795131,(GCF_002008305_PROKKA_00938:0.0202499,GCF_023573625_PROKKA_00887:0.00382307)0.935:0.0163019)0.975:0.090828)1:0.333099);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000812_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000812_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93a9dafd7425fa4faf505f0403d33ac39a9b8d45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000812_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01896:0.105603,(GCF_005280335_PROKKA_01999:0.117891,(GCF_003691675_PROKKA_00659:0.0207319,(GCF_002008305_PROKKA_00940:0.0112844,GCF_023573625_PROKKA_00889:0.0188952)0.774:0.00734739)0.997:0.103734)1:0.105603);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000813_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000813_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02fc9eb586c662b78f2ba6587f8125ffb2f3fad6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000813_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01895:0.274093,(GCF_005280335_PROKKA_01997:0.166615,((GCF_002008305_PROKKA_00941:0,GCF_023573625_PROKKA_00890:0):0.0214864,GCF_003691675_PROKKA_00660:0.0178636):0.0580917):0.274093);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000814_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000814_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db0cbc254416bf4ff62666ba24932388aa8229c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000814_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01894:0.0239152,(GCF_005280335_PROKKA_01996:0.072134,(GCF_023573625_PROKKA_00891:0.00554074,(GCF_002008305_PROKKA_00942:0.00207846,GCF_003691675_PROKKA_00661:0.00999093)0.422:0.00466113)0.968:0.0186051)1:0.0239152);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000819_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000819_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24ef34458249124977b186fe169f51519e1d69d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.767:0.00359585)0.999:0.0713538)1:0.109023);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000820_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000820_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b066f9b728c459a340fc71cee3ee7514d1da7c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.22:0.00420176)1:0.101765)1:0.0980861);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000821_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000821_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6b1d630de2ba92cd416b489b133a49a293f2dde
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.857:0.0305444)0.993:0.183366)1:0.135599);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000822_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000822_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..581021ef5bf6189fda2e8a73885c076dc2e432ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000822_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01876:0.0378861,(GCF_005280335_PROKKA_01925:0.0182478,(GCF_023573625_PROKKA_00909:0.00180937,(GCF_002008305_PROKKA_00963:0.00181162,GCF_003691675_PROKKA_00676:5e-09)0.905:6e-09)0.856:0.00565868)1:0.0378861);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000823_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000823_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dbb7d05ee65b7e1f34213c7b28891729edd97675
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.835:0.00970852)0.435:0.0138289)1:0.0648276);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000824_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000824_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b1ab273c249311151944d9e8c2d4d428b7d532d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.816:0.00480392)0.998:0.0810425)1:0.120709);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000825_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000825_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fda47d236088fbe6760c5f2c8b0104333346e5b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000825_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01868:0.0889186,(GCF_005280335_PROKKA_01920:0.0437435,(GCF_003691675_PROKKA_00680:0.00207806,(GCF_002008305_PROKKA_00967:0.0157121,GCF_023573625_PROKKA_00913:0.00319468)0.523:0.00694742)0.999:0.0519917)1:0.0889186);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000826_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000826_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..daa2df8d1d34234670c7c46e5f9f770c29f6f98f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000826_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01866:0.123357,(GCF_005280335_PROKKA_01918:0.121248,(GCF_002008305_PROKKA_00972:0.0134079,(GCF_003691675_PROKKA_00685:0.0202578,GCF_023573625_PROKKA_00915:0.00319594)0.282:0.00678931)0.994:0.106701)1:0.123357);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000829_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000829_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3513f6a91ed0db69c872e1301ea53c31b45803cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00477261):0.00415892):0.0495534);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000830_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000830_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f94c15a97101d50a8a18860218f9ecdbb8725d33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000830_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01859:0.0330402,(GCF_005280335_PROKKA_01912:0.0129385,(GCF_002008305_PROKKA_00978:0.0044365,(GCF_003691675_PROKKA_00692:0,GCF_023573625_PROKKA_00921:0):5e-09):0.0233025):0.0330402);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000832_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000832_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70d88d927c60453c8311724a715cdce6eb6c5642
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.346879,GCF_005280335_PROKKA_01910:0.126627):0.0409297);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000834_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000834_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5470d61daff509baeeec69c9235956708399146f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.252:0.00148073,(GCF_005280335_PROKKA_01907:0.163335,GCF_023573625_PROKKA_00925:5e-09)0.884:0.00245283)1:0.00473335);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000835_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000835_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e13abf37611bbf416229a25a270b58e69295e07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_003691675_PROKKA_00697:0.0036575):0.00389754):0.00170241);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000840_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000840_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22d33ed1a85969082f38aa6e663e0bb71b20d309
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_003691675_PROKKA_00702:0.00438584):0.00438898):0.00109552);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000843_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000843_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4afc7fb5b110f3e6ed9768e6cf06b8f131c4f72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000843_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01845:0.00233033,(GCF_002008305_PROKKA_00991:0.00695193,(GCF_003691675_PROKKA_00705:0.00322722,(GCF_005280335_PROKKA_01898:0.00374603,GCF_023573625_PROKKA_00934:0.0125801)0.347:0.00232245)0.891:0.006064)1:0.00233033);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000845_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000845_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb2dbf0ff82529dc61d7193f537d49590babd55d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000845_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01841:0.070395,(GCF_005280335_PROKKA_01894:0.104878,(GCF_023573625_PROKKA_00938:0.00376866,(GCF_002008305_PROKKA_00995:0.00373997,GCF_003691675_PROKKA_00709:5e-09)0.764:0.00183505)0.991:0.0401954)1:0.070395);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000846_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000846_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c894987652fb2181876e1d1e01f5f28e6fc08cba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0277728,GCF_005280335_PROKKA_01893:0.0701203):0.113353);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000847_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000847_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9bdeef5d3431c7ef07d833c1404c93dbe30cb40d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0276576,GCF_023573625_PROKKA_00941:5e-09):0.135041):0.103446);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000848_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000848_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e716d5bc97f523438287bc9b142ba77c4d9a324d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.005254,GCF_023573625_PROKKA_00942:0.0110194):0.120882):0.136971);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000849_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000849_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ddc9183974d971858803881f97b12741dea4e7fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000849_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01818:0.0197983,((GCF_002008305_PROKKA_01000:0,GCF_003691675_PROKKA_00714:0,GCF_023573625_PROKKA_00943:0):0.00954688,GCF_005280335_PROKKA_01890:0.00959968):0.0197983);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000854_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000854_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ae8a063299c2c0f1f0fa43cca7b16fa8ea5b6fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000854_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01813:0.10996,(GCF_005280335_PROKKA_01885:0.0392277,((GCF_002008305_PROKKA_01005:0,GCF_003691675_PROKKA_00719:0):5e-09,GCF_023573625_PROKKA_00948:0.0131578):0.1222):0.10996);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000859_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000859_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ebdecb6e2c504c7c100d93c41d61f13819f6918
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000859_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00705:0.721328,(GCF_005280335_PROKKA_01870:5e-09,(GCF_023573625_PROKKA_00961:0.0285509,(GCF_002008305_PROKKA_01017:0.0381542,GCF_003691675_PROKKA_00731:0.00936785)0.874:0.019111)0:5e-09)1:0.721328);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000860_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000860_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54d817c8ad5c39f16a2612eb65fb57bf335ad9cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000860_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01761:0.076889,(GCF_005280335_PROKKA_01869:0.0819807,(GCF_003691675_PROKKA_00732:0.00661994,(GCF_002008305_PROKKA_01018:0.00220344,GCF_023573625_PROKKA_00962:0.00884228)0.888:5e-09)0.295:0.0163446)1:0.076889);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000864_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000864_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd37437319d9864bfc17a11bd906344df412e527
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000864_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00782:0.518983,(GCF_003691675_PROKKA_00736:0.0123144,(GCF_023573625_PROKKA_00966:5e-09,(GCF_002008305_PROKKA_01022:5e-09,GCF_003691675_PROKKA_00737:0.0053597)0.953:0.0174833)0.759:0.0232446)1:0.518983);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000865_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000865_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16ccc5f46cef99992548cb30b3df28f204641eba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.918:0.0104698)0.992:0.160972)1:0.0904837);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000867_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000867_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6423d30ceca8ed7df94f8a0901ea3c429cd8f841
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000867_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01750:0.123961,(GCF_005280335_PROKKA_01860:0.0246271,(GCF_002008305_PROKKA_01025:0.00653187,(GCF_003691675_PROKKA_00740:0,GCF_023573625_PROKKA_00969:0):5e-09):0.0533441):0.123961);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000876_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000876_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c2b5ccf0f2e0ec56c5e7570fb781d1fa7fa85ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000876_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01734:0.415384,(GCF_005280335_PROKKA_00543:0.457529,(GCF_002008305_PROKKA_01043:0.240948,(GCF_003691675_PROKKA_00756:0.0142062,GCF_023573625_PROKKA_00984:0.0055722)1:0.292654)0.933:0.168611)1:0.415384);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000878_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000878_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bb5e1f77a1e99d4adb663acfc55b1b72682120d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000878_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01731:0.0646779,(GCF_005280335_PROKKA_01844:0.0717246,(GCF_023573625_PROKKA_00986:0.00144676,(GCF_003691675_PROKKA_00758:0.00977903,GCF_002008305_PROKKA_01045:0.00395306)0.448:0.00266723)1:0.042894)1:0.0646779);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000880_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000880_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f89c72cd956916501cc47c792bec57e40d7f103f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000880_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01729:0.17292,(GCF_005280335_PROKKA_01841:0.103588,(GCF_023573625_PROKKA_00988:0.00793049,(GCF_002008305_PROKKA_01047:0.00432132,GCF_003691675_PROKKA_00760:5e-09)0.784:0.00946504)0.966:0.079978)1:0.17292);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000883_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000883_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a8d8b96832058fcd2be608fd58165aadbe294c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):6e-09,GCF_023573625_PROKKA_00991:0.00673945):0.0572932):0.0680974);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000884_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000884_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be4c518c288f102322f09a8fdec1f7ae04e79cea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000884_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01725:0.0731402,(GCF_005280335_PROKKA_01835:0.0563529,(GCF_003691675_PROKKA_00764:0.0115168,(GCF_002008305_PROKKA_01051:5e-09,GCF_023573625_PROKKA_00992:0.00334823)0.708:0.00587305)0.989:0.0538604)1:0.0731402);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000886_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000886_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa547bc1586d276f50cd218f4dc8f3651c82b6d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.835:5e-09)0.894:0.0208683)1:0.0721587);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000888_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000888_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0bc4680859732182e542f05f58a3eca558aac148
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.539:0.01025)0.989:0.0823387)1:0.166081);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000893_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000893_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0368e52117727de2b25019d15cb2cac5bd4866f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00601575):0.0435485):0.0731808);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000894_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000894_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b68cc9ada4f812b4af1f3a5a0ebc1d2b837dc35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000894_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01707:0.0528504,((GCF_002008305_PROKKA_01078:0,GCF_003691675_PROKKA_00797:0,GCF_023573625_PROKKA_01027:0):0.00250234,GCF_005280335_PROKKA_01820:0.00892214):0.0528504);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000895_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000895_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14ec7b61c1aa57a8cfba88c88c43ce7b4afa246d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000895_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01706:0.0180147,((GCF_002008305_PROKKA_01079:0,GCF_003691675_PROKKA_00798:0,GCF_023573625_PROKKA_01028:0):0.0519999,GCF_005280335_PROKKA_01819:0.0703708):0.0180147);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000897_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000897_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..662e31c4190593e15f1ee2f83118ed0e75529a90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09):0.0873013):0.110456);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000899_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000899_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb72a5108dad900651da30fbef150a0d37ad589c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000899_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01702:0.174763,(GCF_005280335_PROKKA_01814:0.24357,(GCF_002008305_PROKKA_01083:6e-09,(GCF_003691675_PROKKA_00802:0,GCF_023573625_PROKKA_01032:0):0.00472356):0.0881071):0.174763);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000901_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000901_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1e4498ce7972a313e7c1cd3ad9e6c168b1fb962
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09):0.0198945):0.10423);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000902_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000902_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb0fc42db5b0793981b258ed75f6e27081f7e921
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000902_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01699:0.0465861,(GCF_005280335_PROKKA_01811:0.0305003,(GCF_002008305_PROKKA_01086:0.00388521,(GCF_003691675_PROKKA_00805:0.00204884,GCF_023573625_PROKKA_01035:0.00248124)0.418:0.00547747)0.982:0.0266148)1:0.0465861);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000904_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000904_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7dd488d813842185923e9b1229fcf75c74fa037
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000904_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01697:0.0535447,(GCF_005280335_PROKKA_01808:0.258887,(GCF_002008305_PROKKA_01088:0.00330219,(GCF_003691675_PROKKA_00807:0,GCF_023573625_PROKKA_01037:0):5e-09):0.0608667):0.0535447);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000905_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000905_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b17b2f2da7160f1f4f6f04b0feb725da6a00444
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.060726,GCF_005280335_PROKKA_01807:0.269084):0.0227856);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000906_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000906_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2833b4aeb97a0bd4b80948c98afc45214ccc482a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000906_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01695:0.0290338,(GCF_005280335_PROKKA_01806:0.326613,(GCF_023573625_PROKKA_01039:5e-09,(GCF_002008305_PROKKA_01090:0.00207109,GCF_003691675_PROKKA_00809:5e-09)0.844:0.00207379)0.979:0.0439178)1:0.0290338);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000907_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000907_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..441f3cfd5a7359d8400f3264d1abdd601f9ceafe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000907_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01694:0.0504082,(GCF_005280335_PROKKA_01805:0.0486741,(GCF_002008305_PROKKA_01091:0.00584876,(GCF_003691675_PROKKA_00810:0.00388143,GCF_023573625_PROKKA_01040:0.00194285)0.767:5e-09)0.998:0.0530957)1:0.0504082);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000910_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000910_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad9bd78556664daf17b52e1572a69818ba3956a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000910_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01690:0.145911,((GCF_002008305_PROKKA_01095:0,GCF_003691675_PROKKA_00814:0,GCF_023573625_PROKKA_01044:0):0.0469678,GCF_005280335_PROKKA_01800:0.205807):0.145911);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000911_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000911_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..87dff1e4a76a1e034c5ab08f0794307c3f71a01a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09):0.110354):0.105258);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000912_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000912_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5084c719ef1b6c323aec6a5e25b0935b82bf2021
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000912_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01688:0.0643779,((GCF_002008305_PROKKA_01097:0,GCF_003691675_PROKKA_00816:0,GCF_023573625_PROKKA_01046:0):0.0417753,GCF_005280335_PROKKA_01798:0.111828):0.0643779);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000914_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000914_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fecad9f2e50e7898b30ecb00df350d51fe3b8f55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000914_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01686:0.0802423,(GCF_005280335_PROKKA_01796:0.0316454,((GCF_002008305_PROKKA_01099:0,GCF_003691675_PROKKA_00818:0):5e-09,GCF_023573625_PROKKA_01048:0.053127):0.118962):0.0802423);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000917_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000917_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4bdce9fe47e22059de4fa1a6a1c1503187114aae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000917_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01682:0.015624,((GCF_002008305_PROKKA_01103:0,GCF_003691675_PROKKA_00822:0,GCF_023573625_PROKKA_01052:0):0.00869855,GCF_005280335_PROKKA_01791:0.0143601):0.015624);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000921_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000921_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37c519756a405c025a4b1b5a10ec5e9ba5bb6471
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000921_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01677:0.0328439,(GCF_005280335_PROKKA_01785:0.0235958,(GCF_002008305_PROKKA_01108:0.0013132,(GCF_003691675_PROKKA_00827:0,GCF_023573625_PROKKA_01057:0):0.00764368):0.00823086):0.0328439);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000922_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000922_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c5850c05fa4258cc55e72f9025586d005851002
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000922_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01676:0.218831,(GCF_005280335_PROKKA_01783:0.125907,(GCF_002008305_PROKKA_01109:0.0121877,(GCF_003691675_PROKKA_00828:0,GCF_023573625_PROKKA_01058:0):0.0209297):0.0930002):0.218831);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000923_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000923_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91b4ecc044b2709553331889fc61f8d60cb7c18e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00711023):0.173284):0.3263);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000924_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000924_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf10d805ab29924a069d868898a5ce9d22baad10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000924_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01673:0.148179,(GCF_005280335_PROKKA_01780:0.103714,((GCF_002008305_PROKKA_01113:0,GCF_023573625_PROKKA_01063:0):5e-09,GCF_003691675_PROKKA_00832:0.00619097):0.099736):0.148179);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000925_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000925_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a619fe44924317cb11a028ac43ef8c38719f927c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.365:0.00295978)0.96:0.0151536)1:0.0518545);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000926_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000926_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2bc8aad1b82d6db38b8953ded37067c0f2476ec9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00321585,GCF_005280335_PROKKA_01778:0.0132862):0.00377461):0.107961);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000930_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000930_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95183bb983c6a0c414593a401dcacf386fbf8b90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.796:0.00679961)0.976:0.0418005)1:0.114917);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000931_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000931_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2dde4a4c8019cf27c6ab2ac726253c949699b3f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000931_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01664:0.0450683,(GCF_005280335_PROKKA_01771:0.0282693,((GCF_002008305_PROKKA_01122:0,GCF_023573625_PROKKA_01072:0):0.00302964,GCF_003691675_PROKKA_00841:0.00303007):0.0367898):0.0450683);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000932_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000932_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7acff702075a54992b63a1d35f7a93e372c27315
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000932_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01663:0.0158466,((GCF_002008305_PROKKA_01123:0,GCF_003691675_PROKKA_00842:0,GCF_023573625_PROKKA_01073:0):0.0181003,GCF_005280335_PROKKA_01770:0.0249114):0.0158466);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000936_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000936_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8433ff79d1594d4e28080ae7b16b7215368855db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000936_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01659:0.135562,(GCF_005280335_PROKKA_01765:0.0612326,((GCF_002008305_PROKKA_01127:0,GCF_003691675_PROKKA_00846:0):5e-09,GCF_023573625_PROKKA_01077:0.0117555):0.107961):0.135562);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000937_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000937_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48adb3813cbab36390bdb782c4da1c55840f4f88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0337895,GCF_005280335_PROKKA_01764:0.025213):0.101975);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000938_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000938_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d350e9976f95721a7eb3b7c148de07432cc4f90c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000938_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01657:0.0385923,((GCF_002008305_PROKKA_01129:0,GCF_003691675_PROKKA_00848:0,GCF_023573625_PROKKA_01079:0):0.0332153,GCF_005280335_PROKKA_01763:0.0263766):0.0385923);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000941_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000941_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54aeed389c85ed785926e5c467a2aa697fafad2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000941_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01654:0.0485431,(GCF_005280335_PROKKA_01760:0.0452842,((GCF_002008305_PROKKA_01132:0,GCF_003691675_PROKKA_00851:0):0.00273995,GCF_023573625_PROKKA_01082:5e-09):0.0509861):0.0485431);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000944_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000944_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58bb6ab72581ed237599447c5c302757de8b0901
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000944_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01651:0.0999928,(GCF_005280335_PROKKA_01757:0.06718,((GCF_002008305_PROKKA_01135:0,GCF_003691675_PROKKA_00854:0):5e-09,GCF_023573625_PROKKA_01085:0.00395727):0.0555143):0.0999928);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000946_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000946_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91a734e23299946a3d96c6f5b1212b4bbc860fc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000946_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01649:0.16166,((GCF_002008305_PROKKA_01137:0,GCF_003691675_PROKKA_00856:0,GCF_023573625_PROKKA_01087:0):0.0294978,GCF_005280335_PROKKA_01755:0.0807633):0.16166);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000947_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000947_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9694acf5534b79c18cd934ed86a3ebb30f35ed23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.739:5e-09)0.959:0.0158752)1:0.0221992);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000949_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000949_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..19ef9dcaa7c913c9773dc840303ad54349f2e221
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000949_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01646:0.0174707,(GCF_005280335_PROKKA_01752:0.00911179,(GCF_003691675_PROKKA_00859:0.00250054,(GCF_002008305_PROKKA_01140:0.00389021,GCF_023573625_PROKKA_01090:5e-09)0.177:0.0052836)0.921:0.0158556)1:0.0174707);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000952_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000952_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63aef5e1307d45ddb9c9127984fc0a659503196e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000952_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01643:0.0341386,(GCF_005280335_PROKKA_01748:0.0171695,(GCF_023573625_PROKKA_01093:0.00186492,(GCF_002008305_PROKKA_01143:0.00370813,GCF_003691675_PROKKA_00862:5e-09)0.787:0.00183729)0.877:0.00726522)1:0.0341386);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000953_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000953_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a21e5427c916c2792d0ed0c668dc7a6fbd9dcbb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09):0.0985408):0.114969);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000954_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000954_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b8084854942a59aeb38e84256ed400823d42e79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.813:0.0213947)0.889:0.0978146)1:0.21874);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000955_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000955_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..027ae97d98e2704e3c39693b242efd7437907c7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000955_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01638:0.0272334,(GCF_005280335_PROKKA_01744:0.0504207,(GCF_002008305_PROKKA_01148:0.00673823,(GCF_003691675_PROKKA_00867:0,GCF_023573625_PROKKA_01098:0):0.00891182):0.0357593):0.0272334);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000957_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000957_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..808cfbbce4b0acfeff52ff86a7bd72cd7b6b9873
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000957_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01636:0.0992287,(GCF_005280335_PROKKA_01742:0.0749996,(GCF_002008305_PROKKA_01150:5e-09,(GCF_003691675_PROKKA_00869:0,GCF_023573625_PROKKA_01100:0):0.0109239):0.0823626):0.0992287);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000958_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000958_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7005f0ed763e2591a61e2c25eb6b0b94b3054494
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0035682):0.0739978):0.0547733);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000959_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000959_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc26b58dc098ec882f7f66a4b65505ff4e608b8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000959_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01633:0.00581471,((GCF_002008305_PROKKA_01153:0,GCF_003691675_PROKKA_00872:0,GCF_023573625_PROKKA_01103:0):0.011402,GCF_005280335_PROKKA_01738:0.0118057):0.00581471);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000961_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000961_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfd4ec6dc3707caf3dfb5a534ca7ab736d376105
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000961_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01631:0.1639,(GCF_005280335_PROKKA_01733:0.101856,(GCF_002008305_PROKKA_01156:5e-09,(GCF_003691675_PROKKA_00875:0,GCF_023573625_PROKKA_01106:0):0.00111369):0.106455):0.1639);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000964_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000964_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d15ec4ecc062101199e2bed15859dcae1a5a142
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09):0.0773688):0.0991183);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000966_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000966_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43e6d550a0ea40b3510dbfc91d667d317332384b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000966_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01625:0.147517,(GCF_005280335_PROKKA_01728:0.0717313,(GCF_003691675_PROKKA_00881:0.00543277,(GCF_002008305_PROKKA_01162:0.00215091,GCF_023573625_PROKKA_01112:0.00214575)0.774:0.00542331)0.984:0.0499146)1:0.147517);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000970_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000970_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed96238e25dfc1080960b75ebf6691a1fdb9ca26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000970_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01620:0.0350722,(GCF_005280335_PROKKA_01722:0.113248,((GCF_002008305_PROKKA_01167:0,GCF_003691675_PROKKA_00886:0):0.0123223,GCF_023573625_PROKKA_01117:5e-09):0.0962436):0.0350722);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000974_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000974_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30f64fc42d9c5c32ca53319506ebb9ade8bbf0d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00320837):0.0685294):0.134893);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000976_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000976_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..307069661e7fe7184b00d08f39a146530718ecd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.934:0.0165624)1:0.174246)1:0.22398);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000978_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000978_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c15653ac9b2ec32cafd2b7698b2bc88b250a0a1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.912:5e-09)0.771:0.00826512)1:0.122815);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000986_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000986_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d020be26b33e8d15af4c83f6aafbb4fb31f762c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0461896,GCF_005280335_PROKKA_01704:0.0303743):0.210103);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000987_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000987_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b2f4775efb6d867b07b5f889759b17a2bc14e03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000987_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01602:0.255485,(GCF_005280335_PROKKA_01703:0.0762637,((GCF_002008305_PROKKA_01185:0,GCF_023573625_PROKKA_01135:0):0.0144075,GCF_003691675_PROKKA_00904:0.00365852):0.0859033):0.255485);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000988_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000988_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2843166e8765570154b122807cc4c7cd37e9c5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000988_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01601:0.107019,(GCF_005280335_PROKKA_01702:0.0421881,(GCF_003691675_PROKKA_00905:0.015219,(GCF_002008305_PROKKA_01186:5e-09,GCF_023573625_PROKKA_01136:0.000996967)0.959:0.00810269)1:0.0451305)1:0.107019);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000990_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000990_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1de94300bc1f7bc7a90b02075687f4a9f72a1ce2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000990_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01599:0.0529827,((GCF_002008305_PROKKA_01188:0,GCF_003691675_PROKKA_00907:0,GCF_023573625_PROKKA_01138:0):0.00918321,GCF_005280335_PROKKA_01700:0.0321023):0.0529827);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000992_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000992_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..765c7013e6aabca6ebe73a9bfcd9b8b5a6c5dab0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_003691675_PROKKA_00909:0.00726748):0.0543401):0.0820613);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000995_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000995_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..929173ce51e3677c194c5854894c17e5e2e289dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000995_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01594:0.314897,(GCF_005280335_PROKKA_01695:0.141002,(GCF_003691675_PROKKA_00912:0.0136203,(GCF_002008305_PROKKA_01193:0.0163234,GCF_023573625_PROKKA_01143:6e-09)0.745:0.00825368)0.959:0.129161)1:0.314897);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000998_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000998_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52b83136fbc0328ecbc93ec9a05afec042c255c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0000998_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01589:0.0778183,(GCF_023573625_PROKKA_01150:5e-09,(GCF_005280335_PROKKA_01691:0.0536621,(GCF_002008305_PROKKA_01196:0.0103446,GCF_003691675_PROKKA_00916:5e-09)0:5e-09)0.446:0.0103446)1:0.0778183);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001000_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001000_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00ffd5abd98112ea6e305bab93715d0abebdfb02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001000_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01586:0.0392061,((GCF_002008305_PROKKA_01198:0,GCF_003691675_PROKKA_00918:0,GCF_023573625_PROKKA_01152:0):0.00822182,GCF_005280335_PROKKA_01689:0.0146159):0.0392061);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001001_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001001_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bafb62ad0e627cfe06426fe90261dd29a4ca05d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001001_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01585:0.063038,(GCF_005280335_PROKKA_01688:0.0132318,((GCF_002008305_PROKKA_01199:0,GCF_023573625_PROKKA_01153:0):0.0261633,GCF_003691675_PROKKA_00919:0.00392483):0.0132369):0.063038);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001002_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001002_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..451baa6c38510276708b68d2df4808d848c117fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001002_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01584:0.0642171,(GCF_005280335_PROKKA_01687:0.0152159,(GCF_023573625_PROKKA_01154:0.00547848,(GCF_002008305_PROKKA_01200:0.014173,GCF_003691675_PROKKA_00920:6e-09)0.757:0.00339712)0.446:0.0075677)1:0.0642171);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001003_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001003_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07434ddd24750f9def65e451e265efdebe91b73d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.998:0.0237905,GCF_003691675_PROKKA_00921:0.00555709)0.921:0.0121674)1:0.078874);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001004_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001004_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e0f639c9d39910f6496725d50e4741e6f697cc3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.982:0.0825781)0.953:0.065314)1:0.107515);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001005_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001005_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..585029849aec5f6fd4af28d4d8e86a092bfb198e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001005_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01581:0.0186315,(GCF_005280335_PROKKA_01683:0.00283777,(GCF_023573625_PROKKA_01161:0.00110054,(GCF_002008305_PROKKA_01204:0.0294237,GCF_003691675_PROKKA_00923:0.0094858)0.703:0.00624506)1:0.0308583)1:0.0186315);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001006_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001006_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..01cc59b2637bb16d30080dd0ec9b6f5baabbc78f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.714:0.00270227)0.872:0.0205855)1:0.100304);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001007_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001007_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24b704426938e26c6061f9acb12dbe636c2c53ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001007_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01579:0.0158045,(GCF_005280335_PROKKA_01681:0.023148,((GCF_002008305_PROKKA_01206:0,GCF_003691675_PROKKA_00925:0):5e-09,GCF_023573625_PROKKA_01163:0.00774282):0.0078755):0.0158045);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001011_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001011_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c54d89e6ad2674bde55777d879d441b1701c969
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001011_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01575:0.388866,(GCF_005280335_PROKKA_01677:0.113931,(GCF_003691675_PROKKA_00929:0.00730341,(GCF_002008305_PROKKA_01210:0.0112172,GCF_023573625_PROKKA_01167:5e-09)0.842:0.009537)0.831:0.0413059)1:0.388866);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001012_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001012_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d2541ad6f19c150316fb936ee49b7f1597605c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001012_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01574:0.0653301,(GCF_005280335_PROKKA_01676:0.00984305,((GCF_002008305_PROKKA_01211:0,GCF_023573625_PROKKA_01168:0):0.00691454,GCF_003691675_PROKKA_00930:0.00325796):0.0248098):0.0653301);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001013_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001013_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12ae56cb99d25042a6c895cce112707010ceba14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001013_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01572:0.0378229,(GCF_005280335_PROKKA_01675:0.0199608,(GCF_003691675_PROKKA_00932:0.00461279,(GCF_002008305_PROKKA_01213:0.00171183,GCF_023573625_PROKKA_01170:5e-09)0.719:0.00226074)0.991:0.0342139)1:0.0378229);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001014_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001014_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d24a613db42495f1c13afc294b1c67fb877881d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001014_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01571:0.0809757,(GCF_005280335_PROKKA_01674:0.0291493,(GCF_002008305_PROKKA_01214:0.00311972,(GCF_003691675_PROKKA_00933:5e-09,GCF_023573625_PROKKA_01171:0.00311378)0.779:5e-09)0.977:0.0309655)1:0.0809757);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001015_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001015_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4f57e04847654ea9bd5a6abe0efe78d252700c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.000820604,GCF_003691675_PROKKA_00934:0.00804433):0.0575432):0.135824);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001016_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001016_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b64f98a7653f0947744fa15b2d5d8efe2714197e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.033319,GCF_005280335_PROKKA_01672:0.0644614):0.0545412);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001018_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001018_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..566e6f350da70b94e6d22d7a16f6e447f74b6935
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.843:0.00384596)0.996:0.0823526)1:0.118859);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001023_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001023_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a06fc9ca6b14a2502332c2420ccc2b2bb09772d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.501:0.00415048)0.987:0.0237042)1:0.0298749);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001026_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001026_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3abaf358720870c7a5db61cc89553a657931ed9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001026_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01558:0.0936444,(GCF_005280335_PROKKA_01661:0.0509456,(GCF_002008305_PROKKA_01227:0.00401845,(GCF_003691675_PROKKA_00946:0,GCF_023573625_PROKKA_01185:0):0.00764251):0.0482944):0.0936444);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001029_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001029_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41a50e20dced06ab79d4d7b65deb6547bc0acdfe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001029_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01555:0.189443,(GCF_005280335_PROKKA_01658:0.0593205,(GCF_002008305_PROKKA_01230:0.00908336,(GCF_003691675_PROKKA_00949:0,GCF_023573625_PROKKA_01188:0):0.00609764):0.0257398):0.189443);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001030_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001030_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de791362431f50e379624f54800aab9e56b9d79a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.004235):0.0285051):0.0453156);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001031_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001031_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..285c2b242fe0798a6ad034672d0bd072f4c0e0d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001031_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01553:0.0987905,(GCF_005280335_PROKKA_01656:0.0647405,(GCF_003691675_PROKKA_00951:0.0105507,(GCF_002008305_PROKKA_01232:0.00530363,GCF_023573625_PROKKA_01190:0.0066178)0.867:0.00970442)1:0.123815)1:0.0987905);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001032_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001032_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..72c44d8f1d79f2869affa73f391590b657c95f79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.909:0.0145722)0.987:0.0987666)1:0.117377);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001033_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001033_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b6c415da740668d02321f600b573fc92fc0fe33b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001033_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01551:0.142799,(GCF_005280335_PROKKA_01654:0.0660671,(GCF_023573625_PROKKA_01192:0.00532757,(GCF_002008305_PROKKA_01234:0.00579936,GCF_003691675_PROKKA_00953:0.0058135)0.886:0.00500806)0.995:0.0535306)1:0.142799);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001034_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001034_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8a5ea0f5d485836f142d2ab6d4eaf219123fb0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001034_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01550:0.0577237,(GCF_005280335_PROKKA_01653:0.02506,(GCF_002008305_PROKKA_01235:0.0045999,(GCF_003691675_PROKKA_00954:5e-09,GCF_023573625_PROKKA_01193:0.0022983)0.892:6e-09)0.945:0.0162058)1:0.0577237);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001037_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001037_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8da271887e2dd0018716470087ecbdba9cc98e1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001037_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01547:0.101278,(GCF_005280335_PROKKA_01650:0.028801,(GCF_002008305_PROKKA_01238:0.00462908,(GCF_003691675_PROKKA_00957:0,GCF_023573625_PROKKA_01196:0):5e-09):0.0458569):0.101278);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001038_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001038_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c30dbcc3bc3a564c4d96fb2d4e2c89b016a80dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0160565,GCF_003691675_PROKKA_00958:0.0329465):0.124275):0.121442);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001041_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001041_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41d3e4f5614c022306de54c6839ff068551f3c50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001041_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01543:0.0904146,(GCF_005280335_PROKKA_01646:0.0319502,((GCF_002008305_PROKKA_01242:0,GCF_023573625_PROKKA_01200:0):0.0025505,GCF_003691675_PROKKA_00961:0.00247625):0.0316473):0.0904146);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001042_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001042_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d61414f860918af1d65b44272c3f533a5cb0831
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001042_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01542:0.202598,((GCF_002008305_PROKKA_01243:0,GCF_003691675_PROKKA_00962:0,GCF_023573625_PROKKA_01201:0):0.110314,GCF_005280335_PROKKA_01645:0.130071):0.202598);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001043_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001043_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0fc553e63d0dd9c91f229bf7775bee2d2a3fe3f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_023573625_PROKKA_01203:0.0059041):0.00922539):0.0800257);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001044_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001044_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d6443c6224d92ef248a37f1c49f3b05eda3a4ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0341091,GCF_005280335_PROKKA_01642:0.0668553):0.07353);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001045_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001045_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c7348812f79d5f3c0db717289b6c13422a46fb4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0357284,GCF_005280335_PROKKA_01641:0.0195437):0.0474208);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001047_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001047_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91767d4ea104d6878f421bb2af63a0bdc86a584e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001047_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01536:0.061819,(GCF_005280335_PROKKA_01639:0.0541034,(GCF_002008305_PROKKA_01249:0.00762495,(GCF_003691675_PROKKA_00968:0,GCF_023573625_PROKKA_01207:0):5e-09):0.0153934):0.061819);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001048_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001048_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07872ecc0e2b17ab51be7f855db6cc2b1a9b1eb2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001048_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01535:0.304893,(GCF_005280335_PROKKA_01638:0.0530144,(GCF_002008305_PROKKA_01250:0.00628463,(GCF_003691675_PROKKA_00969:0,GCF_023573625_PROKKA_01208:0):0.00673558):0.110848):0.304893);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001050_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001050_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..905a103ac69a3863ef90e8b22bda45e4d0752ff5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001050_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01533:0.168268,(GCF_005280335_PROKKA_01636:0.0875989,(GCF_002008305_PROKKA_01252:0.0175777,(GCF_003691675_PROKKA_00971:0,GCF_023573625_PROKKA_01210:0):0.0116272):0.0975505):0.168268);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001054_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001054_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5276a19c7dc17567e6ff82c1f4ad6f15592a4599
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00477853):0.00958802):0.0023814);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001057_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001057_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..523db2af7685304fa48dd9406b477d2c1424b5e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001057_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01525:0.169878,(GCF_005280335_PROKKA_00445:0.885196,(GCF_002008305_PROKKA_01260:0.0275488,(GCF_003691675_PROKKA_00979:0,GCF_023573625_PROKKA_01218:0):0.00735053):0.177284):0.169878);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001061_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001061_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd4de421df4aa9c258cef14b3e4251638cff0128
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.72:0.00376014)0.999:0.0748924)1:0.13861);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001062_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001062_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..feb60661f6964173e1e0fd600a114a108fecb9b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001062_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01517:0.0519083,(GCF_005280335_PROKKA_01622:0.0314408,(GCF_002008305_PROKKA_01265:0.00612265,(GCF_003691675_PROKKA_00984:0,GCF_023573625_PROKKA_01223:0):0.00921069):0.0297086):0.0519083);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001063_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001063_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bdc449a7ede1e38d7ff909d24160665d4199eb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001063_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01516:0.0774438,(GCF_005280335_PROKKA_01621:0.037204,(GCF_002008305_PROKKA_01266:0.0114792,(GCF_003691675_PROKKA_00985:0,GCF_023573625_PROKKA_01224:0):0.0114013):0.0525468):0.0774438);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001066_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001066_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e6a2106425ab8e5fece3008d693669dd68aa8d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001066_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01513:0.113225,((GCF_002008305_PROKKA_01269:0,GCF_003691675_PROKKA_00988:0,GCF_023573625_PROKKA_01227:0):0.0523645,GCF_005280335_PROKKA_01618:0.0322143):0.113225);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001067_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001067_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8c0c12c8c3e4d816423a165fdd19f8c72ad96b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001067_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01512:0.106649,(GCF_005280335_PROKKA_01617:0.101481,(GCF_002008305_PROKKA_01270:5e-09,(GCF_003691675_PROKKA_00989:0,GCF_023573625_PROKKA_01228:0):0.00325626):0.0601401):0.106649);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001068_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001068_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d6fa52538e8ad02e052f6009a1c2f12af69d7c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09):0.095283):0.247831);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001071_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001071_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f692a8e5cf5abaf2262de125010798ed5fbb06a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001071_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01507:0.0404738,((GCF_002008305_PROKKA_01275:0,GCF_003691675_PROKKA_00994:0,GCF_023573625_PROKKA_01233:0):0.066095,GCF_005280335_PROKKA_01612:0.0618601):0.0404738);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001072_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001072_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a5b0bf3ab9aedb364ed56bd7b3362f658cb5ef5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001072_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01506:0.094036,(GCF_005280335_PROKKA_01611:0.0798873,(GCF_002008305_PROKKA_01276:0.00351537,(GCF_003691675_PROKKA_00995:5e-09,GCF_023573625_PROKKA_01234:0.00142274)0.932:0.00656378)0.998:0.0559085)1:0.094036);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001075_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001075_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb79016e5e3a66d12139aea789fd8f0e26ed0c79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09):0.117127):0.173909);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001076_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001076_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a371b49c531af53c9cc3947f91682c7b8387efc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.806:0.00235803)0.993:0.0798706)1:0.1179);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001077_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001077_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b7bf226c3d9d6d2efc67e035c885a842e6d76d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001077_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01500:0.102175,(GCF_005280335_PROKKA_01605:0.0911083,(GCF_003691675_PROKKA_01000:0.00175312,(GCF_002008305_PROKKA_01281:0.00820706,GCF_023573625_PROKKA_01239:5e-09)0.642:0.000974302)1:0.119623)1:0.102175);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001078_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001078_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39115d45d895d0278ad327b8f6d38e8210cb5798
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00533023):0.144523):0.298118);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001079_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001079_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b12c4f5d39c8dbadd59311de6e2e49f79bde491e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001079_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01498:0.215553,(GCF_005280335_PROKKA_01602:0.150286,(GCF_002008305_PROKKA_01283:0.000873251,(GCF_003691675_PROKKA_01002:0,GCF_023573625_PROKKA_01241:0):0.0397047):0.0668646):0.215553);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001080_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001080_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0ec7116b04613b55444b033ef3f14fd71d4ab9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001080_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01497:0.253766,((GCF_002008305_PROKKA_01284:0,GCF_003691675_PROKKA_01003:0,GCF_023573625_PROKKA_01242:0):0.16737,GCF_005280335_PROKKA_01601:0.138075):0.253766);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001081_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001081_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97a27cb803a68b32c0eeab58fc052ab7bcb9722c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0107792):0.0936544):0.200244);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001082_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001082_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b913bc43023078cbce3292b29280232a312345c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.925:6e-09)0.996:0.0322865)1:0.0624822);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001083_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001083_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..390af2b62c358c493ffdd920eaa3204b055261e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001083_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01493:0.0342155,(GCF_005280335_PROKKA_01597:0.010496,((GCF_002008305_PROKKA_01295:0,GCF_003691675_PROKKA_01018:0):0.00109017,GCF_023573625_PROKKA_01253:6e-09):0.018703):0.0342155);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001088_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001088_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6313b941a78fe2ede23e2d6a7658ff46725ec1a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.126816,GCF_005280335_PROKKA_01592:0.0355788):0.222785);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001090_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001090_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c6ea358a2e0d978ff52c6afdac827f550fe1c726
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001090_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01486:0.199732,((GCF_002008305_PROKKA_01302:0,GCF_003691675_PROKKA_01025:0,GCF_023573625_PROKKA_01260:0):0.100476,GCF_005280335_PROKKA_01590:0.0579029):0.199732);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001095_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001095_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..29b45817d114d59ced9173008835401cc9df0ed3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00448112):0.0573976):0.162209);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001096_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001096_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cccb30557840c800ac892c01a41ed92d4589cf7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00117694):0.0628016):0.09647);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001097_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001097_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..448a4a1dbc3b949b1fcaec444117175ada4b42b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001097_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01478:0.0767063,((GCF_003691675_PROKKA_01033:0,GCF_023573625_PROKKA_01268:0):0.0415422,(GCF_002008305_PROKKA_01310:0.00487742,GCF_005280335_PROKKA_01582:0.00999476):0.0346356):0.0767063);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001098_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001098_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d30c433602636b816d6336bc406ef38877982b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001098_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01477:0.111431,((GCF_003691675_PROKKA_01034:0.0120203,GCF_023573625_PROKKA_01269:0.00336972)1:0.321027,(GCF_002008305_PROKKA_01311:0.0038297,GCF_005280335_PROKKA_01581:0.00517231)1:0.1746)1:0.111431);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001099_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001099_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..344122e4fc482ba212d6a43acb4361e7fbf142a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001099_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01476:0.0619359,((GCF_002008305_PROKKA_01312:0,GCF_005280335_PROKKA_01580:0):0.0941601,(GCF_003691675_PROKKA_01035:0.00355137,GCF_023573625_PROKKA_01270:0.00564814):0.217142):0.0619359);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001100_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001100_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..61168b90b217b4dda568a80915a6941687f7dd42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001100_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01475:0.0306942,((GCF_003691675_PROKKA_01036:0,GCF_023573625_PROKKA_01271:0):0.145333,(GCF_002008305_PROKKA_01313:5e-09,GCF_005280335_PROKKA_01579:0.00386195):0.0595944):0.0306942);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001102_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001102_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2703848911d3a258c6096caf61255d9ec4d8b6ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)1:0.0293644)1:0.0476177)1:0.117606);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001103_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001103_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..11c2379391cf29392345c3f8fda830f77f50f34c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001103_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01470:0.081894,(GCF_005280335_PROKKA_01574:0.026259,(GCF_002008305_PROKKA_01318:5e-09,(GCF_003691675_PROKKA_01039:0.00275598,GCF_023573625_PROKKA_01274:0.00827678)0.979:0.0167478)0.97:0.0309677)1:0.081894);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001108_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001108_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47f434e87bc49291a883e1433fe65ce67234259e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00631855,GCF_003691675_PROKKA_01044:5e-09):0.0572524):0.148268);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001109_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001109_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a5252be61922a7d82f5cd4bcaabb37ae40d3bdd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.929:0.00952077)0.984:0.0430542)1:0.102715);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001110_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001110_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4247d06e5097093ea9e1613f6c775218d3282daa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.893:6e-09)0.647:0.00423275)1:0.00551603);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001123_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001123_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb1f959cc6f33b233d0c809b2d379a1fcc216753
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.797:0.00315697)0.963:0.0302863)1:0.0630306);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001128_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001128_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..175fb62f100bb55a5c6b3fed9620d3003edb7d49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001128_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01442:0.232256,(GCF_005280335_PROKKA_01546:0.102242,(GCF_002008305_PROKKA_01346:5e-09,(GCF_003691675_PROKKA_01066:0.0351629,GCF_023573625_PROKKA_01301:5e-09)0.368:0.0144522)1:0.253342)1:0.232256);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001129_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001129_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d332fc97e6a7d11fcafb39f927a8a051be3fc339
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001129_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01441:0.148156,(GCF_005280335_PROKKA_01545:0.0358104,(GCF_002008305_PROKKA_01347:0.0205589,(GCF_003691675_PROKKA_01067:0,GCF_023573625_PROKKA_01302:0):5e-09):0.107424):0.148156);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001131_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001131_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5d4667112b564a69d4754b890b95fe70a6737d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.051:0.00718847)0.998:0.128494)1:0.127076);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001132_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001132_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd21e017ea753f2d2437c1239a210746aeb65970
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001132_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01438:0.226962,(GCF_005280335_PROKKA_01542:0.192634,(GCF_023573625_PROKKA_01305:0.020589,(GCF_002008305_PROKKA_01350:0.0234947,GCF_003691675_PROKKA_01070:0.0105036)0.719:0.00782614)0.977:0.116489)1:0.226962);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001133_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001133_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ede55e2834780f109c66906ed8a679f7f7a96c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001133_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01437:0.0203659,(GCF_005280335_PROKKA_01541:0.0335923,(GCF_003691675_PROKKA_01071:0.00490598,(GCF_002008305_PROKKA_01351:5e-09,GCF_023573625_PROKKA_01306:0.00844516)0.825:5e-09)0.989:0.0284659)1:0.0203659);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001138_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001138_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0175f52851643395d794e5064d9f8d0bde9a17dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001138_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01432:0.0672852,(GCF_005280335_PROKKA_01536:0.0603789,(GCF_003691675_PROKKA_01076:0.00178013,(GCF_002008305_PROKKA_01356:0.0129322,GCF_023573625_PROKKA_01311:0.00354836)0.253:0.00385426)0.997:0.0637872)1:0.0672852);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001140_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001140_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2290538f0aef6974a2944b26f148edffe2ad7e25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.911:0.0111797)1:0.0914694)1:0.124131);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001141_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001141_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67e10606c6af0f3874e34ca25177be78d97aca83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.924:0.00758962)0.994:0.058926)1:0.181115);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001143_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001143_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1cf652d02043cf0c771bc0203b6bde870577d7a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00883693,GCF_003691675_PROKKA_01082:0.00283647):0.0225972):0.0835817);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001145_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001145_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f43e4576cde4e21f21776bdda2d66c92eeadcf3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001145_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01424:0.335103,((GCF_002008305_PROKKA_01364:0,GCF_003691675_PROKKA_01084:0,GCF_023573625_PROKKA_01319:0):0.163089,GCF_005280335_PROKKA_01529:0.183885):0.335103);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001148_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001148_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0dd51fb538f092254d0de1045b951a10c0f2341
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001148_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01421:0.110597,(GCF_005280335_PROKKA_01526:0.0623918,((GCF_002008305_PROKKA_01367:0,GCF_003691675_PROKKA_01087:0):0.0073275,GCF_023573625_PROKKA_01322:5e-09):0.0683241):0.110597);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001149_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001149_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..966f0e39213da4b8cae328cccc2f55ea8c1c6ec9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.807:0.0110127)0.856:0.0458706)1:0.274166);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001150_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001150_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4333e2881ce060cfc385d964a9400c30ece9856c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001150_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01418:0.0668969,(GCF_005280335_PROKKA_01522:0.0160504,((GCF_002008305_PROKKA_01370:0,GCF_023573625_PROKKA_01325:0):5e-09,GCF_003691675_PROKKA_01090:0.00209317):0.00727548):0.0668969);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001151_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001151_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f38e75f4d1a4f2cbf49ba48dba8ef5fdb1a44c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001151_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01417:0.0649071,(GCF_005280335_PROKKA_01521:0.0713415,(GCF_003691675_PROKKA_01091:0.038968,(GCF_002008305_PROKKA_01371:5e-09,GCF_023573625_PROKKA_01326:0.00856846)0.299:0.0048674)0.915:0.0320285)1:0.0649071);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001153_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001153_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..773c664b04a18b9b2b349045735b582b62ee77ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001153_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01414:0.132115,(GCF_005280335_PROKKA_01519:0.0556401,(GCF_002008305_PROKKA_01373:0.000516384,(GCF_003691675_PROKKA_01093:6e-09,GCF_023573625_PROKKA_01328:0.00158619)0.864:0.00745668)1:0.0945986)1:0.132115);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001155_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001155_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40b9bc9acb6520bd525f9ece7a24b2e882337b9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001155_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01412:0.0568043,(GCF_005280335_PROKKA_01517:0.0026607,(GCF_002008305_PROKKA_01375:0.00399394,(GCF_003691675_PROKKA_01095:0.00106742,GCF_023573625_PROKKA_01330:0.00397426)0.949:0.00419464)0.945:0.00435658)1:0.0568043);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001156_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001156_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28d435bc80b12f3df61bb84e13ae2f015f4f18fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001156_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01411:0.090208,(GCF_005280335_PROKKA_01516:0.0259163,(GCF_023573625_PROKKA_01331:0.00953291,(GCF_002008305_PROKKA_01376:5e-09,GCF_003691675_PROKKA_01096:0.00534655)0.876:0.0131898)0.865:0.0175083)1:0.090208);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001159_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001159_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2967695c7e4f2078230c41f96a2d5465f20876fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001159_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01408:0.180178,(GCF_005280335_PROKKA_01513:0.119243,(GCF_002008305_PROKKA_01379:5e-09,(GCF_003691675_PROKKA_01099:0,GCF_023573625_PROKKA_01334:0):0.0139244):0.0414146):0.180178);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001160_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001160_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..254e6bc2e00ad23b721c246f1576396720948bb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001160_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01407:0.13028,(GCF_005280335_PROKKA_01512:0.0384695,((GCF_002008305_PROKKA_01380:0,GCF_023573625_PROKKA_01335:0):5e-09,GCF_003691675_PROKKA_01100:0.00758838):0.0253063):0.13028);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001161_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001161_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c88b2bf19c0be83d6ea918bd03035c64222268a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001161_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01406:0.0977852,(GCF_005280335_PROKKA_01511:0.0597574,((GCF_002008305_PROKKA_01381:0,GCF_023573625_PROKKA_01336:0):0.0197091,GCF_003691675_PROKKA_01101:0.00228117):0.0693659):0.0977852);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001162_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001162_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be1f756882d153195ead10d01cd51b37ee79e9ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001162_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01404:0.415627,(GCF_005280335_PROKKA_01492:0.135582,(GCF_002008305_PROKKA_01403:0.012178,(GCF_003691675_PROKKA_01133:0,GCF_023573625_PROKKA_01353:0):0.00550554):0.152048):0.415627);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001163_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001163_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ddee29843c114864b02c44a0f6556a5111878cdb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.777:0.00190463)0.962:0.0131791)1:0.0508645);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001165_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001165_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d0a83881ec3492d398d537ec1c1a1fc2532dc53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001165_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01400:0.0557222,((GCF_002008305_PROKKA_01407:0,GCF_003691675_PROKKA_01137:0,GCF_023573625_PROKKA_01357:0):0.0281805,GCF_005280335_PROKKA_01489:0.0132365):0.0557222);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001170_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001170_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ba8ef24f17e6ad0f99b430f9e5ed17d68166e59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001170_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01390:0.0217681,(GCF_005280335_PROKKA_01483:0.0153455,(GCF_002008305_PROKKA_01416:0.00741918,(GCF_003691675_PROKKA_01147:0.010417,GCF_023573625_PROKKA_01366:5e-09)0.446:0.00821222)0.588:0.0131993)1:0.0217681);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001172_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001172_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54a81e02839855671cbdfd26e9eacfc96add6e75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001172_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01388:0.108125,(GCF_005280335_PROKKA_01480:0.0423142,(GCF_003691675_PROKKA_01150:0.00459973,(GCF_002008305_PROKKA_01419:0.00849075,GCF_023573625_PROKKA_01369:0.00427401)0.948:0.0255193)0.981:0.0553591)1:0.108125);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001173_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001173_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fef318eaba74280d365417ed621a8941cfb487f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001173_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01387:0.103205,(GCF_005280335_PROKKA_01479:0.0485773,(GCF_002008305_PROKKA_01420:0.0325846,(GCF_003691675_PROKKA_01151:0.00334528,GCF_023573625_PROKKA_01370:0.00334667)0.899:5e-09)0.932:0.031767)1:0.103205);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001174_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001174_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1f74a6586e95bed4ea61980720ad9278823a4fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001174_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01386:0.111608,(GCF_005280335_PROKKA_01478:0.0536268,(GCF_002008305_PROKKA_01421:0.0137792,(GCF_003691675_PROKKA_01152:0,GCF_023573625_PROKKA_01371:0):0.0140231):0.0376701):0.111608);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001175_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001175_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b24253ddf77aa4eb3455eeb2d15f2e18c41d58a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.945:0.0219793)1:0.168735)1:0.0907118);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001179_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001179_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a718edb174031f5972953a41277eb14473167aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001179_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01377:0.101187,(GCF_005280335_PROKKA_01470:0.0517588,(GCF_002008305_PROKKA_01429:0.00302007,(GCF_003691675_PROKKA_01161:0.00387928,GCF_023573625_PROKKA_01379:0.00259093)0.85:0.00347666)1:0.0625289)1:0.101187);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001180_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001180_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f913c28b5a913d3cbc75f8e6238df58046f03cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.413:0.00405457)0.966:0.0254736)1:0.0581643);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001183_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001183_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67466db85b85da27e3ead371734c81e3000a6e23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001183_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01373:0.113727,((GCF_002008305_PROKKA_01433:0,GCF_003691675_PROKKA_01165:0,GCF_023573625_PROKKA_01383:0):0.032998,GCF_005280335_PROKKA_01465:0.0543248):0.113727);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001185_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001185_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b553e50f66402e908b76c276f25cd77bd43597b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001185_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01371:0.108602,(GCF_005280335_PROKKA_01463:0.0934779,(GCF_023573625_PROKKA_01385:0.00432313,(GCF_002008305_PROKKA_01435:0.00233658,GCF_003691675_PROKKA_01167:0.00233453)0.742:0.00501775)0.998:0.0879999)1:0.108602);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001187_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001187_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef021c6d6c95e0eefb520bce7f4a1a4414a33240
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.452:0.00480542)1:0.0956826)1:0.0856638);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001191_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001191_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e3b81a16fb2663fc21d9471d338405763e7f1ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001191_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01364:0.489224,(GCF_005280335_PROKKA_01456:0.319233,((GCF_002008305_PROKKA_01442:0,GCF_003691675_PROKKA_01174:0):0.0200611,GCF_023573625_PROKKA_01392:0.00469511):0.258949):0.489224);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001193_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001193_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff60c2aa319fff33eafe171e3cc6908fd0971fe4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.882:0.00279439)0.964:0.0257815)1:0.0785834);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001194_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001194_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62a50393d1ea1b87ce3f6809a44b32bfa3fe2e17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001194_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01357:0.132181,(GCF_005280335_PROKKA_01453:0.109261,(GCF_003691675_PROKKA_01178:6e-09,(GCF_002008305_PROKKA_01446:0.0279141,GCF_023573625_PROKKA_01396:0.00696229)0.446:0.00693951)0.994:0.13923)1:0.132181);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001199_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001199_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3aa2be31398b703c7409672db01fcf908e52494
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001199_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01351:0.136936,((GCF_002008305_PROKKA_01452:0.0119858,GCF_023573625_PROKKA_01402:0.0203546)0.989:0.0732512,(GCF_003691675_PROKKA_01184:0.0713454,GCF_005280335_PROKKA_01447:0.0461422)0.993:0.0901078)1:0.136936);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001200_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001200_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4eb7e3f819e7738d2acbc7f718af4f91d2c6d9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001200_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01349:0.0158804,((GCF_002008305_PROKKA_01454:0,GCF_003691675_PROKKA_01186:0,GCF_023573625_PROKKA_01404:0):0.0153844,GCF_005280335_PROKKA_01446:0.0155938):0.0158804);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001203_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001203_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bef5175bfd182e64bcd64b81b188f4ec83e009c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001203_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01346:0.33794,(GCF_005280335_PROKKA_01443:0.20119,(GCF_002008305_PROKKA_01457:5e-09,(GCF_003691675_PROKKA_01189:0,GCF_023573625_PROKKA_01407:0):0.00621657):0.248437):0.33794);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001205_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001205_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7026d9dd9139c4a207c4d9dbe175a4a46aa24ae2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001205_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01344:0.164217,((GCF_002008305_PROKKA_01459:0,GCF_003691675_PROKKA_01191:0,GCF_023573625_PROKKA_01409:0):0.0696719,GCF_005280335_PROKKA_01441:0.0988651):0.164217);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001206_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001206_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91a8750390ec1a46f75ce3e6cc8b7b6d4793bcc2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0152219):0.206546):0.274978);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001207_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001207_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23bfa1921efdde0105397df0a0184277fd6ea60a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.871:0.0131523)0.857:0.0530581)1:0.259714);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001208_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001208_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91fdf711c3bf60edbf4247bfd3d2da9a3f862c4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.831:0.0131343)0.698:0.0272805)1:0.202495);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001209_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001209_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f721a25a76da467434daeca2bb0e5288e53bad95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001209_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01340:0.295572,(GCF_005280335_PROKKA_01437:0.142971,(GCF_002008305_PROKKA_01463:5e-09,(GCF_003691675_PROKKA_01195:0.0161997,GCF_023573625_PROKKA_01413:5e-09)0.901:0.010826)0.996:0.22511)1:0.295572);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001210_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001210_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64f506ab7ee3665cf4bdc4e8ccda798704491760
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001210_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01339:0.259861,(GCF_005280335_PROKKA_01436:0.204919,((GCF_002008305_PROKKA_01464:0,GCF_023573625_PROKKA_01414:0):5e-09,GCF_003691675_PROKKA_01196:0.019981):0.219411):0.259861);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001212_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001212_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c870a5978b8813f1ed120f8664f5c5c49dd75a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001212_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01337:0.0654034,(GCF_005280335_PROKKA_01434:0.0407413,(GCF_003691675_PROKKA_01198:0.00966888,(GCF_002008305_PROKKA_01466:0.00321468,GCF_023573625_PROKKA_01416:0.00322048)0.842:5e-09)0.982:0.0234475)1:0.0654034);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001216_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001216_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78772293e06ebe8faf7892c3abd64991f693734d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0140191,GCF_003691675_PROKKA_01203:0.00857113):0.0247197):0.0508576);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001217_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001217_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4a6071dacf5a67c43441da02cb24277277be20d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001217_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01330:0.0849687,(GCF_005280335_PROKKA_01428:0.11963,(GCF_023573625_PROKKA_01422:0.0177241,(GCF_002008305_PROKKA_01472:0.0193829,GCF_003691675_PROKKA_01204:0.0068942)0.863:0.0117556)1:0.153232)1:0.0849687);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001219_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001219_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..38b727e496bb7c0d7484cf542a1149ff4b453c5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001219_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01328:0.07129,(GCF_005280335_PROKKA_01426:0.0382615,(GCF_023573625_PROKKA_01424:5e-09,(GCF_002008305_PROKKA_01474:0.00266365,GCF_003691675_PROKKA_01206:6e-09)0.888:0.00801974)0.975:0.0370313)1:0.07129);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001220_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001220_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89a2c6df1d12e6558129bc4dae8045e9f96c60b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.962:0.0120043)0.782:0.00443107)1:0.00440254);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001227_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001227_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7fdb3dd493b7fbad8d9c9187f22e94568e88cd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001227_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01318:0.181559,(GCF_005280335_PROKKA_01418:0.14854,(GCF_023573625_PROKKA_01434:0.00385577,(GCF_002008305_PROKKA_01484:0.0176624,GCF_003691675_PROKKA_01216:5e-09)0.754:0.00267921)0.999:0.119444)1:0.181559);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001229_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001229_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..efb69bb0ab365f16caa0aae18fc44386948e1dff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09):0.0558882):0.0634561);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001232_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001232_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0cf1f216721bf9450a66ae4f41ed3c07a50187cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.777:5e-09)0.979:0.0850486)1:0.224533);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001236_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001236_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cefb581b5a6db177f4a50617b95a3a6197770b9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.775:0.00531479)0.978:0.0748953)1:0.233527);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001237_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001237_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae87e16503f4071591694333f504406a5326b1df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001237_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01305:0.252265,(GCF_005280335_PROKKA_01406:0.110117,(GCF_003691675_PROKKA_01228:0.00329902,(GCF_002008305_PROKKA_01519:0.0110593,GCF_023573625_PROKKA_01446:0.00504374)0.66:0.00775939)0.87:0.0284021)1:0.252265);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001238_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001238_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2dc906eb856b6fbfd4c3c70499025788fd30bdd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001238_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01304:0.158456,(GCF_005280335_PROKKA_01405:0.0827574,(GCF_002008305_PROKKA_01520:0.00585215,(GCF_003691675_PROKKA_01229:0.00257795,GCF_023573625_PROKKA_01447:0.00427997)0.932:0.00456306)1:0.0510535)1:0.158456);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001243_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001243_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1391f47410231c7c485126f62189b486e3183af5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001243_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01299:0.00601477,(GCF_005280335_PROKKA_01400:0.0849719,(GCF_002008305_PROKKA_01525:0.00592864,(GCF_003691675_PROKKA_01234:5e-09,GCF_023573625_PROKKA_01452:0.00296382)0.914:5e-09)0.324:0.00645434)1:0.00601477);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001244_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001244_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfff0023c7be034db732c1623fd0b089edb7cdf7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001244_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00047:0.146162,(GCF_005280335_PROKKA_01399:0.0236874,(GCF_023573625_PROKKA_01453:0.00376052,(GCF_002008305_PROKKA_01526:0.0156753,GCF_003691675_PROKKA_01235:0.0132318)0.744:0.00293962)0.878:0.0138523)1:0.146162);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001246_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001246_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4cb3bb682da61cdb6749be6280582c8a1b5781ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001246_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01288:0.209046,(GCF_005280335_PROKKA_01397:0.0406714,((GCF_002008305_PROKKA_01528:0,GCF_003691675_PROKKA_01238:0):0.0104775,GCF_023573625_PROKKA_01455:0.0205158):0.0573855):0.209046);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001250_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001250_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b82f65797a5c2648050681011fbbf78e7de0c36
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001250_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01284:0.0801338,((GCF_002008305_PROKKA_01532:0,GCF_003691675_PROKKA_01242:0,GCF_023573625_PROKKA_01459:0):0.0571464,GCF_005280335_PROKKA_01393:0.0833558):0.0801338);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001251_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001251_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7d575fb74be3fec9852258ae34a0fbfeb099206
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001251_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01283:0.109717,(GCF_005280335_PROKKA_01392:0.102267,(GCF_002008305_PROKKA_01533:0.00198343,(GCF_003691675_PROKKA_01243:0,GCF_023573625_PROKKA_01460:0):5e-09):0.0701003):0.109717);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001256_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001256_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc40c66cf785b7828f8f2b4b4a092030674fca34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.714:0.0131957)1:0.120908)1:0.128127);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001258_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001258_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ad1b218ec8e56c51b3a2b9c42e656412b674b44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.808:0.00372047)1:0.0525195)1:0.0672452);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001259_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001259_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70160eaf0e1e1e071e571f4873ec401be674dbec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001259_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01274:0.174672,(GCF_005280335_PROKKA_01383:0.0812814,(GCF_003691675_PROKKA_01252:0.00661241,(GCF_002008305_PROKKA_01542:0.0180325,GCF_023573625_PROKKA_01469:0.00322393)0.62:0.00805832)1:0.119127)1:0.174672);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001261_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001261_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7137a4fb47a0323f7adcd5a541651ac520ce085f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001261_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01272:0.0731145,(GCF_005280335_PROKKA_01381:0.0265972,((GCF_002008305_PROKKA_01544:0,GCF_003691675_PROKKA_01254:0):0.00228815,GCF_023573625_PROKKA_01471:0.00482499):0.0328416):0.0731145);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001262_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001262_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb9eeeca8fb0d4a60e8ad71a8b13b5bed6a30b6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001262_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01271:0.183913,(GCF_005280335_PROKKA_01380:0.0790995,((GCF_002008305_PROKKA_01545:0,GCF_003691675_PROKKA_01255:0):0.00611907,GCF_023573625_PROKKA_01472:0.0178224):0.138084):0.183913);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001263_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001263_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9810d340f1cd0a36202606e825734db7d315446
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001263_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01270:0.0902753,(GCF_005280335_PROKKA_01379:0.0648349,((GCF_002008305_PROKKA_01546:0,GCF_003691675_PROKKA_01256:0):0.0203694,GCF_023573625_PROKKA_01473:0.0114445):0.0412066):0.0902753);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001265_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001265_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13821d695f79a4f3465c18216e84d9be8446e2a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001265_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01268:0.474556,(GCF_005280335_PROKKA_01377:0.156515,(GCF_023573625_PROKKA_01475:0.00227969,(GCF_002008305_PROKKA_01548:5e-09,GCF_003691675_PROKKA_01258:0.003372)0.888:0.0113164)0.966:0.13594)1:0.474556);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001266_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001266_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66011aa59ca750b0e27af30f6f65741f81b9f01a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001266_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01266:0.0369241,((GCF_002008305_PROKKA_01550:0,GCF_003691675_PROKKA_01260:0,GCF_023573625_PROKKA_01477:0):5e-09,GCF_005280335_PROKKA_01375:0.0182301):0.0369241);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001267_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001267_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03529fae82fbe00cf76c76d0212816df6ce545ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.699:0.0116179)0.985:0.222254)1:0.223432);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001268_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001268_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..459e2bcded75167f38b9b037bbdd4dba5f7b8710
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.662:0.0111074)0.972:0.0834532)1:0.143603);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001269_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001269_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5a1f72c0c2df758fa7759951d7d49dbdecb1a2f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.796:6e-09)0.991:0.0628322)1:0.0770067);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001272_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001272_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..476601d98e5114bef95fbff7825168509b9541eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001272_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01260:0.0808142,(GCF_005280335_PROKKA_01369:0.0993258,((GCF_002008305_PROKKA_01556:0,GCF_023573625_PROKKA_01483:0):5e-09,GCF_003691675_PROKKA_01266:0.0033155):0.0822026):0.0808142);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001274_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001274_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3539f0854bd6a47012e5fab8eabfceafc42a6b69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001274_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01258:0.0444514,(GCF_005280335_PROKKA_01367:0.0270173,(GCF_003691675_PROKKA_01268:0.00904803,(GCF_002008305_PROKKA_01558:0.00299898,GCF_023573625_PROKKA_01485:5e-09)0.894:5e-09)1:0.103252)1:0.0444514);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001275_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001275_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..484132a661c66dc85cc11fb222d7e210aaafa14c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.762:0.00236705)0.825:0.0152807)1:0.0393277);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001281_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001281_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89bf7e9ad4895058b09faf037f34971d324e659d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001281_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01250:0.150261,(GCF_023573625_PROKKA_01494:0.00231499,((GCF_002008305_PROKKA_01567:0,GCF_003691675_PROKKA_01277:0):0.00401043,GCF_005280335_PROKKA_01359:0.00399335):0.00167265):0.150261);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001282_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001282_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..178c8fd2a0cfcbfb1a000a132d4f7236834b860a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001282_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01249:0.133603,(GCF_005280335_PROKKA_01358:0.0273981,((GCF_002008305_PROKKA_01568:0,GCF_003691675_PROKKA_01278:0):0.0135648,GCF_023573625_PROKKA_01495:0.0191196):0.0139466):0.133603);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001283_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001283_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6203ec63276c0a7be1f85a1d8b83e07364ee96fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.793:0.0112567)0.952:0.0906756)1:0.325294);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001284_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001284_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7706119ddadf1f09b730a6e5799c2f1b805eb1f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.662:0.00507286)0.991:0.0881036)1:0.195866);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001291_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001291_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0f3698d9ab5f19a2693240a59ce9e914c37cb90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001291_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01238:0.0104009,(GCF_002008305_PROKKA_01578:0.00291252,(GCF_023573625_PROKKA_01505:5e-09,(GCF_005280335_PROKKA_01345:0.169894,GCF_003691675_PROKKA_01288:6e-09)0.772:0.00416311)0.781:0.00572839)1:0.0104009);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001292_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001292_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18d639084c6a58637445ee6113918c5551d0c5a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001292_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01237:0.0044442,(GCF_005280335_PROKKA_01344:0.103173,(GCF_002008305_PROKKA_01579:0.00221251,(GCF_003691675_PROKKA_01289:0,GCF_023573625_PROKKA_01506:0):5e-09):5e-09):0.0044442);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001293_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001293_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22b1d831b0e387b58e980da1040d548ca406f5b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.939:0.00936661)0.944:0.00935409)1:2.5e-09);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001295_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001295_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e0ee58c7e6e3c7ecd319ca7af972c79bb2654f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.94:0.0115931)0.973:0.0318377)1:0.191772);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001297_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001297_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..326f73789b6045c671794b1392d2557b5de8eb11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001297_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01215:0.09172,(GCF_005280335_PROKKA_01327:0.223184,((GCF_002008305_PROKKA_01594:0,GCF_023573625_PROKKA_01521:0):0.00727551,GCF_003691675_PROKKA_01306:0.0018849):0.0924736):0.09172);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001299_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001299_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..214c2f6f9a9365223016de89af8088d8d2443790
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001299_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01207:0.0390839,(GCF_005280335_PROKKA_01298:0.0542776,((GCF_002008305_PROKKA_01597:0,GCF_003691675_PROKKA_01309:0):0.00494766,GCF_023573625_PROKKA_01524:0.00655636):0.0633141):0.0390839);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001301_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001301_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4cda5819728c7a4eb103f3183ec9ff2da0d93db3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001301_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01203:0.00203654,(GCF_005280335_PROKKA_01294:0.00410293,(GCF_023573625_PROKKA_01526:0.0070031,(GCF_002008305_PROKKA_01599:5e-09,GCF_003691675_PROKKA_01311:0.00699872)0.192:5e-09)0.886:0.012894)1:0.00203654);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001304_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001304_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8fc4ea91c79eff520dc024e4fca8c1af0069be6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001304_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01199:0.00668236,(GCF_005280335_PROKKA_01291:0.00880306,((GCF_002008305_PROKKA_01603:0,GCF_023573625_PROKKA_01530:0):5e-09,GCF_003691675_PROKKA_01315:0.00881627):0.00437688):0.00668236);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001305_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001305_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..980b29db0697f8a629c3bb805f263c71270af8e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001305_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01193:0.0184841,(GCF_023573625_PROKKA_01536:0.0120957,(GCF_003691675_PROKKA_01321:5e-09,(GCF_002008305_PROKKA_01610:0.00835903,GCF_005280335_PROKKA_01288:0.0980305)0.86:0.00779237)0.296:0.00803321)1:0.0184841);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001306_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001306_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95969c914d4fed0bca3c65933f85e7c3e9cdcfaa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001306_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01192:0.00838915,(GCF_002008305_PROKKA_01611:0.0167465,(GCF_005280335_PROKKA_01287:0.0393648,(GCF_003691675_PROKKA_01322:0.0112046,GCF_023573625_PROKKA_01537:5e-09)0.799:5e-09)0.777:0.00554117)1:0.00838915);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001308_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001308_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18f65c4249648eab7ed59a98fbed17d40064130b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.758:0.00931413)0.347:0.00539971)1:0.00890765);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001309_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001309_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a781f874c4d1684f7d2b7260f3eb23945ddb182
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001309_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01181:0.0627804,(GCF_003691675_PROKKA_01332:0.115661,(GCF_005280335_PROKKA_01271:0.0950432,(GCF_002008305_PROKKA_01626:5e-09,GCF_023573625_PROKKA_01555:0.00622469)0.96:0.0533551)0.96:0.070797)1:0.0627804);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001310_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001310_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7ddcbe1642457f57c3a91f9b65f72edcdffb66c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.878:0.0255577)0.97:0.0646843)1:0.0214355);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001314_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001314_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d40c6c8870dcacf8c9f70f4e53679ce7553a35d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001314_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01172:0.0432193,(GCF_005280335_PROKKA_01263:0.051413,(GCF_002008305_PROKKA_01632:0.0033603,(GCF_003691675_PROKKA_01337:0.0129678,GCF_023573625_PROKKA_01561:5e-09)0.495:0.00968503)0.86:0.0220203)1:0.0432193);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001315_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001315_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d0d050a87db33bad170e43498b66727090d90d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.669:0.00424513)1:0.337219)1:0.172565);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001316_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001316_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..73fcdbd5ede2838d201cd9aebb562f81426a1d93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.806:0.00219545)0.999:0.0997349)1:0.0730982);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001317_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001317_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37aec0d826a5c9484d4d19e4f747396a21c8b4a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001317_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01169:0.0332143,(GCF_005280335_PROKKA_01260:0.161376,((GCF_002008305_PROKKA_01635:0,GCF_023573625_PROKKA_01564:0):5e-09,GCF_003691675_PROKKA_01340:0.0322568):0.0510556):0.0332143);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001319_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001319_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..770d3e40e99019c5a3ee4625262fea6e5929b250
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001319_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01166:0.0332532,(GCF_005280335_PROKKA_01257:0.0388948,((GCF_002008305_PROKKA_01638:0,GCF_003691675_PROKKA_01343:0):5e-09,GCF_023573625_PROKKA_01567:5e-09):0.0288372):0.0332532);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001321_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001321_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5f05098be3ab3379dc270bfea1fd9717d9f18a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.879:0.0195746)0.922:0.0561275)1:0.13395);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001327_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001327_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2d20b5562cdbe46580d66dc24ab2e1a6b92a7fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001327_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01158:0.0977231,(GCF_005280335_PROKKA_01247:0.160746,(GCF_002008305_PROKKA_01646:0.0100722,(GCF_003691675_PROKKA_01351:0.00996988,GCF_023573625_PROKKA_01576:5e-09)0.913:5e-09)0.942:0.0877798)1:0.0977231);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001329_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001329_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45b942d35baea31fc5d9d0fff8629bb3ccde83fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.916:0.00513881)1:0.0531638)1:0.134863);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001331_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001331_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cbb04a4c7e2a8055cc273d67d99a1485cefa071
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001331_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01154:0.1035,(GCF_005280335_PROKKA_01243:0.0852988,(GCF_002008305_PROKKA_01650:5e-09,(GCF_003691675_PROKKA_01355:0.0113472,GCF_023573625_PROKKA_01580:5e-09)0.827:0.00564697)0.983:0.104124)1:0.1035);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001334_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001334_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fffdfc3056949563635098afb7c6f24c587af2d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001334_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01151:0.0211156,(GCF_005280335_PROKKA_01240:0.0150641,(GCF_002008305_PROKKA_01653:0.00700053,(GCF_003691675_PROKKA_01358:0.00179771,GCF_023573625_PROKKA_01583:5e-09)0.731:0.00385966)0.997:0.0243262)1:0.0211156);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001335_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001335_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62daf2edfb4e16882ab2bff9bedef11a3c480ae1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.844:0.00204321)1:0.0606432)1:0.0609631);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001336_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001336_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d38a40aacd0a1f34371c2e557a36f652ad3aadc7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001336_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01148:0.00499657,(GCF_002008305_PROKKA_01657:0.0099627,(GCF_003691675_PROKKA_01362:0,GCF_005280335_PROKKA_01237:0,GCF_023573625_PROKKA_01587:0):5e-09):0.00499657);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001338_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001338_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3700c38e3a0360eda898cf345a392639c153ab2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001338_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01145:2.5e-09,(GCF_005280335_PROKKA_01234:0.104047,(GCF_023573625_PROKKA_01590:0.0081462,(GCF_002008305_PROKKA_01660:0.0109024,GCF_003691675_PROKKA_01365:0.00268701)0.869:0.00544718)0.26:0.00815226)1:2.5e-09);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001340_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001340_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df43813714ac4310b5ef94f8d0730e34d11808b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001340_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01143:0.0368354,(GCF_005280335_PROKKA_01232:0.186564,(GCF_002008305_PROKKA_01662:0.00809712,(GCF_003691675_PROKKA_01367:0.00835264,GCF_023573625_PROKKA_01592:0.0103752)0.721:0.00274039)0.958:0.0351188)1:0.0368354);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001341_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001341_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3900c239b3237e6e91fddf8e40b035caa84191e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001341_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01142:0.242796,(GCF_005280335_PROKKA_01231:0.36041,(GCF_002008305_PROKKA_01663:0.0135629,(GCF_003691675_PROKKA_01368:0.00443035,GCF_023573625_PROKKA_01593:0.0136042)0.361:0.00681464)0.469:0.0312281)1:0.242796);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001342_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001342_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1bde82c1437271b8ad581127829a6aeef7b9f4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.246:0.00242944)1:0.256596)1:0.0602431);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001345_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001345_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7b84d63f14ae9dee60176b8c06e71e049556635
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001345_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01138:0.190687,(GCF_005280335_PROKKA_01227:0.0618713,(GCF_002008305_PROKKA_01667:0.0244931,(GCF_003691675_PROKKA_01372:0,GCF_023573625_PROKKA_01597:0):0.00583034):0.0718976):0.190687);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001346_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001346_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3047980e977ac20788ee83eaaae8aa5085aa352a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.41:0.00285271)0.993:0.0582038)1:0.0522379);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001348_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001348_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7f8152d28b66c122923ad990a3b054c1fbf2bff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001348_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01135:0.134401,(GCF_003691675_PROKKA_01376:0.00933708,(GCF_005280335_PROKKA_01207:0.0528827,(GCF_002008305_PROKKA_01671:0.0123343,GCF_023573625_PROKKA_01601:0.040911)0.787:0.0107757)0.723:0.005949)1:0.134401);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001350_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001350_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d7c9280871122d274db28b4a9fa7645c96341dd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.756:0.0135682)0.978:0.0643532)1:0.13277);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001351_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001351_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37dbe4b7db9f62d1f747fa8176b0eb78147bf1e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.942:0.0148064)0.998:0.110484)1:0.164251);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001353_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001353_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f4c7ec65b73537efdb5f4e2b6748fe1a93f24124
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_023573625_PROKKA_01606:0.00777584):0.0224525):0.106361);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001355_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001355_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..32104a835a60bd701f2156a293da21d470312d53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001355_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01128:0.0669058,(GCF_005280335_PROKKA_01200:0.0540152,((GCF_002008305_PROKKA_01678:0,GCF_003691675_PROKKA_01383:0):0.00475759,GCF_023573625_PROKKA_01608:0.00526659):0.0340536):0.0669058);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001356_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001356_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b1468c901971881559924bc6304cc6807744c3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001356_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01127:0.0339663,(GCF_005280335_PROKKA_01198:0.0288289,(GCF_002008305_PROKKA_01680:0.0032073,(GCF_003691675_PROKKA_01384:0.00323297,GCF_023573625_PROKKA_01609:0.00153133)0.256:0.00332026)0.998:0.0366004)1:0.0339663);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001357_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001357_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d47bce4cc2abd227d34c93184a537ae62e1a9cb6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_003691675_PROKKA_01386:0.00285287):0.0701392):0.0993954);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001358_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001358_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7c35a0db0d130ef42b2f581dba70f5fd30e8484
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001358_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01124:0.0650066,(GCF_005280335_PROKKA_01194:0.130754,(GCF_003691675_PROKKA_01388:0.00689836,(GCF_002008305_PROKKA_01684:5e-09,GCF_023573625_PROKKA_01613:0.00689707)0.76:5e-09)0.998:0.196844)1:0.0650066);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001359_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001359_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14776b8f14cb3d0d359b717bfbfa1fc9a71fce7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001359_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01123:0.304197,((GCF_002008305_PROKKA_01685:0,GCF_003691675_PROKKA_01389:0,GCF_023573625_PROKKA_01614:0):0.146515,GCF_005280335_PROKKA_01193:0.223962):0.304197);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001362_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001362_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9338853f3da3c5dd0d2ca76d45405edfeb32ef52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001362_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01119:0.0240659,(GCF_005280335_PROKKA_01189:0.0206926,((GCF_002008305_PROKKA_01689:0,GCF_023573625_PROKKA_01618:0):0.00598019,GCF_003691675_PROKKA_01396:0.00601885):0.0168947):0.0240659);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001363_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001363_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f3f9d1b6ff429df78de49f2d29b42ac7209e7157
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001363_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01118:0.0277975,(GCF_005280335_PROKKA_01188:5e-09,((GCF_002008305_PROKKA_01690:0,GCF_003691675_PROKKA_01397:0):5e-09,GCF_023573625_PROKKA_01619:0.00672151):0.0202678):0.0277975);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001364_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001364_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98753d24ffb113847d2b5f98afc0a29a5497e90b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001364_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01117:0.178053,(GCF_005280335_PROKKA_01187:0.0656948,(GCF_002008305_PROKKA_01691:0.00681244,(GCF_003691675_PROKKA_01398:0.0100656,GCF_023573625_PROKKA_01620:0.00819364)0.099:0.0056293)0.993:0.0823988)1:0.178053);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001367_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001367_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5d14dea03644f4a240225948839a19be97934e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0140217,GCF_005280335_PROKKA_01184:5e-09):0.00710484);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001368_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001368_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da4e2a1fd1049d138b981986be876f53da605e89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001368_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01695:0,GCF_003691675_PROKKA_01402:0,GCF_005280335_PROKKA_01183:0,GCF_023573625_PROKKA_01624:0):0.0164082,GCF_020097155_PROKKA_01113:0.0164082);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001370_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001370_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4833705312876af33c3c6fc872226fef6e7258bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001370_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01697:0,GCF_003691675_PROKKA_01404:0,GCF_005280335_PROKKA_01181:0,GCF_023573625_PROKKA_01626:0):0.006717,GCF_020097155_PROKKA_01111:0.006717);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001371_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001371_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f6aedb4ac5c54b37012f0b766b57f3b9711d636e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001371_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01110:0.0751001,(GCF_005280335_PROKKA_01180:0.0357574,(GCF_002008305_PROKKA_01698:0.00354723,(GCF_003691675_PROKKA_01405:5e-09,GCF_023573625_PROKKA_01627:0.0070171)0.866:0.00700806)0.995:0.070247)1:0.0751001);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001372_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001372_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e8ca5ef36679841e758d06d052026e5540bac71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001372_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01109:0.077639,(GCF_005280335_PROKKA_01179:0.015693,(GCF_002008305_PROKKA_01699:5e-09,(GCF_003691675_PROKKA_01406:0.00475223,GCF_023573625_PROKKA_01628:0.00473057)0.859:0.00956603)0.949:0.0437913)1:0.077639);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001377_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001377_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..031809dd1f995bea26eb14a448ab252bb017965b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001377_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01104:0.0116921,(GCF_002008305_PROKKA_01704:0.00774441,((GCF_003691675_PROKKA_01411:0,GCF_023573625_PROKKA_01633:0):5e-09,GCF_005280335_PROKKA_01174:0.0156256):5e-09):0.0116921);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001378_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001378_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f139a96580621a6fa100e03bb24e3736ba22ff9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001378_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01103:0.0513463,(GCF_005280335_PROKKA_01173:0.000501605,(GCF_002008305_PROKKA_01705:5e-09,(GCF_003691675_PROKKA_01412:0,GCF_023573625_PROKKA_01634:0):0.0055389):0.0106529):0.0513463);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001381_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001381_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c07b90b6e51afb873d54effa05cff1652c545ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0174217,GCF_005280335_PROKKA_01170:0.0174001):0.0181405);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001382_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001382_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10d45c6f5db9fa4d4cc9de82c4b3f9c00f010f69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00803552,GCF_020097155_PROKKA_01099:0.00803552);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001383_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001383_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c237a88f84ecdd8ec5f495521e19cbe9652f210
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001383_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01098:0.0675942,((GCF_002008305_PROKKA_01710:0,GCF_003691675_PROKKA_01417:0,GCF_023573625_PROKKA_01639:0):0.0357484,GCF_005280335_PROKKA_01168:0.00530366):0.0675942);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001386_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001386_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94be05a1329b0312e615a87107571dcf3aa13ecd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001386_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01095:0.00869368,((GCF_003691675_PROKKA_01420:0,GCF_023573625_PROKKA_01642:0):5e-09,(GCF_002008305_PROKKA_01713:0.00731931,GCF_005280335_PROKKA_01165:0.00855025):5e-09):0.00869368);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001387_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001387_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ab04c5724b0791a184d8bec87554af384ebf0a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001387_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01714:0,GCF_003691675_PROKKA_01421:0,GCF_005280335_PROKKA_01164:0,GCF_023573625_PROKKA_01643:0):0.0120777,GCF_020097155_PROKKA_01094:0.0120777);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001388_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001388_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ebb3930015666aee8bef8e478bfe195f2086c527
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001388_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01715:0,GCF_003691675_PROKKA_01422:0,GCF_005280335_PROKKA_01163:0,GCF_023573625_PROKKA_01644:0):0.00537453,GCF_020097155_PROKKA_01093:0.00537453);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001390_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001390_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c5062b5318e18d555eba88ba96f41d8a803b007
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001390_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01717:0,GCF_003691675_PROKKA_01424:0,GCF_005280335_PROKKA_01161:0,GCF_023573625_PROKKA_01646:0):0.0298265,GCF_020097155_PROKKA_01091:0.0298265);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001391_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001391_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53115f811aece9e0d3456519e1e77a3260d24200
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0136414,GCF_005280335_PROKKA_01160:5e-09):0.0183637);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001392_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001392_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..618489b752d77f34c3c9271e0b70d03afb681b7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001392_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01089:0.0137632,(GCF_005280335_PROKKA_01159:0.0183311,((GCF_002008305_PROKKA_01719:0,GCF_023573625_PROKKA_01648:0):5e-09,GCF_003691675_PROKKA_01426:0.00458129):0.00453969):0.0137632);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001394_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001394_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..af28c8a51a47a145477d7cbd484c548c7d9809f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_003691675_PROKKA_01428:0.0134996):0.226143):0.165641);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001398_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001398_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..166e64cb49b533d635a353c9c3ee2652d2bd48e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00636814,GCF_005280335_PROKKA_01153:5e-09):0.00318706);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001402_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001402_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a9652a4222a26355eecd872ce73bf5058450e40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09):0.00762115):0.0159406);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001403_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001403_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae826903d17a5d86c2ab9312818ba218d5959157
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09):0.0173436):0.0352705);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001404_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001404_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e428771900b42cd8512a7451148ce7c42f1feae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001404_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01076:0.0452094,(GCF_005280335_PROKKA_01147:0.00615263,(GCF_023573625_PROKKA_01660:0.00406457,(GCF_002008305_PROKKA_01731:5e-09,GCF_003691675_PROKKA_01438:0.00406722)0.758:5e-09)0.765:0.0142941)1:0.0452094);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001405_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001405_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30eb0f271b8687de708c5cee9a3a8ec8940d2658
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0174227,GCF_005280335_PROKKA_01146:0.0100587):0.0235205);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001406_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001406_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..33857b908924abb1e153e8e7d7a41af391238502
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.778:0.00474651)0.898:0.03243)1:0.0735912);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001407_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001407_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e2552bc70a1a7e2587e5524ef68a5f2adc88252
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001407_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01073:0.153325,(GCF_005280335_PROKKA_01144:0.0290719,((GCF_002008305_PROKKA_01734:0,GCF_023573625_PROKKA_01663:0):0.0124085,GCF_003691675_PROKKA_01441:5e-09):0.0361365):0.153325);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001408_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001408_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b86fe16515f9584610283dc013e1222c86fa89e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.903:0.00912154)0.996:0.0448412)1:0.0312759);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001409_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001409_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f5abbe92b9c73cf84f23fb64657d86e57a2ac2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001409_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01070:0.0724046,(GCF_005280335_PROKKA_01141:0.0230908,(GCF_002008305_PROKKA_01737:0.0043173,(GCF_023573625_PROKKA_01666:0.0125404,GCF_003691675_PROKKA_01444:0.00834774)0.772:0.00398454)0.968:0.0405116)1:0.0724046);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001413_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001413_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71fbc1252e6f0f3e81f8aab50da20486d8aafe81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001413_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01065:0.492987,(GCF_005280335_PROKKA_01136:0.170578,(GCF_002008305_PROKKA_01741:5e-09,(GCF_003691675_PROKKA_01448:0.0039107,GCF_023573625_PROKKA_01670:5e-09)0.468:0.00390794)0.935:0.13326)1:0.492987);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001414_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001414_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5662ca125e4fb657d71e9ede2160f1c22185c32d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00526125,GCF_023573625_PROKKA_01671:0.00233347):0.0465323):0.131339);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001415_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001415_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b1c5d7b18d5049c559f99273cf8fe4654e79f7e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001415_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01063:0.0924504,((GCF_002008305_PROKKA_01743:0,GCF_003691675_PROKKA_01450:0,GCF_023573625_PROKKA_01672:0):0.0680943,GCF_005280335_PROKKA_01134:0.0326293):0.0924504);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001416_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001416_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3875de03b6efe9fb0d7ac3a75742fbc348f1f4ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001416_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01062:0.0736305,((GCF_002008305_PROKKA_01744:0,GCF_003691675_PROKKA_01451:0,GCF_023573625_PROKKA_01673:0):0.0549009,GCF_005280335_PROKKA_01133:5e-09):0.0736305);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001418_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001418_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d020290c41995202c0d71bc76d3975cceb8f6028
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001418_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01059:0.179784,(GCF_005280335_PROKKA_01131:0.106997,((GCF_002008305_PROKKA_01746:0,GCF_003691675_PROKKA_01453:0):0.0127499,GCF_023573625_PROKKA_01675:5e-09):0.169403):0.179784);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001419_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001419_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f3b50c338dbdeec8fae9678394fb8b273f5fd91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001419_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01058:0.182986,(GCF_005280335_PROKKA_01130:0.100012,((GCF_002008305_PROKKA_01747:0,GCF_003691675_PROKKA_01454:0):0.0121012,GCF_023573625_PROKKA_01676:5e-09):0.0876428):0.182986);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001420_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001420_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0cb79dca5e6c6ff31fb0bf4e980fd8146214c541
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001420_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01057:0.10189,((GCF_002008305_PROKKA_01748:0,GCF_003691675_PROKKA_01455:0,GCF_023573625_PROKKA_01677:0):0.0808164,GCF_005280335_PROKKA_01129:0.0636366):0.10189);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001423_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001423_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e0282da1a38673fdcaf766c71c3fe3f4395fa86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00495213,GCF_023573625_PROKKA_01680:0.0353634):0.0997258):0.166208);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001424_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001424_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..660d7d0bbfb8edde40697217b57541b2f1280348
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001424_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01050:0.0453259,(GCF_005280335_PROKKA_01125:0.0708523,((GCF_002008305_PROKKA_01752:0,GCF_003691675_PROKKA_01459:0):0.00983012,GCF_023573625_PROKKA_01681:0.00287665):0.0597458):0.0453259);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001426_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001426_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b754f2c8c9e899ebb5873baa778e63846d8fc53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_023573625_PROKKA_01683:0.0117601):0.0590642):0.138738);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001428_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001428_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfab9b68f3b7fb9128455ec83d549c28252c62f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001428_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01046:0.170423,((GCF_002008305_PROKKA_01756:0,GCF_003691675_PROKKA_01463:0,GCF_023573625_PROKKA_01685:0):0.0715577,GCF_005280335_PROKKA_01121:0.213955):0.170423);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001430_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001430_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc05acacd5ca7607ca94396769788a6831b53c5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0140853,GCF_023573625_PROKKA_01689:0.0048041):0.032725):0.314184);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001432_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001432_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b038e176d85b74f9af3a383ff84f841b2f8f4fe1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001432_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01040:0.0505434,(GCF_005280335_PROKKA_01115:0.138834,(GCF_023573625_PROKKA_01691:5e-09,(GCF_002008305_PROKKA_01762:0.00233142,GCF_003691675_PROKKA_01469:5e-09)0.915:0.00232937)0.962:0.0384554)1:0.0505434);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001433_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001433_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f3bbfdddbeefdfac527588d35a33947a07c87120
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001433_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01039:0.107667,(GCF_005280335_PROKKA_01114:0.0438545,(GCF_002008305_PROKKA_01763:0.00190692,(GCF_023573625_PROKKA_01692:0.00757008,GCF_003691675_PROKKA_01470:0.0018873)0.762:0.00186378)1:0.0658509)1:0.107667);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001436_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001436_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10129d849f92299ce485497c64fd89e2b25433e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.462:5e-09)0.907:0.0119846)1:0.0460569);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001440_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001440_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bec3d323872907f4295db8505b63b2ad92ac285e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001440_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01029:0.0473677,(GCF_005280335_PROKKA_01104:0.0513869,(GCF_002008305_PROKKA_01773:0.0132063,(GCF_003691675_PROKKA_01480:5e-09,GCF_023573625_PROKKA_01702:0.00654939)0.811:5e-09)0.974:0.0701318)1:0.0473677);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001441_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001441_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce686702a32cc8c78abdde8c886aa17ea33abc76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001441_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01028:0.0361667,(GCF_005280335_PROKKA_01103:0.0731396,(GCF_023573625_PROKKA_01703:0.0128056,(GCF_002008305_PROKKA_01774:0.0125005,GCF_003691675_PROKKA_01481:0.00622564)0.758:0.0063048)0.947:0.0495429)1:0.0361667);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001443_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001443_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..075141c02dcf01b42bd4bf8964d1c14bd902a02b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.77:6e-09)0.998:0.0729685)1:0.0887011);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001444_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001444_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..af878646b803ce7014db9b31d7a2933f086ea707
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001444_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01024:0.158209,(GCF_005280335_PROKKA_01100:0.0931168,(GCF_002008305_PROKKA_01777:0.0152993,(GCF_003691675_PROKKA_01484:0.00149619,GCF_023573625_PROKKA_01706:0.00604657)0.794:0.00300654)0.998:0.107759)1:0.158209);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001445_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001445_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9b0aa2208ebf9a695454d36496b62a004764391
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.845:0.00992183)0.914:0.0860004)1:0.370727);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001446_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001446_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..535fa65dc69c596bf10199ed6c0aea12a145bd48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001446_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01019:0.0450369,(GCF_005280335_PROKKA_01096:0.0707769,(GCF_023573625_PROKKA_01711:0.0106936,(GCF_002008305_PROKKA_01782:0.0043065,GCF_003691675_PROKKA_01489:0.003517)0.507:0.00354221)0.999:0.057836)1:0.0450369);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001447_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001447_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce09e5ef7fd288f3fcee7499834d1f9932fae4f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001447_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01018:0.0285944,(GCF_005280335_PROKKA_01095:0.032845,(GCF_023573625_PROKKA_01712:0.00847621,(GCF_002008305_PROKKA_01783:5e-09,GCF_003691675_PROKKA_01490:0.00281506)0.86:5e-09)0.859:0.0115469)1:0.0285944);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001449_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001449_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac9f0c9fd733971d8936f131c535498db3929020
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001449_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01016:0.077261,(GCF_005280335_PROKKA_01093:0.0646881,((GCF_002008305_PROKKA_01785:0,GCF_003691675_PROKKA_01492:0):5e-09,GCF_023573625_PROKKA_01714:0.00601727):0.0363605):0.077261);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001450_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001450_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7140c0be0fe70a50616f6b0ebd83fef8e2e5fd18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.749:5e-09,(GCF_002008305_PROKKA_01787:0.00602665,GCF_005280335_PROKKA_01089:0.00435728)0.594:0.00199761)1:0.134621);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001451_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001451_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99c134487978f274cd77f45ba3a6898f1e809847
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.769:0.00218414)0.996:0.0377683)1:0.115939);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001452_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001452_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6886595e71f2a70903c5f909b8398c984bd7408
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001452_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01010:0.0209257,(GCF_005280335_PROKKA_01074:0.0136302,(GCF_002008305_PROKKA_01799:5e-09,(GCF_003691675_PROKKA_01496:5e-09,GCF_023573625_PROKKA_01720:0.00916395)0.91:0.00306163)0.914:0.0169043)1:0.0209257);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001453_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001453_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97c3240d62ebc517da7316f81c7ebff66cdb9d02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001453_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01009:0.00178976,((GCF_003691675_PROKKA_01497:0.0111042,GCF_005280335_PROKKA_01073:0.00429916)0.897:0.00750368,(GCF_002008305_PROKKA_01800:0.0133151,GCF_023573625_PROKKA_01721:0.00597269)0.251:0.002356)1:0.00178976);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001454_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001454_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f98a6196e6f5f91ff2631099965efc05dbf4766f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.998:0.0393309,(GCF_002008305_PROKKA_01801:0.0203861,GCF_023573625_PROKKA_01722:0.0154193)0.732:0.00363735)1:0.00189306);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001456_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001456_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..336f59df08b8d7b962a0fde907597a34e9bdaed4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.987:0.194549,(GCF_002008305_PROKKA_01803:0.0433827,GCF_023573625_PROKKA_01724:0.0398436)0.937:0.127672)1:0.147925);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001457_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001457_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a734dd32c46180be9aec338c326cb5f8b99322a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.985:0.161956,(GCF_003691675_PROKKA_01501:5e-09,GCF_005280335_PROKKA_01069:0.00775009)0.923:0.098726)1:0.196099);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001458_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001458_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91328a9cec5363a91d6822810da3ac7ac0651b5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001458_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01002:0.213099,(GCF_005280335_PROKKA_01067:5e-09,(GCF_023573625_PROKKA_01728:5e-09,(GCF_002008305_PROKKA_01807:0.00853895,GCF_003691675_PROKKA_01504:0.00425896)0.833:5e-09)0.868:0.00424163)1:0.213099);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001463_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001463_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f558adc566ed7616743860da4fbc8a8f8ecb9e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001463_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00995:0.0649143,(GCF_005280335_PROKKA_01060:0.0666199,(GCF_023573625_PROKKA_01735:0.00601525,(GCF_002008305_PROKKA_01814:0.00230662,GCF_003691675_PROKKA_01511:0.0120109)0.668:0.00389842)0.999:0.0802371)1:0.0649143);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001464_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001464_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..17c68670ea14a9b7d515005e0b3dd0426b3e486c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001464_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00994:0.0420294,(GCF_005280335_PROKKA_01059:0.0102478,(GCF_023573625_PROKKA_01736:5e-09,(GCF_002008305_PROKKA_01815:5e-09,GCF_003691675_PROKKA_01512:0.0087657)0.859:0.00428899)0.947:0.021477)1:0.0420294);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001466_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001466_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae9dea3c0dc755ce836dc09a4dc00018f3e5e28c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.73:0.00330913)0.986:0.0677131)1:0.0977051);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001467_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001467_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6f55a5009de85224db715ed63cf0d4e3ad7bc3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.885:0.00943901)0.995:0.0604158)1:0.0764292);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001469_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001469_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b750b599682d3087fa84dea19cc526594c6d2917
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.582:0.00180664)1:0.0869942)1:0.0428587);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001470_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001470_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f5d0f8f7bf31b94f014456de5050d0936b52efc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001470_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00987:0.0983813,(GCF_005280335_PROKKA_01048:0.069639,((GCF_002008305_PROKKA_01821:0,GCF_023573625_PROKKA_01742:0):0.0125942,GCF_003691675_PROKKA_01518:0.0269566):0.0644929):0.0983813);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001472_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001472_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..265a81875124aae023aeed496ee348c1033a458f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.767:0.0025311)1:0.0579309)1:0.0724627);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001473_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001473_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4384fcd7a91fc05a754b1a3ddf58b796329b7ea8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.881:0.0201688)0.809:0.0619865)1:0.28559);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001474_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001474_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..324e0b46099853a3c1ff12826093342a41f6ef8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.802:0.0113411)0.707:0.0612688)1:0.254462);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001475_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001475_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ebc475246e10110e53886431e94deb1b0e4cb33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001475_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00982:0.252052,(GCF_005280335_PROKKA_01043:0.0954285,((GCF_002008305_PROKKA_01826:0,GCF_023573625_PROKKA_01747:0):0.0104507,GCF_003691675_PROKKA_01523:0.0274871):0.162691):0.252052);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001476_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001476_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ff669f7e1c7dc0c612ce777f07075327e4344e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001476_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00981:0.315366,(GCF_005280335_PROKKA_01042:0.169154,(GCF_003691675_PROKKA_01524:0.0140283,(GCF_002008305_PROKKA_01827:0.00921749,GCF_023573625_PROKKA_01748:0.0122119)0.893:0.0174279)0.939:0.0810875)1:0.315366);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001478_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001478_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb043a8f1a2d190a512c602dac4c9e9e042dda1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001478_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00979:0.154979,(GCF_005280335_PROKKA_01040:0.14391,(GCF_023573625_PROKKA_01750:0.0104158,(GCF_002008305_PROKKA_01829:0.0112816,GCF_003691675_PROKKA_01526:0.0228561)0.862:0.0159031)0.976:0.0925994)1:0.154979);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001481_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001481_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..136b0f76220e16502abb82e8833f5c14e5233ee4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.423:0.00588151,GCF_002008305_PROKKA_01833:0.0301716)0.616:0.00762276)1:0.476591);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001482_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001482_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5979270d99323ac517df704449cf205744bda3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001482_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00975:0.315572,(GCF_005280335_PROKKA_01034:0.0786708,(GCF_023573625_PROKKA_01755:0.0174509,(GCF_002008305_PROKKA_01834:0.0330323,GCF_003691675_PROKKA_01531:6e-09)0.776:0.0150388)0.708:0.0996048)1:0.315572);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001485_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001485_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..783e323f7fb73a807ec36234847320322b9513ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001485_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00971:0.213476,(GCF_005280335_PROKKA_01030:0.101759,(GCF_002008305_PROKKA_01838:0.0187547,(GCF_003691675_PROKKA_01535:0,GCF_023573625_PROKKA_01759:0):0.0292112):0.14597):0.213476);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001490_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001490_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d63997f785519d0f59ae8f18479981bc61f26442
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001490_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00966:0.0583345,(GCF_005280335_PROKKA_01025:0.119594,((GCF_002008305_PROKKA_01843:0,GCF_003691675_PROKKA_01540:0):0.00321821,GCF_023573625_PROKKA_01764:5e-09):0.188832):0.0583345);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001491_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001491_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80ac1fee5249c2c3145cea838aaba67008853793
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001491_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00963:0.0779007,((GCF_002008305_PROKKA_01847:0,GCF_003691675_PROKKA_01543:0,GCF_023573625_PROKKA_01767:0):0.0324827,GCF_005280335_PROKKA_01021:0.0456468):0.0779007);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001492_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001492_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5877e5b1372125b3557ee4e119f092d9e47fd88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001492_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00962:0.219269,(GCF_005280335_PROKKA_01020:0.14751,(GCF_023573625_PROKKA_01768:0.0353782,(GCF_002008305_PROKKA_01848:5e-09,GCF_003691675_PROKKA_01544:0.0122601)0.786:0.0271395)0.747:0.0663398)1:0.219269);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001494_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001494_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20f51b9851ac29f4f331381af628cf8023565e12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001494_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00960:0.255653,(GCF_005280335_PROKKA_01018:0.132507,(GCF_003691675_PROKKA_01546:0.00212215,(GCF_002008305_PROKKA_01850:0.00207284,GCF_023573625_PROKKA_01770:0.00430657)0.908:0.0128954)0.999:0.158771)1:0.255653);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001495_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001495_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..33255804dd7ee8fc344d5273d64972f497c24b2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.793:0.00627446)0.958:0.0478233)1:0.220692);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001498_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001498_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aee6b813f893fd783612f25aae2a351d24e87b34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001498_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00953:0.247938,(GCF_005280335_PROKKA_01009:0.091211,((GCF_002008305_PROKKA_01855:0,GCF_023573625_PROKKA_01775:0):0.0178966,GCF_003691675_PROKKA_01551:0.0186644):0.0892055):0.247938);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001500_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001500_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..033933801554bad497a4140ae466730706244aa2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.755:0.00253609)0.964:0.0285645)1:0.0937729);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001502_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001502_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ca9a5a53984d1b87d557e34e991a6a5db8cc632
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001502_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00947:0.103875,(GCF_005280335_PROKKA_01004:0.0559301,(GCF_002008305_PROKKA_01859:0.0063397,(GCF_003691675_PROKKA_01555:5e-09,GCF_023573625_PROKKA_01779:0.00317026)0.851:5e-09)0.996:0.0697383)1:0.103875);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001505_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001505_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..940b54202d4a30238f30715ce2b58f2fe506f3f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0151196,GCF_003691675_PROKKA_01558:0.0096625):0.00879936):0.0805853);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001506_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001506_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b4265678c4fb5aa1436a7712cee1f8480c54333
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001506_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00936:0.225682,(GCF_005280335_PROKKA_00997:0.0778884,(GCF_023573625_PROKKA_01783:5e-09,(GCF_003691675_PROKKA_01559:0.0232622,GCF_002008305_PROKKA_01863:0.00252254)0.764:0.00250686)0.996:0.108456)1:0.225682);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001507_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001507_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..73c95eb09dfd1b229c47dc35b58314b07f6cefc6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.963:0.0260216)0.908:5e-09)1:0.523686);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001508_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001508_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..008af813c52de535decb990206429575ef0dda67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.614:0.0022837)0.975:0.0699369)1:0.133215);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001512_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001512_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eaedea9ef573b2ae64c42e4e48ce9f4653829f34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_023573625_PROKKA_01789:0.00402861):0.0639693):0.115833);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001513_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001513_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30dda25a456967fdc828e71c2aa1a82fd12a6e2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.807:0.0107783)0.989:0.132383)1:0.268967);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001519_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001519_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15f7eb7af185aeeebcd5d62f6b3236d7fbf535d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001519_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00921:0.0241287,((GCF_003691675_PROKKA_01572:0.00471146,GCF_023573625_PROKKA_01796:0.00464167)0.807:0.00356647,(GCF_002008305_PROKKA_01876:0.00812403,GCF_005280335_PROKKA_00983:0.00434507)0.361:0.00321643)1:0.0241287);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001522_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001522_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5374244af1d90b6704a9939984841e26f9c30d8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001522_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00914:0.14355,((GCF_002008305_PROKKA_01882:0,GCF_023573625_PROKKA_01802:0):0.0667573,(GCF_003691675_PROKKA_01578:0.00568643,GCF_005280335_PROKKA_00976:0.0576307):0.0524043):0.14355);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001526_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001526_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd6b712d21fe2414c406fbdee773c48bcccc5be5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.112935,GCF_003691675_PROKKA_01582:0.00177466):0.133061):0.253324);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001528_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001528_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4bc1968feab179963c28867e60b19b4b44ad6b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001528_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00908:0.206035,(GCF_005280335_PROKKA_00970:0.0387569,(GCF_003691675_PROKKA_01584:5e-09,(GCF_002008305_PROKKA_01888:0.110767,GCF_023573625_PROKKA_01808:5e-09)0.948:0.0162992)0.968:0.0942305)1:0.206035);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001530_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001530_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5a55a01810d3906814035364366d8c58855fe7da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.835:0.0241759)0.959:0.0495395)1:0.137887);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001532_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001532_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d495994370f195e986d06631d605289261a2417
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00302569,GCF_003691675_PROKKA_01592:0.00292646):0.0835093):0.08551);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001536_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001536_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4fdcdb705cbe24a2b000e8bf008133b7e66354c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.799:0.00132365)0.999:0.0705425)1:0.0949595);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001538_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001538_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14466340f628417e20c7cce4c79acf90641c5a8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.891:0.0108803)0.986:0.158656)1:0.209223);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001539_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001539_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e4bf3a94945d3a9d01fc2e646d35ce98d0abcc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001539_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00893:0.256425,(GCF_005280335_PROKKA_00953:0.358169,(GCF_002008305_PROKKA_01905:0.017071,(GCF_003691675_PROKKA_01601:0.0345536,GCF_023573625_PROKKA_01825:5e-09)0.197:5e-09)0.37:0.0769791)1:0.256425);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001540_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001540_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31fe33ffc9a1b5a7ef0956e3da19efd737b1953b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001540_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00892:0.226956,(GCF_005280335_PROKKA_00952:0.125038,(GCF_003691675_PROKKA_01602:0.00424132,(GCF_023573625_PROKKA_01826:0.0269754,GCF_002008305_PROKKA_01906:0.00888235)0.773:0.00905303)1:0.252233)1:0.226956);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001542_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001542_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99297f1f685f704b540e96259581cffc087685f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001542_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01908:0,GCF_003691675_PROKKA_01604:0,GCF_005280335_PROKKA_00950:0,GCF_023573625_PROKKA_01828:0):0.0349436,GCF_020097155_PROKKA_00890:0.0349436);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001543_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001543_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bfa1d991eebd50b61eb2e258b86b63f6e65d8d6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001543_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00889:0,(GCF_005280335_PROKKA_00949:0,(GCF_002008305_PROKKA_01909:0,GCF_003691675_PROKKA_01605:0,GCF_023573625_PROKKA_01829:0):0.0177769):0);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001544_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001544_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4299692b4ca346d4ec2f51e5a428568c16485e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001544_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00888:0.0124847,((GCF_002008305_PROKKA_01910:0,GCF_005280335_PROKKA_00948:0,GCF_023573625_PROKKA_01830:0):5e-09,GCF_003691675_PROKKA_01606:0.012385):0.0124847);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001545_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001545_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef7466e364eb5dad2d369431133c221e55b1e4f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001545_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00884:0.0526024,(GCF_005280335_PROKKA_00943:0.168953,(GCF_002008305_PROKKA_01911:0.0244557,(GCF_003691675_PROKKA_01607:0.00402675,GCF_023573625_PROKKA_01831:0.00385464)0.731:0.00740376)1:0.134835)1:0.0526024);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001546_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001546_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a8d4c41add9171a28af45ac83bfb7f0553a80f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.769:0.00326335,(GCF_005280335_PROKKA_00942:0.0334068,GCF_023573625_PROKKA_01838:0.00745059)0.548:0.00271499)1:0.023034);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001548_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001548_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f4f802ccad0c128740fc8156dfcf1dd5556bc48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001548_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00875:0.160459,(GCF_005280335_PROKKA_00940:0.0731538,(GCF_023573625_PROKKA_01840:0.00222073,(GCF_002008305_PROKKA_01920:5e-09,GCF_003691675_PROKKA_01616:0.00544374)0.885:0.0142604)0.889:0.0361233)1:0.160459);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001550_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001550_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2de71b965e321c8c98681141d32d324c31a87270
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001550_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00872:0.0026526,((GCF_002008305_PROKKA_01923:0,GCF_003691675_PROKKA_01619:0,GCF_023573625_PROKKA_01843:0):0.0282662,GCF_005280335_PROKKA_00937:0.24336):0.0026526);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001552_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001552_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f1d5641e59201f003f33e9f924fd06109ac1406
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001552_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00866:0.00992087,(GCF_005280335_PROKKA_00935:0.20981,(GCF_003691675_PROKKA_01622:0.0113585,(GCF_002008305_PROKKA_01926:5e-09,GCF_023573625_PROKKA_01845:0.00564355)0.754:5e-09)0.662:0.00350033)1:0.00992087);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001557_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001557_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47725f4062e3a57231ff8a16b20d8d22c921c3b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001557_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00861:0.352251,(GCF_005280335_PROKKA_00927:0.158655,(GCF_023573625_PROKKA_01851:0.00412214,(GCF_002008305_PROKKA_01932:0.02087,GCF_003691675_PROKKA_01628:0.00295698)0.84:0.010713)0.991:0.174643)1:0.352251);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001559_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001559_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..76b788f18a868f8c6c292ec9856ead7f50dbab41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001559_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00859:0.1132,(GCF_005280335_PROKKA_00925:0.241094,(GCF_023573625_PROKKA_01853:0.00488619,(GCF_002008305_PROKKA_01934:0.00277969,GCF_003691675_PROKKA_01630:0.00276248)0.777:0.00624597)0.999:0.135219)1:0.1132);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001560_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001560_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b35b52bcd1b3d6fe3acfeec89413911bc9c10785
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.358:0.00171756)1:0.119356)1:0.0749175);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001562_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001562_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f6384c598715a199b30a129a79497df86d40d39
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001562_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00856:0.0922899,(GCF_005280335_PROKKA_00922:0.0428066,((GCF_002008305_PROKKA_01937:0,GCF_023573625_PROKKA_01856:0):0.0120514,GCF_003691675_PROKKA_01633:0.01219):0.0840841):0.0922899);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001563_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001563_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6eb8f558468542411066901dee3a3a2eb255bfca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00540822,GCF_003691675_PROKKA_01634:0.00537842):0.0537362):0.266874);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001565_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001565_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6899c2ded92830d4437879f38b6566164923ac5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001565_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00852:0.0146994,((GCF_003691675_PROKKA_01638:0,GCF_023573625_PROKKA_01861:0):0.00781663,(GCF_002008305_PROKKA_01942:0.0104402,GCF_005280335_PROKKA_00914:0.0230825):0.00299213):0.0146994);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001567_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001567_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4d0b5b277ee16835446f3156fdbaf463f92ef81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.789:5e-09)0.88:0.00498353)1:0.00629716);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001568_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001568_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aac0b69181380225df679e51847bc7de5d8081ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001568_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00847:0.00911944,(GCF_023573625_PROKKA_01866:0.00760072,(GCF_005280335_PROKKA_00911:0.466072,(GCF_002008305_PROKKA_01947:0.0113381,GCF_003691675_PROKKA_01641:0.022233)0.729:0.00362795)0.728:0.0036903)1:0.00911944);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001569_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001569_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66fb7009c98c984bd2f52baf03ac24e0b38a2e37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0149691):0);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001570_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001570_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d3b2b2816595c6fb5570bb50d0d180e9d2b9c59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001570_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01951:1.51696,GCF_020097155_PROKKA_00845:5e-09)0:2.5e-09,(GCF_020097155_PROKKA_00292:1.63256,(GCF_023573625_PROKKA_01872:0.0191164,GCF_005280335_PROKKA_00906:0.0119095)0.463:0.0106857)0:2.5e-09);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001571_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001571_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63467e4e246ecd4212e68a5d969873d7c0f772d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001571_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00439:0.936183,GCF_020097155_PROKKA_00834:0.424046)0.944:0.110952,(GCF_023573625_PROKKA_01889:0.0075977,(GCF_002008305_PROKKA_01963:0.00430501,GCF_005280335_PROKKA_00894:0.0234587)0.569:0.0107445)0.944:0.110952);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001572_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001572_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df68eeb6b6326a5e35fd5f3b29d897c179872734
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.94:0.0158424)0.305:0.00785108)1:0.431785);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001573_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001573_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43341642ceaf0e21a3ddd40dd632a643a96f6b1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001573_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00832:0.167712,(GCF_003691675_PROKKA_01662:5e-09,(GCF_023573625_PROKKA_01894:0.0236553,(GCF_005280335_PROKKA_00891:0.0229202,GCF_002008305_PROKKA_01968:0.0254241)0.612:0.0071641)0.906:0.00760877)1:0.167712);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001576_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001576_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3b9c698e89d0690ffa44b58642148ab9cd32b57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.363:0.0106341)1:0.145812)1:0.192366);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001577_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001577_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1eece93a4ea22a745a5030794762a89bfaf6d81f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00352355):0.0345751):0.16598);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001578_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001578_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f38fd31a1c186c22bed8befbd1fd72300603bae3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.712:0.00574648)0.875:0.106898)1:0.310623);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001580_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001580_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d561aba60c3e237cf86f8635e0f8407af956a89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.973:0.00902247)0.753:0.00177752)1:0.00916695);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001585_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001585_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d858b128e81ac3ed4a245dab7ea5266fa617248
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001585_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00807:0.0124104,((GCF_002008305_PROKKA_01986:0,GCF_005280335_PROKKA_00871:0):5e-09,(GCF_003691675_PROKKA_01680:0.00305158,GCF_023573625_PROKKA_01912:0.00305687):0.00305319):0.0124104);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001586_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001586_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b76126b2a94ebdfce75941213ad2360e0df1f7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001586_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00806:0.0619037,(GCF_005280335_PROKKA_00869:0.0160977,(GCF_023573625_PROKKA_01914:0.00344292,(GCF_002008305_PROKKA_01988:0.006912,GCF_003691675_PROKKA_01682:0.00690785)0.738:5e-09)0.757:0.0154958)1:0.0619037);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001587_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001587_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c33db61b4e61f619402052275ae085dca01e62b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.779:0.0149932)0.998:0.282663)1:0.432367);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001589_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001589_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c189e883fdfd4c9ed4fb04e101dd8fd45d14e316
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.745:0.00179419)0.959:0.0681649)1:0.00848506);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001590_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001590_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c1b96c9b650348001be3d200a0c1b707e287790
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.753:0.00356145)0.933:0.0152502)1:0.00615878);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001591_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001591_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b81c67589243b0bc69ac03ca1adc0f673681cbc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.721:5e-09)0.972:0.0165515)1:0.0131461);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001592_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001592_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa2e3539ff90dc1843db7853f5a11bfca0a3fadd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001592_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00801:0.009759,(GCF_005280335_PROKKA_00863:0.106953,(GCF_003691675_PROKKA_01688:5e-09,(GCF_002008305_PROKKA_01994:0.00787141,GCF_023573625_PROKKA_01920:0.00259126)0.82:0.0026111)0.996:0.0454817)1:0.009759);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001593_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001593_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fe1204e6f5c78b0d7dedd378498d35f58ba3b42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.747:0.00633693)1:0.216666)1:0.0164524);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001594_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001594_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99d66f2b99eb6b60082631723038b35a8bf2805c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001594_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00795:0.228747,(GCF_005280335_PROKKA_00859:0.321123,(GCF_002008305_PROKKA_01998:0.0131897,(GCF_003691675_PROKKA_01692:0.00960341,GCF_023573625_PROKKA_01924:0.0151968)0.561:0.000100259)0.919:0.0535728)1:0.228747);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001596_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001596_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..af0d87811f6d519fdf8b770c8317f2e4e52083dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.12182,GCF_005280335_PROKKA_00857:0.099087):0.229723);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001597_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001597_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b0df1424f14f2c08b7187d705de749264739204
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.621:0.00700393)0.989:0.0485822)1:0.100741);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001598_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001598_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9df482b16b3992737a07857a286035c4928770b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001598_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00775:0.207717,(GCF_005280335_PROKKA_00838:0.071004,(GCF_002008305_PROKKA_02004:5e-09,(GCF_003691675_PROKKA_01714:0.00408356,GCF_023573625_PROKKA_01942:0.00824463)0.689:0.00824961)0.99:0.110008)1:0.207717);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001599_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001599_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0fe2df673f23fb0ca0384650bc7e7e3bce9f52c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001599_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00773:0.568101,(GCF_005280335_PROKKA_00836:0.24233,(GCF_002008305_PROKKA_02006:0.0387745,(GCF_003691675_PROKKA_01716:0.0212873,GCF_023573625_PROKKA_01944:0.0221452)0.801:0.0122104)0.991:0.219775)1:0.568101);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001600_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001600_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc24e4781fb4e4e7eb053cd41a1b7053dc4224a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001600_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00772:0.533691,(GCF_005280335_PROKKA_00835:0.0909539,(GCF_023573625_PROKKA_01945:5e-09,(GCF_002008305_PROKKA_02007:0.0406391,GCF_003691675_PROKKA_01717:0.0131638)0.746:0.00657068)0.988:0.291724)1:0.533691);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001601_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001601_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..314e1c5ab25603f2c1e8723d1ccd45f11776681f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.912:5e-09)0.926:0.0179016)1:0.0115535);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001603_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001603_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc8cba93e65f03bccb3a1e129b766c07d664d478
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.834:0.00360198)0.997:0.0682384)1:0.05807);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001607_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001607_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e4457f7337fcdd6d55e57dd15ead93f9c92709b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.842:0.00369008)0.273:0.0047956)1:0.00481378);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001608_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001608_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f37f362a38d87e1b1a80d1be2c5c578ec347df26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.775:0.00464099)0.391:0.00378446)1:0.00811437);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001609_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001609_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d57e2f52511ae3ae41c759b1eb689f5d388dd487
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.41312,GCF_023573625_PROKKA_01956:0.0245429):0.0152347):2.5e-09);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001610_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001610_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eecc4516df345291cb7c27660bde7e89d103d9ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.843:0.0144764,(GCF_005280335_PROKKA_00802:0.453848,GCF_023573625_PROKKA_01957:0.0167494)0.567:0.0201204)1:0.0185899);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001611_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001611_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a24047e8e0bf715eb0d9d98996473e57df446405
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001611_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00759:0.00340125,(GCF_005280335_PROKKA_00798:0.0852773,(GCF_002008305_PROKKA_02021:5e-09,(GCF_003691675_PROKKA_01730:0.0066719,GCF_023573625_PROKKA_01958:0.0136659)0.764:0.00685394)0.759:5e-09)1:0.00340125);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001613_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001613_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2d7b56be7a6153c31a8a75f3b5c8c2376f834c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.34:0.00139252)0.903:0.00809137)1:0.0525974);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001615_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001615_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4486005a672cdbd2888186d0b98088bf31c39e11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001615_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00756:0.461984,(GCF_005280335_PROKKA_00794:0.39683,(GCF_023573625_PROKKA_01962:0.0142124,(GCF_002008305_PROKKA_02025:0.0182323,GCF_003691675_PROKKA_01734:0.0170032)0.754:0.0115437)0.979:0.261382)1:0.461984);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001616_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001616_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..860059b49f978411e5d3fa4d39cd8a727ecb2f6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001616_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00754:0.00989769,(GCF_005280335_PROKKA_00793:0.236974,(GCF_002008305_PROKKA_02026:0.0135662,(GCF_003691675_PROKKA_01735:0,GCF_023573625_PROKKA_01963:0):0.00659026):0.0513393):0.00989769);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001617_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001617_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69cce75dd1d2103a6a2fdc6c10afc9bfd4d2f97a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001617_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00753:0.011127,(GCF_005280335_PROKKA_00792:0.0203729,(GCF_002008305_PROKKA_02027:5e-09,(GCF_023573625_PROKKA_01964:0.0022426,GCF_003691675_PROKKA_01736:0.00223565)0.817:0.00223575)0.874:0.00512861)1:0.011127);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001620_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001620_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f5ce5a4901f0c04082e5c5806065a9a662641c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001620_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00749:0.00290921,((GCF_002008305_PROKKA_02034:5e-09,GCF_003691675_PROKKA_01741:5e-09)0.906:0.00578743,(GCF_005280335_PROKKA_00783:0.0429694,GCF_023573625_PROKKA_01969:0.00412643)0.748:0.0026915)1:0.00290921);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001621_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001621_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a72ba0f14c06125ae4c8018f477adc3343084c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001621_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00748:0.00855579,(GCF_005280335_PROKKA_00781:0.0107308,((GCF_002008305_PROKKA_02035:0,GCF_003691675_PROKKA_01742:0):0.00818759,GCF_023573625_PROKKA_01970:0.0123048):0.0176665):0.00855579);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001622_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001622_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..181a41a1f861e512fedff1a5b1418f387b64530d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001622_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00747:0.00483905,((GCF_003691675_PROKKA_01743:0,GCF_023573625_PROKKA_01971:0):0.0112772,(GCF_002008305_PROKKA_02036:0.00986959,GCF_005280335_PROKKA_00780:0.140549):0.00868505):0.00483905);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001624_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001624_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2039203de5e4f86bb3705f99182c4052313c559d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001624_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00735:0.0251802,GCF_020097155_PROKKA_00741:0.78908)0.695:0.002324,(GCF_003691675_PROKKA_01751:0.0110803,(GCF_002008305_PROKKA_02045:0.00631454,GCF_023573625_PROKKA_01979:0.0210076)0.823:0.00781843)0.695:0.002324);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001629_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001629_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf1abea8d27d6015f91183534cda120a4ac39d8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001629_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00727:0.0792879,(GCF_005280335_PROKKA_00763:0.109032,(GCF_002008305_PROKKA_02057:0.00850281,(GCF_023573625_PROKKA_01991:0.0217679,GCF_003691675_PROKKA_01763:0.0110875)0.399:0.00663856)0.998:0.100098)1:0.0792879);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001631_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001631_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c237875054a5d608261a337f3f46921e0248097
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001631_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00487:0.16799,(GCF_005280335_PROKKA_00559:0.10586,(GCF_005280335_PROKKA_00742:0.101279,(GCF_002008305_PROKKA_02071:0.00479683,GCF_023573625_PROKKA_01999:0.00347983)0.999:0.100728)0.585:0.0551715)1:0.16799);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001633_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001633_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e08cfce179f8384ce838665f97794d44c7752635
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001633_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00613:0.00498257,((GCF_002008305_PROKKA_02081:0,GCF_023573625_PROKKA_02019:0):0.00495448,(GCF_005280335_PROKKA_00703:0.00993926,GCF_003691675_PROKKA_01785:5e-09):5e-09):0.00498257);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001634_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001634_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aecfaaf4a2599b19f4535d1f42f003ca8d6604b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001634_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00611:0.00889803,((GCF_002008305_PROKKA_02082:0,GCF_003691675_PROKKA_01787:0):5e-09,(GCF_005280335_PROKKA_00701:0.0178518,GCF_023573625_PROKKA_02021:5e-09):0.00590013):0.00889803);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001635_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001635_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d32a73574c05119ef5f25000d51e4edbf611aeb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001635_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00610:0.00642428,(GCF_005280335_PROKKA_00700:0.012618,((GCF_002008305_PROKKA_02083:0,GCF_003691675_PROKKA_01788:0):5e-09,GCF_023573625_PROKKA_02022:0.00630514):0.0192367):0.00642428);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001638_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001638_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ef9190aeb5d29b1ace7202b6a9cb2a9d8ecdeaf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001638_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00607:0.00340803,(GCF_005280335_PROKKA_00697:0.00450474,((GCF_002008305_PROKKA_02086:0,GCF_003691675_PROKKA_01791:0):0.0022582,GCF_023573625_PROKKA_02025:0.00450895):0.00681377):0.00340803);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001639_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001639_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3611805b61fc4077ef609c1fc4231fe3682a6a46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00242715,GCF_005280335_PROKKA_00696:0.0130723):0.0044182):0.0031992);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001642_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001642_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16c2b9d233553432732e0c7aaaeca6e2db9cfddb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001642_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00598:0.0102736,(GCF_005280335_PROKKA_00683:0.0430619,(GCF_002008305_PROKKA_02095:0.0328076,(GCF_003691675_PROKKA_01803:0.0342552,GCF_023573625_PROKKA_02034:0.0460647)0.227:0.0055941)0.576:0.00587213)1:0.0102736);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001644_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001644_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..799d8a87121f18cd6c1070dcdbba570f5d3c3108
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_023573625_PROKKA_02042:0.00890499):0.476136):0.49996);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001647_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001647_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bde4ab53f7d4afc4e05fa0916deec8052f2a5d0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00139466,GCF_023573625_PROKKA_02045:0.00217604):0.0670327):0.154457);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001648_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001648_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0398a9609c9c0ab6b5db7b06a23950bc7ee7e30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001648_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00589:0.13655,(GCF_005280335_PROKKA_00673:0.0484408,(GCF_023573625_PROKKA_02046:0.00307474,(GCF_002008305_PROKKA_02106:0.00322772,GCF_003691675_PROKKA_01813:5e-09)0.758:0.00356868)0.999:0.104728)1:0.13655);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001649_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001649_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..571114a101f441d674d42b3bc04f8a609f8d178e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.00267476,GCF_023573625_PROKKA_02047:5e-09):0.0545039):0.321309);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001650_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001650_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..471dd2a4e03f48a43cafe57785a66cefaef90333
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.45:0.0049039)0.808:0.0200568)1:0.175237);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001658_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001658_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50d169d6b22207350a7a0a8c809771695a19e861
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001658_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00577:0.120162,((GCF_002008305_PROKKA_02120:0,GCF_003691675_PROKKA_01828:0,GCF_023573625_PROKKA_02058:0):0.0668224,GCF_005280335_PROKKA_00660:0.150063):0.120162);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001661_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001661_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77cd218185aad1f81bfea4313f552a49b88c8d9f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001661_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00572:0.00983387,(GCF_005280335_PROKKA_00655:0.10814,(GCF_003691675_PROKKA_01833:0.00951477,(GCF_002008305_PROKKA_02125:0.0378289,GCF_023573625_PROKKA_02063:0.00931741)0.893:5e-09)0.757:0.0185973)1:0.00983387);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001663_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001663_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e99593923242829a1add83da323d3433dbab254f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.965:0.0179826,(GCF_003691675_PROKKA_01835:0.0107767,GCF_005280335_PROKKA_00653:0.0266426)0.453:0.00351498)1:0.0170439);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001665_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001665_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2df949afe0e9c44fc310a825a176eacb1499213f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.793:0.00198084)0.77:0.00196844)1:0.00296408);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001668_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001668_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..599380f5238f8361ccf4ec1b6b7058a23349f355
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001668_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00564:0.00917263,(GCF_005280335_PROKKA_00648:0.0258389,((GCF_002008305_PROKKA_02132:0,GCF_023573625_PROKKA_02070:0):0.0127265,GCF_003691675_PROKKA_01840:0.00927034):0.0164556):0.00917263);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001670_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001670_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..002615c6e637b90faf26462f86c07d74a6ccbd37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001670_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00561:0.191151,(GCF_005280335_PROKKA_00638:0.0379881,(GCF_002008305_PROKKA_02134:0.0200172,(GCF_003691675_PROKKA_01842:0.00382054,GCF_023573625_PROKKA_02072:0.00383231)0.977:0.0320643)0.982:0.0671238)1:0.191151);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001674_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001674_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3aa118443444606834f9ef7bdf5a0c3d03925cf5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001674_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00557:0.136046,((GCF_002008305_PROKKA_02139:0,GCF_003691675_PROKKA_01847:0,GCF_023573625_PROKKA_02077:0):0.0849337,GCF_005280335_PROKKA_00633:0.0944563):0.136046);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001675_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001675_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7da24ed7cbedcea4c3f635a23ff1da2082c79a65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09,GCF_023573625_PROKKA_02078:0.00699099):0.0713705):0.149694);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001679_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001679_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f00abc39673d74d19414caa3af099a4e04d2c81e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001679_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00551:0.0150161,((GCF_003691675_PROKKA_01852:0.00490061,GCF_023573625_PROKKA_02082:0.000615738)1:0.0994,(GCF_002008305_PROKKA_02145:0.0377263,GCF_005280335_PROKKA_00627:0.0344222)1:0.0814167)1:0.0150161);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001680_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001680_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66f06fefb292e335cbb20edadbb90aa93b154771
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001680_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00550:0.0744693,(GCF_002008305_PROKKA_02146:0.329947,((GCF_003691675_PROKKA_01853:0,GCF_023573625_PROKKA_02083:0):0.0718568,GCF_005280335_PROKKA_00626:1.00096):0.176511):0.0744693);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001683_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001683_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16b9bb655c87767d509cd895e2b2aa452d8306a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.98:0.011901)0.994:0.0887066)1:0.214259);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001684_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001684_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e70dca9ad032ec5cdb04b2284421315fd5d211b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001684_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00536:0.172816,(GCF_005280335_PROKKA_00612:0.0818839,((GCF_002008305_PROKKA_02150:0,GCF_003691675_PROKKA_01863:0):0.0161366,GCF_023573625_PROKKA_02093:0.00447407):0.0503299):0.172816);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001686_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001686_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c5b9070808bd6d636c026057baf8ada1cab5730
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.744:0.00233229)1:0.184287)1:0.0381437);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001690_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001690_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b12773e81351b1805281ac73a22dabf28f848e11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.882:0.00943068)0.999:0.149047)1:0.14051);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001691_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001691_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54d28a7cf5e166a80f1502070f0a4b1c0afa7d48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001691_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00519:0.423917,(GCF_005280335_PROKKA_00596:0.385768,((GCF_002008305_PROKKA_02161:0,GCF_023573625_PROKKA_02105:0):5e-09,GCF_003691675_PROKKA_01874:0.0219793):0.125767):0.423917);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001693_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001693_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81dc019d3d04c4dcb165fe3d015b6df24aee4f61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001693_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00516:0.202699,(GCF_005280335_PROKKA_00593:0.158089,(GCF_002008305_PROKKA_02164:0.0290591,(GCF_003691675_PROKKA_01878:0,GCF_023573625_PROKKA_02109:0):0.0189405):0.174881):0.202699);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001694_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001694_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0067c2734931ce8e1e5a141279d3156f05134415
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001694_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00512:0.0784919,(GCF_005280335_PROKKA_00585:0.0586368,(GCF_023573625_PROKKA_02112:0.0308832,(GCF_002008305_PROKKA_02167:0.00421767,GCF_003691675_PROKKA_01881:0.011271)0.205:0.00482563)0.997:0.0413508)1:0.0784919);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001698_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001698_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b3f5d9b98716be4ef69ba8ffe2a8d6d75731067
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.491:5e-09)1:0.121589)1:0.0613411);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001700_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001700_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f04b44e31383b3b5295a3c8222c5e4c8b1d8ad34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.895:0.021478)1:0.155009)1:0.0909285);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001702_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001702_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27bc65671cee8b9fd3ec86b21cfeb2736aa935bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.815:0.0087089)0.975:0.0393025)1:0.138397);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001703_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001703_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8fdc5529535c0bf47d3cbc8bd7ed29750d8a4935
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.472:0.0118453)0.963:0.0932218)1:0.217705);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001704_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001704_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd40a064af3df183ebb42aa101f64d2e4e65432c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001704_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00496:0.140615,(GCF_005280335_PROKKA_00569:0.110787,(GCF_003691675_PROKKA_01895:5e-09,(GCF_002008305_PROKKA_02181:0.00783563,GCF_023573625_PROKKA_02126:0.0077617)0.422:0.00779473)0.922:0.0514654)1:0.140615);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001705_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001705_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84a105332cc9dc1aaed5212d2649a7cdda612740
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001705_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00495:0.0729596,(GCF_005280335_PROKKA_00568:0.29918,(GCF_003691675_PROKKA_01896:0.0034419,(GCF_002008305_PROKKA_02182:0.0176202,GCF_023573625_PROKKA_02127:0.0109388)0.734:0.0119182)1:0.233759)1:0.0729596);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001707_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001707_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c6c253b3663e9aaba87d35a18e08d9d9c65c907
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.006435,GCF_023573625_PROKKA_02130:5e-09):0.219122):0.267517);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001708_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001708_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..082e2e7706933a3632a5e589b35d71fd5b2c290b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.888:0.0140809)0.972:0.0719268)1:0.133851);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001712_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001712_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..751427ed13390b7e0fde145e7ce6bc4757eccc4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001712_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00478:0.254845,(GCF_005280335_PROKKA_00549:0.00864649,(GCF_023573625_PROKKA_02139:0.000623869,(GCF_002008305_PROKKA_02195:0.00480934,GCF_003691675_PROKKA_01908:0.00366747)0.953:0.00669565)0.92:0.0159165)1:0.254845);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001713_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001713_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca929d3a15e2edc59bc36807c483870a524e1a7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001713_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00479:0.38788,((GCF_002008305_PROKKA_02196:0,GCF_023573625_PROKKA_02140:0):0.00201738,(GCF_003691675_PROKKA_01909:0.019216,GCF_005280335_PROKKA_00548:0.0308315):0.00926621):0.38788);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001714_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001714_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8757f93a06d3ae61c9e82bfab66c38de269c93db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001714_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00480:0.437123,((GCF_002008305_PROKKA_02197:0,GCF_003691675_PROKKA_01910:0,GCF_023573625_PROKKA_02141:0):5e-09,GCF_005280335_PROKKA_00547:0.0397178):0.437123);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001715_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001715_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84f9f4145f8165f6db17eecb7d4af9aeec0ff78d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001715_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00481:0.188911,(GCF_005280335_PROKKA_00545:0.210805,(GCF_023573625_PROKKA_02142:0.00787981,(GCF_002008305_PROKKA_02198:5e-09,GCF_003691675_PROKKA_01911:0.00786958)0.89:5e-09)0.958:0.0991709)1:0.188911);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001716_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001716_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b2557f838b385ca2a436a8a8ad368afb28d0d07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.212896,GCF_005280335_PROKKA_00542:0.0635682):0.611508);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001718_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001718_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f37d8c15d1a69c710ab0f5792ede4513e0afa5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001718_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00472:0.121805,((GCF_002008305_PROKKA_02202:0,GCF_003691675_PROKKA_01915:0,GCF_023573625_PROKKA_02146:0):0.0599344,GCF_005280335_PROKKA_00541:0.14819):0.121805);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001719_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001719_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..83610b20fbf50efbbac36fb4a6a964d9a7a6021a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001719_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00469:0.248911,((GCF_002008305_PROKKA_02206:0,GCF_003691675_PROKKA_01919:0,GCF_023573625_PROKKA_02150:0):0.109088,GCF_005280335_PROKKA_00539:0.103845):0.248911);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001720_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001720_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b600d6d710c1cc4f82311d8492156c770f0646a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0181684):0.0524191):0.144715);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001723_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001723_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6cc410f1cfb099b8e0573607c7f6444b429c4ff1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.85:0.011698)1:0.316338)1:0.0643187);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001724_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001724_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cdd63faa1cc28f7c46e30827057691dda7b07705
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001724_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00442:0.00276939,((GCF_002008305_PROKKA_02239:0.0111266,GCF_023573625_PROKKA_02171:0.00553289)0.761:0.00184643,(GCF_003691675_PROKKA_01941:0.00369214,GCF_005280335_PROKKA_00506:0.0681571)0.885:6e-09)1:0.00276939);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001729_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001729_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e8417407fbd2714b09a2f4dd4ea9c277c181056
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001729_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00437:0.0090704,(GCF_002008305_PROKKA_02247:6e-09,((GCF_003691675_PROKKA_01949:0.0327525,GCF_005280335_PROKKA_00499:0.150596)0.962:0.0222391,GCF_023573625_PROKKA_02179:0.00586401)0.517:0.00398956)1:0.0090704);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001730_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001730_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a43d0c18c9c4ced85c412b441f881cbf590129c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001730_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00432:0.0400424,(GCF_002008305_PROKKA_02254:0.00149959,(GCF_005280335_PROKKA_00477:0.024235,(GCF_003691675_PROKKA_01954:0.0158877,GCF_023573625_PROKKA_02185:0.00397854)0.828:5e-09)0.72:0.0025005)1:0.0400424);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001732_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001732_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8086972d8fccae2278108509c25bca70b93bb0d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001732_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00430:0.0129981,((GCF_002008305_PROKKA_02256:0,GCF_003691675_PROKKA_01956:0,GCF_023573625_PROKKA_02187:0):0.00967445,GCF_005280335_PROKKA_00475:0.0264426):0.0129981);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001733_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001733_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80e06bb3c77f495bbbbeac9a7c02de21d360013b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001733_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00429:0.0200618,((GCF_002008305_PROKKA_02257:0,GCF_003691675_PROKKA_01957:0,GCF_023573625_PROKKA_02188:0):0.0102215,GCF_005280335_PROKKA_00474:0.0317468):0.0200618);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001735_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001735_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f769ba1e0a9670165a3a0cd05b4c7f0d1b9e6abe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001735_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00494:0.150339,(GCF_005280335_PROKKA_00461:0.00662733,(GCF_023573625_PROKKA_02202:6e-09,(GCF_002008305_PROKKA_02270:0.00765032,GCF_003691675_PROKKA_01963:0.00190308)0.271:0.00190737)0.922:0.0106221)1:0.150339);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001738_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001738_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4882d2c673fab98ccdd4f985ae64dafe195422ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0:5e-09)0.756:0.00692559)1:0.104153);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001739_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001739_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..901ddaa1d4b12a452883a7a42799a7a5ec5d16c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.853:0.00552156)0.95:0.0238265)1:0.082108);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001740_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001740_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5650c251c1ea99afcc3bde5136768f322684984d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001740_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00401:0.079864,(GCF_005280335_PROKKA_00449:0.0416908,(GCF_002008305_PROKKA_02289:0.00622818,(GCF_003691675_PROKKA_01981:0,GCF_023573625_PROKKA_02229:0):5e-09):0.024615):0.079864);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001744_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001744_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7381360ad07f3961ab52232b7ad490aee3ee0ed3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001744_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00396:0.14034,(GCF_005280335_PROKKA_00443:0.0444307,(GCF_002008305_PROKKA_02293:0.0115184,(GCF_003691675_PROKKA_01986:0.00602334,GCF_023573625_PROKKA_02234:5e-09)0.588:0.000556321)0.979:0.0476111)1:0.14034);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001748_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001748_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78f9adfc124f74711ba72c0e53bccaa1fcec9af2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001748_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00390:0.0586942,(GCF_005280335_PROKKA_00437:0.0375652,(GCF_003691675_PROKKA_01992:0.0105126,(GCF_002008305_PROKKA_02299:0.00208822,GCF_023573625_PROKKA_02240:5e-09)0.902:5e-09)0.992:0.0369371)1:0.0586942);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001752_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001752_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..73006508b5d08f2adfa0bbcaa5a8576f215e3ec8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001752_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00383:0.0608184,(GCF_005280335_PROKKA_00430:0.0287768,(GCF_003691675_PROKKA_01999:0.00929069,(GCF_002008305_PROKKA_02306:0.00928589,GCF_023573625_PROKKA_02247:6e-09)0.747:0.00308033)0.966:0.036198)1:0.0608184);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001753_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001753_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..468b416d28479d342624358b72c80bd9675beaff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.814:0.00422773)0.924:0.0348261)1:0.130709);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001754_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001754_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c4e46dea0e6409140787ae0872fcba3ff4d55e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001754_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00381:0.111193,(GCF_005280335_PROKKA_00428:0.0830991,(GCF_023573625_PROKKA_02249:0.00484398,(GCF_002008305_PROKKA_02308:0.00493002,GCF_003691675_PROKKA_02001:0.0098709)0.77:0.00503932)0.992:0.0999468)1:0.111193);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001758_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001758_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff25e0c46c6f7b4a583f15a8cb34bd6846e46f75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0220324,GCF_005280335_PROKKA_00424:0.0217087):0.0107115);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001763_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001763_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..36ae1b34f44087623bffd1f6e8ac4638841ae933
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001763_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00538:0.0367762,(GCF_005280335_PROKKA_00614:0.0482035,((GCF_003691675_PROKKA_01860:0,GCF_023573625_PROKKA_02090:0):0.162128,GCF_005280335_PROKKA_02660:0.406327):0.130634):0.0367762);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001766_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001766_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..892a20e3026ff374ecf5dbc7f6d11550cdc1d256
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001766_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00455:0.0370052,(GCF_005280335_PROKKA_00514:0.124229,((GCF_003691675_PROKKA_02211:0,GCF_023573625_PROKKA_00218:0):0.0215002,GCF_005280335_PROKKA_00528:1.18129):0.198478):0.0370052);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001767_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001767_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c8d1f18708c7971182326fc3b91d237f7b9b1501
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001767_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_01863:0.525036,GCF_020097155_PROKKA_01752:0.197757)0.993:0.366972,(GCF_020097155_PROKKA_01765:0.412877,(GCF_005280335_PROKKA_00149:0.869659,GCF_020097155_PROKKA_01759:0.222491)0.933:0.317597)0.993:0.366972);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001768_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001768_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49454e1986c60e73c519b25dacaddf9f50408917
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001768_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00388:0.00223321,(GCF_020097155_PROKKA_00656:0.00342505,(GCF_020097155_PROKKA_01831:0.101037,(GCF_020097155_PROKKA_00330:0.236543,GCF_020097155_PROKKA_01209:0.136666)1:1.23393)0.623:5e-09)1:0.00223321);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001770_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001770_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c9db5e661823328557c0225ab543fbf81c60af2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001770_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00384:0.141765,((GCF_002008305_PROKKA_00012:0,GCF_003691675_PROKKA_02030:0):0.00803238,GCF_023573625_PROKKA_00012:0.0325095):0.141765);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001772_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001772_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..17b596d444a8a292edc77300e739b4353f9b536a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001772_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00296:0.090183,(GCF_002008305_PROKKA_00048:0.0122886,(GCF_003691675_PROKKA_02061:5e-09,GCF_023573625_PROKKA_00043:0.00200482)0.45:5e-09)1:0.090183);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001773_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001773_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f3158c2700b2244906fe530b26075119fcd776c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.74:0.00846763)1:0.089077);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001774_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001774_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b5bf0cb0ef5c78e84226596dd44a6e0abbabffa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.761:5e-09)1:0.0540747);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001775_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001775_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3892d393ab0395437b2818d094db3a6e7a1c2874
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001775_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00336:0.214285,(GCF_002008305_PROKKA_00059:5e-09,(GCF_003691675_PROKKA_02072:0.0107047,GCF_023573625_PROKKA_00054:0.0162644)0.762:0.00537379)1:0.214285);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001776_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001776_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de944aa39f1d7695734a35c340b0c07498d06cb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001776_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00261:0.514961,(GCF_003691675_PROKKA_02086:0.0528263,(GCF_002008305_PROKKA_00073:0.0224324,GCF_023573625_PROKKA_00067:0.0217804)0.614:5e-09)1:0.514961);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001777_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001777_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d06f6a517e1cab19a2a9df3bfad511008ce03ffb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001777_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00309:0.121799,(GCF_002008305_PROKKA_00083:0.00699661,(GCF_003691675_PROKKA_02096:0.00644556,GCF_023573625_PROKKA_00077:0.0322255)0.773:0.00526)1:0.121799);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001778_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001778_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7343ad674f75a44f4c000e8b8539136d4e184b59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001778_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00306:0.0427416,(GCF_002008305_PROKKA_00085:0.00430756,(GCF_003691675_PROKKA_02098:0.00663099,GCF_023573625_PROKKA_00080:0.0167271)0.752:0.00182262)1:0.0427416);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001783_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001783_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aac5c766a41e2f5c34f4326385b524db96b84f41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001783_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00230:0.140658,(GCF_003691675_PROKKA_02167:0.0020765,(GCF_002008305_PROKKA_00153:0.00251885,GCF_023573625_PROKKA_00161:0.00827757)0.747:0.00601751)1:0.140658);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001786_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001786_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b08602b35a7d9a898bbd7a43b4e3aaff8fbba80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001786_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00194:0.141943,((GCF_002008305_PROKKA_00199:0,GCF_023573625_PROKKA_00202:0):0.0321838,GCF_003691675_PROKKA_02195:0.00604122):0.141943);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001787_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001787_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68d20be7c9c57b9e48866b2d21ce51934fa9ba17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001787_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00125:1.4766,GCF_020097155_PROKKA_00145:0.168787)0.919:0.0755741,(GCF_002008305_PROKKA_00200:0.27748,GCF_005280335_PROKKA_00189:0.240166)0.919:0.0755741);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001788_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001788_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8da323efd30a42bb26437d1119a087bd541a85c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001788_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00205:0.129275,(GCF_002008305_PROKKA_00201:0.0048483,(GCF_003691675_PROKKA_02196:0.0154785,GCF_023573625_PROKKA_00203:0.0196201)0.785:0.00432328)1:0.129275);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001790_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001790_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3469a340ba3e580d17032e325fc4de64c445e3b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.905:0.00958576)1:0.0808036);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001792_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001792_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21ac92ddb34ba58fffad4408db6fd2ab6f0392c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001792_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00127:0.0221305,(GCF_002008305_PROKKA_00243:0.012867,(GCF_003691675_PROKKA_02255:0.010497,GCF_023573625_PROKKA_00243:0.00555825)0.888:0.0121893)1:0.0221305);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001793_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001793_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2509f14eb0e8a00757dff60a736a61a337f50694
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.852:0.00728319)1:0.0990267);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001797_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001797_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e9f433c41a2dbb4ae1485e0189276ba5ed87f643
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001797_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00083:0.119122,(GCF_002008305_PROKKA_00273:0.000896394,(GCF_003691675_PROKKA_02288:0,GCF_023573625_PROKKA_00271:0):0.00186615):0.119122);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001798_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001798_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..709692b67524aafc6c5f83de28cf58c1db9c910e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)1:0.0420036)1:0.224631);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001801_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001801_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a94125cacb330f664426651023cddc4e99a28ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001801_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00052:0.144874,(GCF_002008305_PROKKA_00302:0.0271037,(GCF_003691675_PROKKA_00010:0.00487166,GCF_023573625_PROKKA_00309:0.012239)0.938:0.0215386)1:0.144874);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001805_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001805_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0254a97ce4e8188332c9943f40563d942e5aaea0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001805_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02624:0.0582522,(GCF_023573625_PROKKA_00352:0.00979276,(GCF_002008305_PROKKA_00345:5e-09,GCF_003691675_PROKKA_00061:0.00154)0.988:0.0191623)1:0.0582522);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001810_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001810_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92e9f856ad6ff983c9e922eddbb35ee11a681b5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001810_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02526:0.15968,(GCF_023573625_PROKKA_00434:0.0047656,(GCF_003691675_PROKKA_00152:5e-09,GCF_002008305_PROKKA_00431:0.0247376)0.67:0.00506639)1:0.15968);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001811_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001811_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac32348bc547b62588422074955211f647b0102b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001811_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02368:0.223469,(GCF_002008305_PROKKA_00463:5e-09,(GCF_003691675_PROKKA_00181:0.0060724,GCF_023573625_PROKKA_00463:0.00301061)0.478:0.0030353)1:0.223469);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001814_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001814_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7a96c9fa38b9b4567daab020edb26d3635e98f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001814_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02309:0.0958525,(GCF_005280335_PROKKA_02426:0.198887,(GCF_002008305_PROKKA_00523:0.00727704,GCF_023573625_PROKKA_00523:0.00590729)0.998:0.172824)1:0.0958525);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001815_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001815_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54a03b5c1722243c13fb9348a87151941b51625b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):5e-09):0.0831457);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001818_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001818_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd0fba831396530a93320eb06c185732047b1a35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001818_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02356:0.00193103,((GCF_002008305_PROKKA_00577:0,GCF_003691675_PROKKA_00309:0):5e-09,GCF_023573625_PROKKA_00578:0.00193056):0.00193103);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001820_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001820_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84f9c89e04a95c02c94a732900f6491d529af2ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001820_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02352:0.134223,(GCF_023573625_PROKKA_00582:0.0264608,(GCF_002008305_PROKKA_00581:0.0447347,GCF_003691675_PROKKA_00314:0.023511)0.781:0.0246309)1:0.134223);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001823_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001823_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a9a48516338d60cc8756ae95307d0a0262c5fd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001823_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02201:2.5e-09,(GCF_002008305_PROKKA_00628:0.00385745,(GCF_005280335_PROKKA_00400:0.00583169,GCF_023573625_PROKKA_00603:0.00578527)0.217:5e-09)1:2.5e-09);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001824_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001824_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f52a8d1a131b24866e4c1ca9639c20d1dc05f948
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.776:5e-09)1:0.001717);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001827_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001827_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f2bccf8c604bd361c03cde871599b903a340a68
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.74:0.00349096)1:0.0107889);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001828_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001828_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae9dafe8c255835315b309443e804243f4ba36ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001828_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02185:0.00962543,(GCF_003691675_PROKKA_00377:0.0095949,(GCF_002008305_PROKKA_00640:0.270214,GCF_023573625_PROKKA_00609:0.0250641)0.668:0.00463975)1:0.00962543);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001829_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001829_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f11d1b29e0145dc50519f922e6f1d8947d3b93ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.856:0.00487328)1:0.139748);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001831_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001831_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea97ea572263613361537c7f146b5149acde26bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001831_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02297:0.0167991,(GCF_002008305_PROKKA_00665:0.0101748,(GCF_003691675_PROKKA_00402:0,GCF_023573625_PROKKA_00635:0):0.00248688):0.0167991);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001833_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001833_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e53697d09edabbfff9cdb1e597a2d4f71351cb9f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001833_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02295:0.0648245,(GCF_002008305_PROKKA_00667:0.0168777,(GCF_003691675_PROKKA_00404:0.00663332,GCF_023573625_PROKKA_00637:0.00995014)0.805:0.00645951)1:0.0648245);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001834_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001834_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc3d78ceb7c778e4c7e887831a86b272348cff50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.773:5e-09)1:0.181693);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001836_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001836_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1d9088f6841654f22f86a230cb912519e05aad7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.867:0.0247515)1:0.19984);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001837_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001837_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..729ffad25ee605bf622d792faf48b353af13f507
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001837_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02037:0.233582,((GCF_002008305_PROKKA_00787:0,GCF_003691675_PROKKA_00518:0):0.0291857,GCF_023573625_PROKKA_00754:0.0183241):0.233582);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001838_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001838_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..882e309769b1020909911297923de659114146a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.844:0.0208704)1:0.223001);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001839_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001839_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3fc1ccee367a587ec803a926958fbec4bd90b478
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001839_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01971:0.121472,(GCF_023573625_PROKKA_00817:0.00401878,(GCF_003691675_PROKKA_00580:0.00973442,GCF_002008305_PROKKA_00858:0.00560125)0.393:5e-09)1:0.121472);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001841_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001841_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..35a682940d1dbae3b1f184836d9dbaf53ab9a4a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001841_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01881:0.23727,(GCF_003691675_PROKKA_00671:5e-09,(GCF_002008305_PROKKA_00958:0.0017939,GCF_023573625_PROKKA_00904:0.0162467)0.709:0.00360715)1:0.23727);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001842_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001842_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d85b0b6734a5b9614fadc4256b3172614f42f15d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001842_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01840:0.26274,(GCF_003691675_PROKKA_00710:6e-09,(GCF_002008305_PROKKA_00996:0.00620343,GCF_023573625_PROKKA_00939:0.0124894)0.84:0.00614622)1:0.26274);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001846_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001846_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..092dd4245eb7df7a821ed5ebff6e038c43592d94
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.845:0.00458123)1:0.105009);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001851_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001851_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..83b2da90c34237b415c2ffbd26c5510bc59ae41c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.996:0.0120832)1:0.0442941);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001852_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001852_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5fc55fa21e38fe0926c20aa7444695686f7adbe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0451574):0.238171);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001853_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001853_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9db405737d20481307fb0b4be6a585dddd57af23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001853_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01155:0,GCF_003691675_PROKKA_00874:0,GCF_023573625_PROKKA_01105:0):0.261638,GCF_005280335_PROKKA_01734:0.261638);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001855_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001855_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2228d68b6df396967bec5c01d35a536bf370b9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.746:0.00329945)1:0.105462);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001858_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001858_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..550582dfa6c663d08a3f47467dc0eaf483805f6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001858_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00710:0.0844762,((GCF_002008305_PROKKA_01290:0,GCF_003691675_PROKKA_01009:0):0.0172337,GCF_023573625_PROKKA_01248:5e-09):0.0844762);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001859_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001859_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca6e4d427aaff6baa2d05b75d2092f896ceb2f3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001859_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01482:0.278687,((GCF_002008305_PROKKA_01306:0,GCF_003691675_PROKKA_01029:0):5e-09,GCF_023573625_PROKKA_01264:0.0144057):0.278687);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001861_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001861_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e906dc1804055e51357ac150e2078e59cc87694f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001861_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01431:0.111004,((GCF_002008305_PROKKA_01357:0,GCF_023573625_PROKKA_01312:0):0.00598297,GCF_003691675_PROKKA_01077:0.00504743):0.111004);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001862_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001862_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5a7414fb50cd8d5e9499676bc7dfab0feff0e817
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001862_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01893:0.266579,((GCF_002008305_PROKKA_01382:0,GCF_023573625_PROKKA_01337:0):0.00860321,GCF_003691675_PROKKA_01102:0.0144755):0.266579);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001864_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001864_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d1153164b835a464cb3cf3085edd5ddc952e848
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001864_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01397:0.0770026,(GCF_023573625_PROKKA_01359:0.0018269,(GCF_002008305_PROKKA_01409:0.0150234,GCF_003691675_PROKKA_01139:0.00412576)0.529:0.00248819)1:0.0770026);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001865_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001865_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6dbf3253e14d9ca1dbad9595e029e5fefded2c33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.703:0.00763499)1:0.308018);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001869_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001869_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..423dc09a8c338cb1e125d1e1c3b294b891edc2f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001869_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01350:0.0321738,(GCF_003691675_PROKKA_01185:6e-09,(GCF_002008305_PROKKA_01453:0.00750575,GCF_023573625_PROKKA_01403:5e-09)0.667:0.00751388)1:0.0321738);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001874_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001874_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..913d5b67155292d005ebc87ed160eb3f608a99e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001874_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01411:0.0393985,((GCF_002008305_PROKKA_01514:0,GCF_003691675_PROKKA_01223:0):0.00292785,GCF_023573625_PROKKA_01441:0.0058193):0.0393985);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001875_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001875_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fb2f210791a6b5acafe4e13c81000db3bab9da6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001875_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01339:0.00446455,(GCF_023573625_PROKKA_01510:0.00296768,(GCF_002008305_PROKKA_01583:0.00295422,GCF_003691675_PROKKA_01294:0.0240688)0.779:0.00299202)1:0.00446455);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001876_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001876_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..268d67cf935bc5ec0635054ad0a56b0c2ffb860f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001876_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01586:0,GCF_003691675_PROKKA_01297:0,GCF_023573625_PROKKA_01513:0):0.0072449,GCF_005280335_PROKKA_01336:0.0072449);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001877_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001877_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03a11941189e019930610c645bfe8e259914d884
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001877_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01334:0.0122582,((GCF_002008305_PROKKA_01588:0,GCF_023573625_PROKKA_01515:0):0.0020435,GCF_003691675_PROKKA_01299:0.0019815):0.0122582);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001878_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001878_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..084fe72db2ea549b96e6f7e06d03d90f7669284b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001878_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01221:0.144378,(GCF_023573625_PROKKA_01519:5e-09,(GCF_002008305_PROKKA_01592:0.00589281,GCF_003691675_PROKKA_01304:5e-09)0.965:0.00588497)1:0.144378);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001879_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001879_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..76d4e2a899b46b904d7fa44b8cd324d5eaff2b51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.748:0.00524755)1:0.00542795);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001881_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001881_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4c637ae1c5bd41a03b774b5337bd204db801876
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001881_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_PROKKA_01655:2.5e-09,(GCF_023573625_PROKKA_01552:1.30937,(GCF_003691675_PROKKA_01360:5e-09,GCF_023573625_PROKKA_01585:0.00916582)0.939:0.0153561)1:2.5e-09);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001884_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001884_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..742b821bb8ed5347e1ea7966e64f23cf16170e76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001884_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01195:0.179963,(GCF_002008305_PROKKA_01683:0.00368168,(GCF_003691675_PROKKA_01387:0.0118162,GCF_023573625_PROKKA_01612:0.0078488)0.716:0.00425114)1:0.179963);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001886_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001886_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0654b62e9e83d6d65d61b5c0db3c9015086f26a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001886_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01021:0.185352,(GCF_023573625_PROKKA_01709:0.00592956,(GCF_002008305_PROKKA_01780:0.00455313,GCF_003691675_PROKKA_01487:5e-09)0.887:0.0364351)1:0.185352);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001887_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001887_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65b1b1f315022ea1d9125354325e343ae4afe17e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.857:0.0107777)1:0.092199);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001888_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001888_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..751858d04ef32fd630fa2e130112fdc19d30b7c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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):0.0147124):0.129565);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001889_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001889_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..32dd5bde30954864591f464b4689c32d7ca79ee5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001889_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01022:0.0720409,(GCF_023573625_PROKKA_01766:0.00637661,(GCF_002008305_PROKKA_01846:0.00321826,GCF_003691675_PROKKA_01542:5e-09)0.783:0.00975323)1:0.0720409);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001890_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001890_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4348dc658e05f70fb6a6c18a5034ce15f60dd021
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.99:0.164276)1:0.183998);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001891_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001891_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da06be46d12ebfdc578f37f9d31d65635a511160
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001891_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00981:0.0974429,(GCF_023573625_PROKKA_01798:0.0164862,(GCF_002008305_PROKKA_01878:0.00789957,GCF_003691675_PROKKA_01574:0.00636698)0.933:0.010114)1:0.0974429);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001893_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001893_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..32d1bf2934f511fdd895a79dd78e74f444ac85d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001893_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00966:0.0398734,(GCF_003691675_PROKKA_01588:0.0104213,(GCF_002008305_PROKKA_01892:0.00774917,GCF_023573625_PROKKA_01812:0.00385677)0.484:0.00522768)1:0.0398734);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001894_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001894_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53760b8efb0212bbb31766344ccca1c26038f9e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001894_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00903:0.184635,((GCF_002008305_PROKKA_01893:0,GCF_003691675_PROKKA_01589:0):6e-09,GCF_023573625_PROKKA_01813:0.0448194):0.184635);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001895_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001895_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f4aa77997db60da4f6a27576b5bb13e0d0fd29df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001895_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00963:0.0542452,((GCF_002008305_PROKKA_01895:0,GCF_023573625_PROKKA_01815:0):0.0126,GCF_003691675_PROKKA_01591:0.00821494):0.0542452);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001897_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001897_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bba00c0b04562c71599830b6b3ca6b8d3a3f15f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001897_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00883:0.0630811,(GCF_002008305_PROKKA_01912:0.00994707,(GCF_003691675_PROKKA_01608:0.00201426,GCF_023573625_PROKKA_01832:0.00255837)0.888:0.0114792)1:0.0630811);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001898_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001898_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ec2c6cf0939f2b3bbdc2a805b764bc3a92eafd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001898_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00882:0.0763199,((GCF_002008305_PROKKA_01913:0,GCF_023573625_PROKKA_01833:0):0.00751735,GCF_003691675_PROKKA_01609:0.00736406):0.0763199);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001900_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001900_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a96336b65a2af741471babacea59cccec7d982b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001900_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00879:0.15045,(GCF_002008305_PROKKA_01916:0.00496274,(GCF_023573625_PROKKA_01836:0.0170517,GCF_003691675_PROKKA_01612:0.00167809)0.553:0.00348728)1:0.15045);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001901_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001901_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e711ce0196231c2116ef8a97056928ccef756d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001901_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00878:0.0542101,(GCF_023573625_PROKKA_01837:5e-09,(GCF_002008305_PROKKA_01917:5e-09,GCF_003691675_PROKKA_01613:0.00764739)0.875:0.00381661)1:0.0542101);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001902_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001902_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1df05d51998e730d495b402841e1aef9f28ecea6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001902_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00929:0.0733432,(GCF_003691675_PROKKA_01627:0.00300298,(GCF_002008305_PROKKA_01931:0.0065568,GCF_023573625_PROKKA_01850:0.00411108)0.267:0.0019187)1:0.0733432);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001903_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001903_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e22da1acc72ec6785caaddfd45e76cbad62311d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001903_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00919:0.201383,((GCF_002008305_PROKKA_01940:0,GCF_023573625_PROKKA_01859:0):0.0282315,GCF_003691675_PROKKA_01636:0.0118387):0.201383);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001904_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001904_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a308c10443251c7e89e0bd848577e9d6d406df3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001904_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00848:0.00268334,((GCF_002008305_PROKKA_01946:0,GCF_023573625_PROKKA_01865:0):5e-09,GCF_005280335_PROKKA_00916:0.42454):0.00268334);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001905_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001905_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..665660e3220e8d1d01ee27899570f9f3816bed0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001905_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01967:0,GCF_003691675_PROKKA_01661:0,GCF_023573625_PROKKA_01893:0):0.0678055,GCF_005280335_PROKKA_00892:0.0678055);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001908_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001908_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..703896b4bf5359576a4b93245ceed08adcce7948
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001908_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00797:0.164456,((GCF_002008305_PROKKA_01996:0,GCF_003691675_PROKKA_01690:0):0.0106102,GCF_023573625_PROKKA_01922:0.0136929):0.164456);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001909_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001909_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f28cfcfd0038e50a367626e1f665b92772ded18a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001909_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00796:0.505125,(GCF_002008305_PROKKA_01997:0.00655672,(GCF_003691675_PROKKA_01691:0.0195436,GCF_023573625_PROKKA_01923:0.0196374)0.705:0.0131414)1:0.505125);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001911_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001911_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5299e1943d37c429bad42f121933381c2e308b6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001911_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00788:0.00647742,(GCF_002008305_PROKKA_02032:0.00636268,(GCF_003691675_PROKKA_01739:0.00520651,GCF_023573625_PROKKA_01967:0.00830765)0.347:0.00193575)1:0.00647742);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001912_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001912_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f4e064b9d4a09038344e0fd933184bac9193520b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001912_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00104:0.0994383,(GCF_005280335_PROKKA_00142:0.195113,(GCF_002008305_PROKKA_02037:1.26127,GCF_005280335_PROKKA_00807:0.669052)0.971:0.391367)1:0.0994383);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001913_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001913_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b556fd9519a24e793792c98d4c19731e714ddfcf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.423:0.00562601)1:0.100677);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001914_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001914_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..217adac55eac447342f3c3bef3338aa3404ad4ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001914_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00734:0.00377122,(GCF_002008305_PROKKA_02046:0.00506155,(GCF_003691675_PROKKA_01752:0.00752229,GCF_023573625_PROKKA_01980:0.0176484)0.761:5e-09)1:0.00377122);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001915_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001915_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57a3db089a1d89338b973b5a6fb9a2e0365522f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001915_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00732:0.167474,(GCF_002008305_PROKKA_02048:5e-09,(GCF_023573625_PROKKA_01982:0.00546666,GCF_003691675_PROKKA_01754:0.00683627)0.364:0.00272596)1:0.167474);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001916_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001916_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb3cba0015cd704dc28dbdd4e0992b89f79e6b55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001916_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00731:0.118255,(GCF_002008305_PROKKA_02049:0.0024427,(GCF_003691675_PROKKA_01755:0.00726801,GCF_023573625_PROKKA_01983:5e-09)0.164:0.00479291)1:0.118255);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001917_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001917_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..972ef65550c4314c443173cc6c2efd8517106338
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001917_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00766:0.299536,(GCF_003691675_PROKKA_01760:0.0232954,(GCF_002008305_PROKKA_02054:0.023817,GCF_023573625_PROKKA_01988:0.0823796)0.876:0.072511)1:0.299536);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001918_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001918_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d2b83b0a2da266258a672d1f81b0dbba28226a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001918_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_PROKKA_02062:2.5e-09,(GCF_020097155_PROKKA_02222:0.00623576,(GCF_020097155_PROKKA_02426:0.971759,GCF_020097155_PROKKA_02440:1.62407)0.915:0.323516)1:2.5e-09);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001919_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001919_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1359cbd29ef8f5b7e4299c499ed62f62d6e9a42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001919_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00604:0.011451,(GCF_002008305_PROKKA_02090:0.0150939,(GCF_003691675_PROKKA_01798:0.00737896,GCF_005280335_PROKKA_00688:0.0228915)0.893:0.0156266)1:0.011451);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001921_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001921_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9460fe71c89acaee67bfee2b38aff66112ca15aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.94:0.0199149)1:0.0984581);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001929_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001929_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31dce66661939d93c61aa7fffc957e9d5cb01c35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001929_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00604:0.171446,(GCF_023573625_PROKKA_02099:0.00431173,(GCF_002008305_PROKKA_02156:0.00430731,GCF_003691675_PROKKA_01869:5e-09)0.757:5e-09)1:0.171446);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001933_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001933_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..160b2437df71b12b9a7f6c647e4010b5aab13a89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001933_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00561:0.0435833,(GCF_002008305_PROKKA_02188:0.0408009,(GCF_003691675_PROKKA_01902:0.0288515,GCF_023573625_PROKKA_02133:0.00929494)0.83:0.0232413)1:0.0435833);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001936_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001936_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9559677bed25032460e22f96863a408756843bf7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001936_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_02203:0,GCF_003691675_PROKKA_01916:0,GCF_023573625_PROKKA_02147:0):0.105077,GCF_005280335_PROKKA_00540:0.105077);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001942_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001942_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb64598d80ec29638100df6869ee575d9ca2dddd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001942_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00516:0.190927,(GCF_003691675_PROKKA_01937:0.0055358,(GCF_002008305_PROKKA_02221:0.0202619,GCF_023573625_PROKKA_02160:0.0049845)0.76:0.00459648)1:0.190927);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001944_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001944_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78f61e5661b776cf2b3e8b1b6674f50e2964bbd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.672:0.00309558)1:0.193694);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001946_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001946_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2121cc34ba27acdf4e1dd74a86c43543bd1a1b0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001946_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00428:0.0245352,(GCF_023573625_PROKKA_02194:0.013355,(GCF_002008305_PROKKA_02263:0.00436185,GCF_003691675_PROKKA_01958:0.00773076)0.844:0.00729261)1:0.0245352);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001948_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001948_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aad97845a923c836c4a13bc6356a761269cd544c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001948_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00408:0.0304936,(GCF_002008305_PROKKA_02273:0.0327176,(GCF_003691675_PROKKA_01965:0.0159355,GCF_005280335_PROKKA_00459:0.0184343)0.864:5e-09)1:0.0304936);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001953_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001953_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e53ed5460f99527137eb9e4fa0e465860581a01d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001953_tree.txt
@@ -0,0 +1 @@
+((GCF_003691675_PROKKA_00094:0.618319,GCF_005280335_PROKKA_00775:0.869187)1:0.42855,(GCF_003691675_PROKKA_01796:0.0156881,GCF_005280335_PROKKA_00690:0.0143179)1:0.42855);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001957_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001957_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d8dca920466a7220089265c3aeff6223d85fc38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001957_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01825:0.00318969,((GCF_003691675_PROKKA_00323:0,GCF_005280335_PROKKA_02273:0):5e-09,GCF_023573625_PROKKA_00592:0.00451553):0.00318969);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001958_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001958_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f59e73b91f14837fb1a1fc5fd8371521289ced4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001958_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00844:0.00219033,(GCF_005280335_PROKKA_00905:0.00280856,(GCF_003691675_PROKKA_01643:0.0179321,GCF_023573625_PROKKA_01873:0.342438)0.899:0.0129122)1:0.00219033);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001959_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001959_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc34271e300e525a7b92a622f390a0cb0ccec131
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001959_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00843:2.5e-09,(GCF_005280335_PROKKA_00904:0.0019442,(GCF_003691675_PROKKA_01644:0.00884065,GCF_023573625_PROKKA_01874:0.189836)0.998:0.0352906)1:2.5e-09);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001960_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001960_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c1cc757a10bb453d01c50f1f658e2d11c935e3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001960_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00842:0,(GCF_005280335_PROKKA_00903:0,(GCF_003691675_PROKKA_01645:0.00330695,GCF_023573625_PROKKA_01875:0.00642957):0.0769338):0);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001961_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001961_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09c7fcb5f5fbc6ef016b08aed6c50b30d695c49e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001961_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00841:0.00501088,(GCF_005280335_PROKKA_00902:0.0226941,(GCF_003691675_PROKKA_01646:0.0101556,GCF_023573625_PROKKA_01876:0.0117644)0.697:0.00399846)1:0.00501088);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001964_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001964_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3bdfec641d82662c04f5e2b412de76211a375985
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001964_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00790:0.142347,(GCF_023573625_PROKKA_00737:1.40246,(GCF_003691675_PROKKA_01698:0.0702517,GCF_005280335_PROKKA_00853:0.0364395)0.977:0.255957)1:0.142347);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001966_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001966_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bae1880ac62e6d684bb9db293db1df44b965eeab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001966_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00787:0.0358652,(GCF_005280335_PROKKA_00850:0.0347342,(GCF_003691675_PROKKA_01701:0.00384942,GCF_023573625_PROKKA_01929:5e-09)0.992:0.0498003)1:0.0358652);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001968_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001968_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..607c4e1cf94f1b1fdda1967e9fa1078ce31cc58d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001968_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00785:0.096882,(GCF_005280335_PROKKA_00848:0.303104,(GCF_003691675_PROKKA_01703:5e-09,GCF_023573625_PROKKA_01931:0.00329337)0.995:0.129209)1:0.096882);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001969_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001969_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0b28d8815cc112d3a2679f95cae4dd51d2d47120
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.944:0.0479524)1:0.0390988);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001972_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001972_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b7ecf91bd6d1c79e18ff45b25dd28a69a48e0c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001972_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00612:0.012874,((GCF_003691675_PROKKA_01786:0,GCF_023573625_PROKKA_02020:0):0.00500841,GCF_005280335_PROKKA_00702:0.0102652):0.012874);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001973_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001973_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7003a113102c58d73cb81049962713c5d4f93c0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)1:0.144794)1:2.5e-09);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001974_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001974_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5dbe5a6a2f264640cb8e0ad5eded903926c8059b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001974_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00539:0.102207,((GCF_003691675_PROKKA_01859:0,GCF_023573625_PROKKA_02089:0):0.134855,GCF_005280335_PROKKA_00615:0.473987):0.102207);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001975_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001975_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc2e3ee52f493d899e90021ccdc7325432da365d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)0.516:0.0272194)1:0.0100616);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001977_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001977_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63b39a5160f6e44807896688b1e02b8f9866ed70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001977_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00712:0.138561,(GCF_020097155_PROKKA_00421:0.269298,(GCF_020097155_PROKKA_00697:0.0106707,GCF_020097155_PROKKA_00721:0.0233057)0.992:0.248001)1:0.138561);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001979_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001979_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4ecb53cb1364f63deb8b21d3728cb2236bca3b5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001979_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02089:0.0914122,(GCF_005280335_PROKKA_02190:0.197534,(GCF_005280335_PROKKA_02581:1.44457,GCF_005280335_PROKKA_02669:0.628906)0.763:0.179976)1:0.0914122);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001980_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001980_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13a563325db263ef5f28514e23f8f3ce371c38a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001980_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02247:0.0426205,(GCF_020097155_PROKKA_02120:5e-09,(GCF_020097155_PROKKA_00402:0.829223,GCF_020097155_PROKKA_00715:1.07201)1:0.859699)1:0.0426205);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001981_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001981_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f15aafc008b7c2d8acec1ae1576b6fc6644dc97e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/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)1:0);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001982_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001982_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..334ddc34c5938ab2ea61931624b6d9fcf8c47cc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001982_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00310:0.107075,(GCF_020097155_PROKKA_01773:0.216174,(GCF_020097155_PROKKA_00409:1.24894,GCF_020097155_PROKKA_00655:0.634764)1:1.37521)1:0.107075);
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001985_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001985_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a5d9e363cb0375fcda6a044158a954dba2c9424e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Gene_Trees/OG0001985_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00675:0.167866,(GCF_020097155_PROKKA_02226:0.307761,(GCF_020097155_PROKKA_00674:0.550358,GCF_020097155_PROKKA_02225:0.292006)0.916:0.199923)1:0.167866);
\ No newline at end of file